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Thompson N, Kyaw KWY, Singh L, Cikomola JC, Singh NS, Roberts B. The effect of COVID-19 on the non-COVID health outcomes of crisis-affected peoples: a systematic review. Confl Health 2024; 18:37. [PMID: 38664834 PMCID: PMC11044391 DOI: 10.1186/s13031-024-00592-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic posed considerable risks to populations affected by humanitarian crises in low- and middle-income countries (LMICs). However, there is limited understanding of how the pandemic may have affected non-COVID health outcomes among crisis-affected populations. Our aim was to examine the evidence on the impact of the COVID-19 pandemic on non-COVID-19 health outcomes for crisis-affected populations in LMICs. METHODS A systematic review methodology was applied following PRISMA guidelines. Eligibility criteria were: crisis-affected populations in LMICS; COVID-19; and all health topics, except for sexual and reproductive health which was covered in a linked review. Five bibliographic databases and additional grey literature sources were searched. The search period was from 2019 to 31 July 2022. Eligible papers were extracted and analysed using a narrative synthesis approach based on the study objectives and relevant health access and systems frameworks. A quality appraisal was also conducted. FINDINGS 4320 articles were screened, and 15 eligible studies were identified and included in this review. Ten studies collected health outcomes data. Eight related to mental health, which generally showed worse mental health outcomes because of the pandemic, and pandemic-related stressors were identified. Two studies assessed physical health outcomes in children, while none addressed physical health outcomes among adults. Nine studies reported on access to healthcare, revealing worse access levels due to the pandemic and noting key barriers to care. Seven studies reported on the impact on health systems, with key challenges including reduced and distorted health care funding, reduced staff capacity, interrupted medicines and supplies, weak information and mixed-messaging, and weak leadership. All fifteen studies on the social determinants of health, particularly highlighting the effect of increasing poverty, the role of gender, and food insecurity on health outcomes. The quality of papers was limited overall. CONCLUSION This review found some limited evidence indicating negative mental health effects, increased barriers to accessing care, damage to health systems and magnified impacts on the social determinants of health for crisis-affected people during the COVID-19 pandemic. However, the small number and limited quality of the studies make the overall strength of evidence quite weak.
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Affiliation(s)
- N Thompson
- Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, UK
| | - K W Y Kyaw
- Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, UK
| | - L Singh
- Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, UK
| | - J C Cikomola
- Faculty of Medicine, Université Catholique de Bukavu, Democratic Republic of the Congo, Central African Republic
| | - N S Singh
- Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, UK
| | - Bayard Roberts
- Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, UK.
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Dorward J, Sookrajh Y, Lessells R, Bulo E, Bodley N, Singh L, Moodley P, Samsunder N, Drain PK, Hayward G, Butler CC, Garrett N. Viremia and HIV Drug Resistance Among People Receiving Dolutegravir Versus Efavirenz-Based First-Line Antiretroviral Therapy. J Acquir Immune Defic Syndr 2024; 95:e8-e11. [PMID: 38489494 PMCID: PMC10927299 DOI: 10.1097/qai.0000000000003385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Supplemental Digital Content is Available in the Text.
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Affiliation(s)
- Jienchi Dorward
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu–Natal, Durban, South Africa
| | | | - Richard Lessells
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu–Natal, Durban, South Africa
- KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa
| | - Elliot Bulo
- eThekwini Municipality Health Unit, Durban, South Africa
| | - Nicola Bodley
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu–Natal, Durban, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa
| | - Pravikrishnen Moodley
- Department of Virology, University of KwaZulu-Natal and National Health Laboratory Service, Inkosi Albert Luthuli Central Hospital, KwaZulu-Natal, South Africa
| | - Natasha Samsunder
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu–Natal, Durban, South Africa
| | - Paul K. Drain
- Department of Global Health, Schools of Medicine and Public Health, University of Washington, Seattle, WA
- Department of Medicine, School of Medicine, University of Washington, Seattle, WA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA; and
| | - Gail Hayward
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Christopher C. Butler
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu–Natal, Durban, South Africa
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
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3
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Ahsan MR, Singh L, Varma H, Mukherjee A. Exploiting benzilic acid as a modular template: controlling photoreactivity and solid to liquid transition during photodimerization. Chem Commun (Camb) 2023; 59:12711-12714. [PMID: 37811973 DOI: 10.1039/d3cc04257j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
A well-known molecule, benzilic acid, is used as a [2+2] photodimerization template by using third-generation crystal engineering principles. This template utilizes orthogonality and non-covalent interactions in an optimized way and is shown to be effective in tuning the photoreactivity of styryl pyridine derivatives. The photo-induced crystal-to-liquid transformation was observed during photodimerization. This phenomenon is explained based on slip plane and energy framework analysis.
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Affiliation(s)
- Mollah Rohan Ahsan
- Department of Chemistry, Birla Institute of Science and Technology (BITS) Pilani, Hyderabad campus, Hyderabad 500078, Telangana, India.
| | - Lavanya Singh
- Department of Chemistry, Birla Institute of Science and Technology (BITS) Pilani, Hyderabad campus, Hyderabad 500078, Telangana, India.
| | - Harshit Varma
- Department of Chemistry, Birla Institute of Science and Technology (BITS) Pilani, Hyderabad campus, Hyderabad 500078, Telangana, India.
| | - Arijit Mukherjee
- Department of Chemistry, Birla Institute of Science and Technology (BITS) Pilani, Hyderabad campus, Hyderabad 500078, Telangana, India.
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Francisco NM, van Wyk S, Moir M, San JE, Sebastião CS, Tegally H, Xavier J, Maharaj A, Neto Z, Afonso P, Jandondo D, Paixão J, Miranda J, David K, Inglês L, Pereira A, Paulo A, Carralero RR, Freitas HR, Mufinda F, Lutucuta S, Ghafari M, Giovanetti M, Giandhari J, Pillay S, Naidoo Y, Singh L, Tshiabuila D, Martin DP, Chabuka L, Choga W, Wanjohi D, Mwangi S, Pillay Y, Kebede Y, Shumba E, Ondoa P, Baxter C, Wilkinson E, Tessema SK, Katzourakis A, Lessells R, de Oliveira T, Morais J. Insights into SARS-CoV-2 in Angola during the COVID-19 peak: Molecular epidemiology and genome surveillance. Influenza Other Respir Viruses 2023; 17:e13198. [PMID: 37744993 PMCID: PMC10515134 DOI: 10.1111/irv.13198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/25/2023] [Accepted: 08/27/2023] [Indexed: 09/26/2023] Open
Abstract
Background In Angola, COVID-19 cases have been reported in all provinces, resulting in >105,000 cases and >1900 deaths. However, no detailed genomic surveillance into the introduction and spread of the SARS-CoV-2 virus has been conducted in Angola. We aimed to investigate the emergence and epidemic progression during the peak of the COVID-19 pandemic in Angola. Methods We generated 1210 whole-genome SARS-CoV-2 sequences, contributing West African data to the global context, that were phylogenetically compared against global strains. Virus movement events were inferred using ancestral state reconstruction. Results The epidemic in Angola was marked by four distinct waves of infection, dominated by 12 virus lineages, including VOCs, VOIs, and the VUM C.16, which was unique to South-Western Africa and circulated for an extended period within the region. Virus exchanges occurred between Angola and its neighboring countries, and strong links with Brazil and Portugal reflected the historical and cultural ties shared between these countries. The first case likely originated from southern Africa. Conclusion A lack of a robust genome surveillance network and strong dependence on out-of-country sequencing limit real-time data generation to achieve timely disease outbreak responses, which remains of the utmost importance to mitigate future disease outbreaks in Angola.
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Affiliation(s)
- Ngiambudulu M. Francisco
- Grupo de Investigação Microbiana e ImunológicaInstituto Nacional de Investigação em SaúdeLuandaAngola
| | - Stephanie van Wyk
- Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational ThinkingStellenbosch UniversityStellenboschSouth Africa
| | - Monika Moir
- Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational ThinkingStellenbosch UniversityStellenboschSouth Africa
| | - James Emmanuel San
- Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational ThinkingStellenbosch UniversityStellenboschSouth Africa
- KwaZulu‐Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of MedicineUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Cruz S. Sebastião
- Grupo de Investigação Microbiana e ImunológicaInstituto Nacional de Investigação em SaúdeLuandaAngola
- Centro de Investigação em Saúde de Angola (CISA)CaxitoAngola
| | - Houriiyah Tegally
- Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational ThinkingStellenbosch UniversityStellenboschSouth Africa
- KwaZulu‐Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of MedicineUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Joicymara Xavier
- Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational ThinkingStellenbosch UniversityStellenboschSouth Africa
| | - Akhil Maharaj
- Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational ThinkingStellenbosch UniversityStellenboschSouth Africa
| | | | - Pedro Afonso
- Grupo de Investigação Microbiana e ImunológicaInstituto Nacional de Investigação em SaúdeLuandaAngola
| | - Domingos Jandondo
- Grupo de Investigação Microbiana e ImunológicaInstituto Nacional de Investigação em SaúdeLuandaAngola
| | - Joana Paixão
- Grupo de Investigação Microbiana e ImunológicaInstituto Nacional de Investigação em SaúdeLuandaAngola
| | - Julio Miranda
- Grupo de Investigação Microbiana e ImunológicaInstituto Nacional de Investigação em SaúdeLuandaAngola
| | - Kumbelembe David
- Grupo de Investigação Microbiana e ImunológicaInstituto Nacional de Investigação em SaúdeLuandaAngola
| | - Luzia Inglês
- Grupo de Investigação Microbiana e ImunológicaInstituto Nacional de Investigação em SaúdeLuandaAngola
| | - Amilton Pereira
- Grupo de Investigação Microbiana e ImunológicaInstituto Nacional de Investigação em SaúdeLuandaAngola
| | - Agostinho Paulo
- Grupo de Investigação Microbiana e ImunológicaInstituto Nacional de Investigação em SaúdeLuandaAngola
| | - Raisa Rivas Carralero
- Grupo de Investigação Microbiana e ImunológicaInstituto Nacional de Investigação em SaúdeLuandaAngola
| | | | | | | | - Mahan Ghafari
- KwaZulu‐Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of MedicineUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Marta Giovanetti
- Reference Laboratory of FlavivirusOswaldo Cruz FoundationRio de JaneiroBrazil
| | - Jennifer Giandhari
- KwaZulu‐Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of MedicineUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Sureshnee Pillay
- KwaZulu‐Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of MedicineUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Yeshnee Naidoo
- Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational ThinkingStellenbosch UniversityStellenboschSouth Africa
| | - Lavanya Singh
- KwaZulu‐Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of MedicineUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Derek Tshiabuila
- Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational ThinkingStellenbosch UniversityStellenboschSouth Africa
| | - Darren Patrick Martin
- Division of Computational Biology, Department of Integrative Biomedical SciencesUniversity of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape TownCape TownSouth Africa
| | - Lucious Chabuka
- Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational ThinkingStellenbosch UniversityStellenboschSouth Africa
| | - Wonderful Choga
- Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational ThinkingStellenbosch UniversityStellenboschSouth Africa
| | - Dorcas Wanjohi
- Africa CDC Institute of Pathogen GenomicsAfrica Centre for Disease Control and PreventionAddis AbabaEthiopia
| | - Sarah Mwangi
- Africa CDC Institute of Pathogen GenomicsAfrica Centre for Disease Control and PreventionAddis AbabaEthiopia
| | - Yusasha Pillay
- Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational ThinkingStellenbosch UniversityStellenboschSouth Africa
| | - Yenew Kebede
- Africa CDC Institute of Pathogen GenomicsAfrica Centre for Disease Control and PreventionAddis AbabaEthiopia
| | - Edwin Shumba
- African Society for Laboratory MedicineAddis AbabaEthiopia
| | - Pascale Ondoa
- African Society for Laboratory MedicineAddis AbabaEthiopia
| | - Cheryl Baxter
- Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational ThinkingStellenbosch UniversityStellenboschSouth Africa
- KwaZulu‐Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of MedicineUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Eduan Wilkinson
- Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational ThinkingStellenbosch UniversityStellenboschSouth Africa
- KwaZulu‐Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of MedicineUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Sofonias Kifle Tessema
- Africa CDC Institute of Pathogen GenomicsAfrica Centre for Disease Control and PreventionAddis AbabaEthiopia
| | - Aris Katzourakis
- Department of BiologyOxford UniversityOxfordUK
- Big Data Institute, Nuffield Department of MedicineUniversity of OxfordOxfordUK
| | - Richard Lessells
- KwaZulu‐Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of MedicineUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Tulio de Oliveira
- Center for Epidemic Response and Innovation (CERI), School of Data Science and Computational ThinkingStellenbosch UniversityStellenboschSouth Africa
- KwaZulu‐Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of MedicineUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Joana Morais
- Grupo de Investigação Microbiana e ImunológicaInstituto Nacional de Investigação em SaúdeLuandaAngola
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5
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Aimetta A, Moscheni M, Singh L, Marsden C, Scarabosio A, Sertoli M, Sladkomedova A, Subba F, Varje J, Wu H. Forward modelling of Dα camera view in ST40 informed by experimental data. Fusion Engineering and Design 2023. [DOI: 10.1016/j.fusengdes.2023.113513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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6
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Ismael N, van Wyk S, Tegally H, Giandhari J, San JE, Moir M, Pillay S, Utpatel C, Singh L, Naidoo Y, Ramphal U, Mabunda N, Abílio N, Arnaldo P, Xavier J, Amoako DG, Everatt J, Ramphal Y, Maharaj A, de Araujo L, Anyaneji UJ, Tshiabuila D, Viegas S, Lessells R, Engelbrecht S, Gudo E, Jani I, Niemann S, Wilkinson E, de Oliveira T. Genomic epidemiology of SARS-CoV-2 during the first four waves in Mozambique. PLOS Glob Public Health 2023; 3:e0001593. [PMID: 36963096 PMCID: PMC10021167 DOI: 10.1371/journal.pgph.0001593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/20/2023] [Indexed: 03/08/2023]
Abstract
Mozambique reported the first case of coronavirus disease 2019 (COVID-19) in March 2020 and it has since spread to all provinces in the country. To investigate the introductions and spread of SARS-CoV-2 in Mozambique, 1 142 whole genome sequences sampled within Mozambique were phylogenetically analyzed against a globally representative set, reflecting the first 25 months of the epidemic. The epidemic in the country was marked by four waves of infection, the first associated with B.1 ancestral lineages, while the Beta, Delta, and Omicron Variants of Concern (VOCs) were responsible for most infections and deaths during the second, third, and fourth waves. Large-scale viral exchanges occurred during the latter three waves and were largely attributed to southern African origins. Not only did the country remain vulnerable to the introductions of new variants but these variants continued to evolve within the borders of the country. Due to the Mozambican health system already under constraint, and paucity of data in Mozambique, there is a need to continue to strengthen and support genomic surveillance in the country as VOCs and Variants of interests (VOIs) are often reported from the southern African region.
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Affiliation(s)
- Nalia Ismael
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Stephanie van Wyk
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - James Emmanuel San
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Lavanya Singh
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Yeshnee Naidoo
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Upasana Ramphal
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Nédio Mabunda
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Nuro Abílio
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Paulo Arnaldo
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Joicymara Xavier
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
- Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brasil
| | - Daniel Gyamfi Amoako
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Johannesburg, South Africa
- School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
| | - Josie Everatt
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Johannesburg, South Africa
| | - Yajna Ramphal
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Arisha Maharaj
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Leonardo de Araujo
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Ugochukwu J. Anyaneji
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Derek Tshiabuila
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Sofia Viegas
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Richard Lessells
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Eduardo Gudo
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Ilesh Jani
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
| | - Túlio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of Kwazulu-Natal, Durban, South Africa
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7
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Majam M, Segal B, Fieggen J, Smith E, Hermans L, Singh L, Phatsoane M, Arora L, Lalla-Edward S. Utility of a machine-guided tool for assessing risk behaviour associated with contracting HIV in three sites in South Africa. Inform Med Unlocked 2023; 37:101192. [PMID: 36911795 PMCID: PMC9993399 DOI: 10.1016/j.imu.2023.101192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction Digital data collection and the associated mobile health technologies have allowed for the recent exploration of artificial intelligence as a tool for combatting the HIV epidemic. Machine learning has been found to be useful both in HIV risk prediction and as a decision support tool for guiding pre-exposure prophylaxis (PrEP) treatment. This paper reports data from two sequential studies evaluating the viability of using machine learning to predict the susceptibility of adults to HIV infection using responses from a digital survey deployed in a high burden, low-resource setting. Methods 1036 and 593 participants were recruited across two trials. The first trial was a cross-sectional study in one location and the second trial was a cohort study across three trial sites. The data from the studies were merged, partitioned using standard techniques, and then used to train and evaluate multiple different machine learning models and select and evaluate a final model. Variable importance estimates were calculated using the PIMP and SHAP methodologies. Results Characteristics associated with HIV were consistent across both studies. Overall, HIV positive patients had a higher median age (34 [IQR: 29-39] vs 26 [IQR 22-33], p < 0.001), and were more likely to be female (155/703 [22%] vs 107/927 [12%], p < 0.001). HIV positive participants also had more commonly gone a year or more since their last HIV test (183/262 [70%] vs 540/1368 [39%], p < 0.001) and were less likely to report consistent condom usage (113/262 [43%] vs 758/1368 [55%], p < 0.001). Patients who reported TB symptoms were more likely to be HIV positive. The trained models had accuracy values (AUROCs) ranging from 78.5% to 82.8%. A boosted tree model performed best with a sensitivity of 84% (95% CI 72-92), specificity of 71% (95% CI 67-76), and a negative predictive value of 95% (95% CI 93-96) in a hold-out dataset. Age, duration since last HIV test, and number of male sexual partners were consistently three of the four most important variables across both variable importance estimates. Conclusions This study has highlighted the synergies present between mobile health and machine learning in HIV. It has been demonstrated that a viable ML model can be built using digital survey data from an low-middle income setting with potential utility in directing health resources.
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Affiliation(s)
- M. Majam
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - B. Segal
- Phithos Technologies, Johannesburg, South Africa
| | - J. Fieggen
- Phithos Technologies, Johannesburg, South Africa
| | - Eli Smith
- Phithos Technologies, Johannesburg, South Africa
| | - L. Hermans
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
- Infectious Diseases Unit, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - L. Singh
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - M. Phatsoane
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - L. Arora
- Phithos Technologies, Johannesburg, South Africa
| | - S.T. Lalla-Edward
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Corresponding author. Ezintsha, Building C, Sunnyside Office Park, 32 Princess of Wales Terrace, Parktown, Gauteng, 2000, South Africa.
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Tegally H, San JE, Cotten M, Moir M, Tegomoh B, Mboowa G, Martin DP, Baxter C, Lambisia AW, Diallo A, Amoako DG, Diagne MM, Sisay A, Zekri ARN, Gueye AS, Sangare AK, Ouedraogo AS, Sow A, Musa AO, Sesay AK, Abias AG, Elzagheid AI, Lagare A, Kemi AS, Abar AE, Johnson AA, Fowotade A, Oluwapelumi AO, Amuri AA, Juru A, Kandeil A, Mostafa A, Rebai A, Sayed A, Kazeem A, Balde A, Christoffels A, Trotter AJ, Campbell A, Keita AK, Kone A, Bouzid A, Souissi A, Agweyu A, Naguib A, Gutierrez AV, Nkeshimana A, Page AJ, Yadouleton A, Vinze A, Happi AN, Chouikha A, Iranzadeh A, Maharaj A, Batchi-Bouyou AL, Ismail A, Sylverken AA, Goba A, Femi A, Sijuwola AE, Marycelin B, Salako BL, Oderinde BS, Bolajoko B, Diarra B, Herring BL, Tsofa B, Lekana-Douki B, Mvula B, Njanpop-Lafourcade BM, Marondera BT, Khaireh BA, Kouriba B, Adu B, Pool B, McInnis B, Brook C, Williamson C, Nduwimana C, Anscombe C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Mapanguy CM, Loucoubar C, Onwuamah CK, Ihekweazu C, Malaka CN, Peyrefitte C, Grace C, Omoruyi CE, Rafaï CD, Morang’a CM, Erameh C, Lule DB, Bridges DJ, Mukadi-Bamuleka D, Park D, Rasmussen DA, Baker D, Nokes DJ, Ssemwanga D, Tshiabuila D, Amuzu DSY, Goedhals D, Grant DS, Omuoyo DO, Maruapula D, Wanjohi DW, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong’era EM, Ngabana EN, Abworo EO, Otieno E, Shumba E, Barasa E, Ahmed EB, Ahmed EA, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Manuel E, Leendertz F, Taweh FM, Wasfi F, Abdelmoula F, Takawira FT, Derrar F, Ajogbasile FV, Treurnicht F, Onikepe F, Ntoumi F, Muyembe FM, Ragomzingba FEZ, Dratibi FA, Iyanu FA, Mbunsu GK, Thilliez G, Kay GL, Akpede GO, van Zyl GU, Awandare GA, Kpeli GS, Schubert G, Maphalala GP, Ranaivoson HC, Omunakwe HE, Onywera H, Abe H, Karray H, Nansumba H, Triki H, Kadjo HAA, Elgahzaly H, Gumbo H, Mathieu H, Kavunga-Membo H, Smeti I, Olawoye IB, Adetifa IMO, Odia I, Ben Boubaker IB, Mohammad IA, Ssewanyana I, Wurie I, Konstantinus IS, Halatoko JWA, Ayei J, Sonoo J, Makangara JCC, Tamfum JJM, Heraud JM, Shaffer JG, Giandhari J, Musyoki J, Nkurunziza J, Uwanibe JN, Bhiman JN, Yasuda J, Morais J, Kiconco J, Sandi JD, Huddleston J, Odoom JK, Morobe JM, Gyapong JO, Kayiwa JT, Okolie JC, Xavier JS, Gyamfi J, Wamala JF, Bonney JHK, Nyandwi J, Everatt J, Nakaseegu J, Ngoi JM, Namulondo J, Oguzie JU, Andeko JC, Lutwama JJ, Mogga JJH, O’Grady J, Siddle KJ, Victoir K, Adeyemi KT, Tumedi KA, Carvalho KS, Mohammed KS, Dellagi K, Musonda KG, Duedu KO, Fki-Berrajah L, Singh L, Kepler LM, Biscornet L, de Oliveira Martins L, Chabuka L, Olubayo L, Ojok LD, Deng LL, Ochola-Oyier LI, Tyers L, Mine M, Ramuth M, Mastouri M, ElHefnawi M, Mbanne M, Matsheka MI, Kebabonye M, Diop M, Momoh M, Lima Mendonça MDL, Venter M, Paye MF, Faye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina MG, Owusu M, Wiley MR, Tatfeng MY, Ayekaba MO, Abouelhoda M, Beloufa MA, Seadawy MG, Khalifa MK, Matobo MM, Kane M, Salou M, Mbulawa MB, Mwenda M, Allam M, Phan MVT, Abid N, Rujeni N, Abuzaid N, Ismael N, Elguindy N, Top NM, Dia N, Mabunda N, Hsiao NY, Silochi NB, Francisco NM, Saasa N, Bbosa N, Murunga N, Gumede N, Wolter N, Sitharam N, Ndodo N, Ajayi NA, Tordo N, Mbhele N, Razanajatovo NH, Iguosadolo N, Mba N, Kingsley OC, Sylvanus O, Femi O, Adewumi OM, Testimony O, Ogunsanya OA, Fakayode O, Ogah OE, Oludayo OE, Faye O, Smith-Lawrence P, Ondoa P, Combe P, Nabisubi P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Okokhere PO, Bejon P, Dussart P, Bester PA, Mbala PK, Kaleebu P, Abechi P, El-Shesheny R, Joseph R, Aziz RK, Essomba RG, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Neto Rodrigues RMDESA, Audu RA, Carr RAA, Gargouri S, Masmoudi S, Bootsma S, Sankhe S, Mohamed SI, Femi S, Mhalla S, Hosch S, Kassim SK, Metha S, Trabelsi S, Agwa SH, Mwangi SW, Doumbia S, Makiala-Mandanda S, Aryeetey S, Ahmed SS, Ahmed SM, Elhamoumi S, Moyo S, Lutucuta S, Gaseitsiwe S, Jalloh S, Andriamandimby SF, Oguntope S, Grayo S, Lekana-Douki S, Prosolek S, Ouangraoua S, van Wyk S, Schaffner SF, Kanyerezi S, Ahuka-Mundeke S, Rudder S, Pillay S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Mohale T, Le-Viet T, Velavan TP, Schindler T, Maponga TG, Bedford T, Anyaneji UJ, Chinedu U, Ramphal U, George UE, Enouf V, Nene V, Gorova V, Roshdy WH, Karim WA, Ampofo WK, Preiser W, Choga WT, Ahmed YA, Ramphal Y, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Ouma AEO, von Gottberg A, Githinji G, Moeti M, Tomori O, Sabeti PC, Sall AA, Oyola SO, Tebeje YK, Tessema SK, de Oliveira T, Happi C, Lessells R, Nkengasong J, Wilkinson E. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. Science 2022; 378:eabq5358. [PMID: 36108049 PMCID: PMC9529057 DOI: 10.1126/science.abq5358] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022]
Abstract
Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.
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Affiliation(s)
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James E. San
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Matthew Cotten
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Bryan Tegomoh
- The Biotechnology Centre of the University of Yaoundé I, Yaoundé, Cameroon
- CDC Foundation, Atlanta, Georgia, Nebraska Department of Health and Human Services, Lincoln, NE, USA
| | - Gerald Mboowa
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | | | - Amadou Diallo
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Daniel G. Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | | | - Abay Sisay
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abdel-Rahman N. Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Abdou Salam Gueye
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Abdoul K. Sangare
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
| | - Abdoul-Salam Ouedraogo
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | | | - Abdualmoniem O. Musa
- Faculty of Medicine and Health Sciences, Kassala University, Kassala City, Sudan
- Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan
- General Administration of Laboratories and Blood Banks, Ministry of Health, Kassala State, Sudan
| | | | - Abe G. Abias
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | | | - Adamou Lagare
- Center for Medical and Sanitary Research (CERMES), Niamey, Niger
| | | | - Aden Elmi Abar
- Laboratoire de la Caisse Nationale de Sécurité Sociale, Djibouti, Republic of Djibouti
| | - Adeniji A. Johnson
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeola Fowotade
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeyemi O. Oluwapelumi
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
- The Pirbright Institute, Woking, UK
| | - Adrienne A. Amuri
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Agnes Juru
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Ahmed Kandeil
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ahmed Sayed
- Genomics and Epigenomics Program, Research Department CCHE57357, Cairo, Egypt
| | - Akano Kazeem
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Aladje Balde
- Laboratório de Biologia Molecular Jean Piaget, Bissau, Guinea-Bissau
- University Jean Piaget in Guinea-Bissau, Bissau, Guinea-Bissau
| | - Alan Christoffels
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
- SAMRC Bioinformatics Unit, SA Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | | | - Allan Campbell
- Central Public Health Reference Laboratories, Freetown, Sierra Leone
| | - Alpha K. Keita
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier University, 34090, Montpellier, France
| | - Amadou Kone
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Amal Bouzid
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Amel Naguib
- Central Public Health Laboratories (CPHL), Cairo, Egypt
| | | | | | | | - Anges Yadouleton
- Laboratoire des Fièvres Hémorragiques Virales du Benin, Cotonou, Benin
| | - Anika Vinze
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Anise N. Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Anissa Chouikha
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Apporach and Technological Innovation for a Better Health”, LR20IPT02, Pasteur Institute, Tunis 1002, Tunisia
| | - Arash Iranzadeh
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arisha Maharaj
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Armel L. Batchi-Bouyou
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Marien Ngouabi, Brazzaville, Republic of the Congo
| | - Arshad Ismail
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Augustina A. Sylverken
- Kwame Nkrumah University of Science and Technology, Department of Theoretical and Applied Biology, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Augustine Goba
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Ayoade Femi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Ayotunde E. Sijuwola
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Baba Marycelin
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Borno State, Nigeria
| | - Babatunde L. Salako
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Bamidele S. Oderinde
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bankole Bolajoko
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Bassirou Diarra
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Belinda L. Herring
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | | | - Bernard Lekana-Douki
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
- Département de Parasitologie-Mycologie Université des Sciences de la Santé (USS), Libreville, Gabon
| | - Bernard Mvula
- National HIV Reference Laboratory, Community Health Sciences Unit, Ministry of Health, Lilongwe, Malawi
| | | | | | - Bouh Abdi Khaireh
- National Medical and Molecular Biology Laboratory, Ministry of Health, Djibouti, Republic of Djibouti
- Africa CDC, Rapid Responder, Team Djibouti, Djibouti, Djibouti
| | - Bourema Kouriba
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
| | - Bright Adu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Brigitte Pool
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health Seychelles, Victoria, Seychelles
| | - Bronwyn McInnis
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Cara Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Carolyn Williamson
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | - Catherine Anscombe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Chantal G. Akoua-Koffi
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
- UFR Sciences Médicales, Universite Alassane Ouattara, Bouaké, Côte d’Ivoire
| | - Charles N. Agoti
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Public Health, Pwani University, Kilifi, Kenya
| | - Chastel M. Mapanguy
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Faculty of Science and Techniques, University Marien Ngouabi, Brazzaville, Republic of the Congo
| | | | - Chika K. Onwuamah
- Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Chikwe Ihekweazu
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Christian N. Malaka
- Laboratoire des Arbovirus, Fièvres Hémorragiques virales, Virus Emergents et Zoonoses, Institut Pasteur de Bangui, Bangui, Central African Republic
| | | | - Chukwa Grace
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Chukwuma E. Omoruyi
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Clotaire D. Rafaï
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
| | - Collins M. Morang’a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Cyril Erameh
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Daniel B. Lule
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | | | - Daniel Mukadi-Bamuleka
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
| | - Danny Park
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David A. Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | | | - David J. Nokes
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Deogratius Ssemwanga
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Dominic S. Y. Amuzu
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Dominique Goedhals
- PathCare Vermaak, Pretoria, South Africa and Division of Virology, University of the Free State, Bloemfontein, South Africa
| | - Donald S. Grant
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | | | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Dorcas W. Wanjohi
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | | | - Eddy K. Lusamaki
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier University, 34090, Montpellier, France
| | | | | | - Edith N. Ngabana
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Edward O. Abworo
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Edward Otieno
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Edwin Shumba
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | - Edwine Barasa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - El Bara Ahmed
- INRSP, Nouakchott, Mauritania
- Faculté de Médecine de Nouakchott, Nouakchott, Mauritani
| | - Elhadi A. Ahmed
- Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan
| | - Emmanuel Lokilo
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
| | | | - Eromon Philomena
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Etilé A. Anoh
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | - Eusebio Manuel
- Direcção Nacional da Saúde Pública, Ministério da Saúde, Luanda, Angola
| | | | - Fahn M. Taweh
- National Public Health Reference Laboratory–National Public Health Institute of Liberia, Monrovia, Liberia
| | - Fares Wasfi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
| | - Fatma Abdelmoula
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | | | - Fawzi Derrar
- National Influenza Centre, Institut Pasteur d’Algérie, Algiers, Algeria
| | - Fehintola V. Ajogbasile
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Florette Treurnicht
- Department of Virology, National Health Laboratory Service (NHLS), Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Folarin Onikepe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Francine Ntoumi
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Francisca M. Muyembe
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | | | - Fred A. Dratibi
- WHO Int Comoros, Moroni, Union of Comoros
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Fred-Akintunwa Iyanu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Gabriel K. Mbunsu
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | | | | | - George O. Akpede
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Gert U. van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Grace S. Kpeli
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | | | - Gugu P. Maphalala
- Ministry of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
| | | | - Hannah E. Omunakwe
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Nigeria
| | - Harris Onywera
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Hela Karray
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Henda Triki
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
| | | | - Hesham Elgahzaly
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Hlanai Gumbo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Hota Mathieu
- Doctoral School of Technical and Environmental Sciences, Department of Biology and Human Health, N’Djamena, Chad
| | - Hugo Kavunga-Membo
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
| | - Ibtihel Smeti
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Idowu B. Olawoye
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Ifedayo M. O. Adetifa
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Ikponmwosa Odia
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Ilhem Boutiba Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory LR99ES09, Tunis, Tunisia
| | - Iluoreh Ahmed Mohammad
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Isatta Wurie
- College of Medicine and Allied Health Science, University of Sierra Leone, Freetown, Sierra Leone
| | | | | | - James Ayei
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | - Janaki Sonoo
- Virology/Molecular Biology Department, Central Health Laboratory, Victoria Hospital, Ministry of Health and Wellness, Port Louis, Mauritius
| | - Jean-Claude C. Makangara
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Jean-Jacques M. Tamfum
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Jean-Michel Heraud
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | - Jessica N. Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Jinal N. Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Joana Morais
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
- Departamento de Bioquímica, Faculdade de Medicina, Universidade Agostinho Neto, Luanda, Angola
| | | | - John D. Sandi
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - John K. Odoom
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - John O. Gyapong
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - John T. Kayiwa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Johnson C. Okolie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Joicymara S. Xavier
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
| | - Jones Gyamfi
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | - Joseph H. K. Bonney
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Joseph Nyandwi
- National Institute of Public Health, Bujumbura, Burundi
- Faculty of Medicine, University of Burundi, Bujumbura, Burundi
| | - Josie Everatt
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Joyce M. Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | | | - Judith U. Oguzie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Julia C. Andeko
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | | | - Katherine J. Siddle
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Kayode T. Adeyemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Kefentse A. Tumedi
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
| | | | | | | | | | - Kwabena O. Duedu
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | - Lamia Fki-Berrajah
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Lenora M. Kepler
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Leon Biscornet
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health Seychelles, Victoria, Seychelles
| | | | | | - Luicer Olubayo
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
| | - Lul Deng Ojok
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | - Lul Lojok Deng
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | | | - Lynn Tyers
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Magalutcheemee Ramuth
- Virology/Molecular Biology Department, Central Health Laboratory, Victoria Hospital, Ministry of Health and Wellness, Port Louis, Mauritius
| | - Maha Mastouri
- Laboratory of Transmissible Diseases and Biologically Active Substances (LR99ES27), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Mahmoud ElHefnawi
- Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, Cairo, Egypt
| | - Maimouna Mbanne
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | | | - Mamadou Diop
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mambu Momoh
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- Eastern Technical University of Sierra Leone, Kenema, Sierra Leone
| | | | - Marietjie Venter
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Marietou F. Paye
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Martin Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | | | - Matoke-Muhia Damaris
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Maximillian G. Mpina
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- Ifakara Health Insitute, Ifakara, Tanzania
| | - Michael Owusu
- Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Michael R. Wiley
- University of Nebraska Medical Center (UNMC), Omaha, NE, USA
- PraesensBio, Lincoln, NE, USA
| | - Mirabeau Y. Tatfeng
- Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
| | | | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo, Egypt
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | | | - Mohamed G. Seadawy
- Biological Prevention Department, Ministry of Defence, Cairo, Egypt
- Faculty of Science, Fayoum University, Fayoum, Egypt
| | | | | | - Mouhamed Kane
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | | | | | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - My V. T. Phan
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biologically Active Substances (LR99ES27), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- High Institute of Biotechnology of Monastir, University of Monastir, Rue Taher Haddad 5000, Monastir, Tunisia
| | - Nadine Rujeni
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Nadir Abuzaid
- Department of Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Sudan
| | - Nalia Ismael
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | | | | | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Nédio Mabunda
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Nei-yuan Hsiao
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | - Ngiambudulu M. Francisco
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
| | - Ngonda Saasa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Nicholas Bbosa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | | | - Nicksy Gumede
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Nicole Wolter
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Nikita Sitharam
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Nnaemeka Ndodo
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Nnennaya A. Ajayi
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Noël Tordo
- Institut Pasteur de Guinée, Conarky, Guinea
| | - Nokuzola Mbhele
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Nosamiefan Iguosadolo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Nwando Mba
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Ojide C. Kingsley
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Okogbenin Sylvanus
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Oladiji Femi
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences. College of Health Sciences. University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Olubusuyi M. Adewumi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olumade Testimony
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Olusola A. Ogunsanya
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Oluwatosin Fakayode
- Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
| | - Onwe E. Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Ope-Ewe Oludayo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Pascale Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | | | - Patricia Nabisubi
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | | | - Paul E. Oluniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Paulo Arnaldo
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Peter Kojo Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Peter O. Okokhere
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- Department of Medicine, Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Edo State, Nigeria
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Phillip A. Bester
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | - Placide K. Mbala
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Pontiano Kaleebu
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Priscilla Abechi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Rabeh El-Shesheny
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
- Infectious Hazards Preparedness, World Health Organization, Eastern Mediterranean Regional Office, Cairo, Egypt
| | - Rageema Joseph
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Ramy Karam Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Microbiology and Immunology Research Program, Children’s Cancer Hospital Egypt, Cairo, Egypt
| | - René G. Essomba
- National Public Health Laboratory, Ministry of Public Health of Cameroon, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon
| | - Reuben Ayivor-Djanie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | - Richard Njouom
- Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
| | - Richard O. Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richmond Gorman
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Rosa Maria D. E. S. A. Neto Rodrigues
- Coordenadora da rede do Diagnóstico Tuberculose/HIV/COVID-19 na Instituição - Laboratório Nacional de Referência da Tuberculose em São Tomé e Príncipe, São Tomé, São Tomé and Principe
- Ponto focal para Melhoria da qualidade dos Laboratórios (SLIPTA) ao nível de São Tomé e Príncipe, São Tomé, São Tomé and Principe
| | - Rosemary A. Audu
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Rosina A. A. Carr
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | - Saba Gargouri
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Safietou Sankhe
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Saibu Femi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Salma Mhalla
- University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory LR99ES09, Tunis, Tunisia
- Faculty of Medicine of Monastir, University of Monastir, Monastir, Tunisia
| | - Salome Hosch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Samar Kamal Kassim
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Samar Metha
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sameh Trabelsi
- Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
| | - Sara Hassan Agwa
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Sarah Wambui Mwangi
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Seydou Doumbia
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Sheila Makiala-Mandanda
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Sherihane Aryeetey
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | | | - Siham Elhamoumi
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Silvia Lutucuta
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simbirie Jalloh
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | | | - Sobajo Oguntope
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Sonia Lekana-Douki
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Soumeya Ouangraoua
- Centre MURAZ, Ouagadougou, Burkina Faso
- National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
| | - Stephanie van Wyk
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Stephen F. Schaffner
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Stephen Kanyerezi
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | - Steve Ahuka-Mundeke
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | | | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Susan Nabadda
- Central Public Health Laboratories (CPHL), Kampala, Uganda
| | - Sylvie Behillil
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
| | | | - Sylvie van der Werf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
| | - Tapfumanei Mashe
- National Microbiology Reference Laboratory, Harare, Zimbabwe
- World Health Organization, Harare, Zimbabwe
| | - Thabo Mohale
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Thirumalaisamy P. Velavan
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
| | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- University of Basel, Basel, Switzerland
| | - Tongai G. Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ugwu Chinedu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
| | - Uwem E. George
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Vincent Enouf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
| | - Vishvanath Nene
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Vivianne Gorova
- World Health Organization, WHO Lesotho, Maseru, Lesotho
- Med24 Medical Centre, Ruwa, Zimbabwe
| | | | - Wasim Abdul Karim
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - William K. Ampofo
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Wonderful T. Choga
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Yahaya Ali Ahmed
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Yajna Ramphal
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Yemaachi Biotech, Accra, Ghana
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Yvan Butera
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
| | | | - Africa Pathogen Genomics Initiative (Africa PGI)
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- The Biotechnology Centre of the University of Yaoundé I, Yaoundé, Cameroon
- CDC Foundation, Atlanta, Georgia, Nebraska Department of Health and Human Services, Lincoln, NE, USA
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
- West African Health Organisation, Bobo-Dioulasso, Burkina Faso
- Faculty of Medicine and Health Sciences, Kassala University, Kassala City, Sudan
- Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan
- General Administration of Laboratories and Blood Banks, Ministry of Health, Kassala State, Sudan
- MRC Unit The Gambia at LSHTM, Fajara, Gambia
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
- Libyan Biotechnology Research Center, Tripoli, Libya
- Center for Medical and Sanitary Research (CERMES), Niamey, Niger
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Laboratoire de la Caisse Nationale de Sécurité Sociale, Djibouti, Republic of Djibouti
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
- The Pirbright Institute, Woking, UK
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Genomics and Epigenomics Program, Research Department CCHE57357, Cairo, Egypt
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- Laboratório de Biologia Molecular Jean Piaget, Bissau, Guinea-Bissau
- University Jean Piaget in Guinea-Bissau, Bissau, Guinea-Bissau
- SAMRC Bioinformatics Unit, SA Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
- Quadram Institute Bioscience, Norwich, UK
- Central Public Health Reference Laboratories, Freetown, Sierra Leone
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier University, 34090, Montpellier, France
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Central Public Health Laboratories (CPHL), Cairo, Egypt
- National Institute of Public Health, Bujumbura, Burundi
- Laboratoire des Fièvres Hémorragiques Virales du Benin, Cotonou, Benin
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Apporach and Technological Innovation for a Better Health”, LR20IPT02, Pasteur Institute, Tunis 1002, Tunisia
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Marien Ngouabi, Brazzaville, Republic of the Congo
- Kwame Nkrumah University of Science and Technology, Department of Theoretical and Applied Biology, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Borno State, Nigeria
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
- Département de Parasitologie-Mycologie Université des Sciences de la Santé (USS), Libreville, Gabon
- National HIV Reference Laboratory, Community Health Sciences Unit, Ministry of Health, Lilongwe, Malawi
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
- National Medical and Molecular Biology Laboratory, Ministry of Health, Djibouti, Republic of Djibouti
- Africa CDC, Rapid Responder, Team Djibouti, Djibouti, Djibouti
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health Seychelles, Victoria, Seychelles
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- National Health Laboratory Service (NHLS), Cape Town, South Africa
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
- University of Nebraska Medical Center (UNMC), Omaha, NE, USA
- SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
- UFR Sciences Médicales, Universite Alassane Ouattara, Bouaké, Côte d’Ivoire
- School of Public Health, Pwani University, Kilifi, Kenya
- Faculty of Science and Techniques, University Marien Ngouabi, Brazzaville, Republic of the Congo
- Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
- Laboratoire des Arbovirus, Fièvres Hémorragiques virales, Virus Emergents et Zoonoses, Institut Pasteur de Bangui, Bangui, Central African Republic
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- PATH, Lusaka, Zambia
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- Uganda Virus Research Institute, Entebbe, Uganda
- PathCare Vermaak, Pretoria, South Africa and Division of Virology, University of the Free State, Bloemfontein, South Africa
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Macha Research Trust, Choma, Zambia
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- INRSP, Nouakchott, Mauritania
- Faculté de Médecine de Nouakchott, Nouakchott, Mauritani
- Rwanda National Reference Laboratory, Kigali, Rwanda
- Robert Koch-Institute, Berlin, Germany
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Paris, France
- Direcção Nacional da Saúde Pública, Ministério da Saúde, Luanda, Angola
- National Public Health Reference Laboratory–National Public Health Institute of Liberia, Monrovia, Liberia
- Faculty of Pharmacy of Monastir, Monastir, Tunisia
- National Influenza Centre, Institut Pasteur d’Algérie, Algiers, Algeria
- Department of Virology, National Health Laboratory Service (NHLS), Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
- Ministère de Santé Publique et de la Solidarité Nationale, Ndjamena, Chad
- WHO Int Comoros, Moroni, Union of Comoros
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
- Ministry of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Nigeria
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
- Central Public Health Laboratories (CPHL), Kampala, Uganda
- Institut Pasteur de Côte d’Ivoire, Departement des Virus Epidemiques, Abidjan, Côte d’Ivoire
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
- Doctoral School of Technical and Environmental Sciences, Department of Biology and Human Health, N’Djamena, Chad
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
- Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory LR99ES09, Tunis, Tunisia
- College of Medicine and Allied Health Science, University of Sierra Leone, Freetown, Sierra Leone
- Namibia Institute of Pathology, Windhoek, Namibia
- National Institute of Hygiene, Lomé, Togo
- Virology/Molecular Biology Department, Central Health Laboratory, Victoria Hospital, Ministry of Health and Wellness, Port Louis, Mauritius
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
- WHO Burundi, Gitega, Burundi
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
- Departamento de Bioquímica, Faculdade de Medicina, Universidade Agostinho Neto, Luanda, Angola
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
- WHO South Sudan, Juba, South Sudan
- Faculty of Medicine, University of Burundi, Bujumbura, Burundi
- Pasteur Network, Institut Pasteur, Paris, France
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- Instituto Nacional de Saúde Pública, Praia, Cape Verde
- Zambia National Public Health Institute, Lusaka, Zambia
- Public Health Institute of Malawi, Lilongwe, Malawi
- National Health Laboratory, Gaborone, Botswana
- Laboratory of Transmissible Diseases and Biologically Active Substances (LR99ES27), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
- Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, Cairo, Egypt
- Ministry of Health and Wellness, Gaborone, Botswana
- Eastern Technical University of Sierra Leone, Kenema, Sierra Leone
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- National Reference Laboratory Lesotho, Maseru, Lesotho
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- Ifakara Health Insitute, Ifakara, Tanzania
- Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- PraesensBio, Lincoln, NE, USA
- Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo, Egypt
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
- Biological Prevention Department, Ministry of Defence, Cairo, Egypt
- Faculty of Science, Fayoum University, Fayoum, Egypt
- Molecular Pathology Lab, Children’s Cancer Hospital, Cairo, Egypt
- Laboratoire Biolim FSS/Université de Lomé, Lomé, Togo
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
- High Institute of Biotechnology of Monastir, University of Monastir, Rue Taher Haddad 5000, Monastir, Tunisia
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Department of Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Sudan
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
- Institut Pasteur de Guinée, Conarky, Guinea
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences. College of Health Sciences. University of Ilorin, Ilorin, Kwara State, Nigeria
- Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
- Mayotte Hospital Center, Mayotte, France
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
- Department of Medicine, Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Edo State, Nigeria
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
- Infectious Hazards Preparedness, World Health Organization, Eastern Mediterranean Regional Office, Cairo, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Microbiology and Immunology Research Program, Children’s Cancer Hospital Egypt, Cairo, Egypt
- National Public Health Laboratory, Ministry of Public Health of Cameroon, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon
- Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
- Coordenadora da rede do Diagnóstico Tuberculose/HIV/COVID-19 na Instituição - Laboratório Nacional de Referência da Tuberculose em São Tomé e Príncipe, São Tomé, São Tomé and Principe
- Ponto focal para Melhoria da qualidade dos Laboratórios (SLIPTA) ao nível de São Tomé e Príncipe, São Tomé, São Tomé and Principe
- National Public Health Reference Laboratory (NPHRL), Mogadishu, Somalia
- Faculty of Medicine of Monastir, University of Monastir, Monastir, Tunisia
- University of Basel, Basel, Switzerland
- Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre MURAZ, Ouagadougou, Burkina Faso
- National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
- World Health Organization, Harare, Zimbabwe
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
- World Health Organization, WHO Lesotho, Maseru, Lesotho
- Med24 Medical Centre, Ruwa, Zimbabwe
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Yemaachi Biotech, Accra, Ghana
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Ahmed E. O. Ouma
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Matshidiso Moeti
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Pardis C. Sabeti
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Amadou A. Sall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Samuel O. Oyola
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Yenew K. Tebeje
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Sofonias K. Tessema
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - John Nkengasong
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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Ismael N, Wilkinson E, Mahumane I, Gemusse H, Giandhari J, Bauhofer A, Vubil A, Mambo P, Singh L, Mabunda N, Bila D, Engelbrecht S, Gudo E, Lessells R, de Oliveira T. Molecular Epidemiology and Trends in HIV-1 Transmitted Drug Resistance in Mozambique 1999–2018. Viruses 2022; 14:v14091992. [PMID: 36146798 PMCID: PMC9505726 DOI: 10.3390/v14091992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/20/2022] Open
Abstract
HIV drug resistance (HIVDR) can become a public health concern, especially in low- and middle-income countries where genotypic testing for people initiating antiretroviral therapy (ART) is not available. For first-line regimens to remain effective, levels of transmitted drug resistance (TDR) need to be monitored over time. To determine the temporal trends of TDR in Mozambique, a search for studies in PubMed and sequences in GenBank was performed. Only studies covering the pol region that described HIVDR and genetic diversity from treatment naïve patients were included. A dataset from seven published studies and one novel unpublished study conducted between 1999 and 2018 were included. The Calibrated Population Resistance tool (CPR) and REGA HIV-1 Subtyping Tool version 3 for sequences pooled by sampling year were used to determine resistance mutations and subtypes, respectively. The prevalence of HIVDR amongst treatment-naïve individuals increased over time, reaching 14.4% in 2018. The increase was most prominent for non-nucleoside reverse transcriptase inhibitors (NNRTIs), reaching 12.7% in 2018. Subtype C was predominant in all regions, but a higher genetic variability (19% non-subtype C) was observed in the north region of Mozambique. These findings confirm a higher diversity of HIV in the north of the country and an increased prevalence of NNRTI resistance among treatment naïve individuals over time.
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Affiliation(s)
- Nalia Ismael
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
- Correspondence: (N.I.); (T.d.O.)
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Isabel Mahumane
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Hernane Gemusse
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Adilson Bauhofer
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Adolfo Vubil
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Pirolita Mambo
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Nédio Mabunda
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Dulce Bila
- Elizabeth Glaser Pediatric AIDS Foundation in Mozambique, Avenida Agostinho Neto, Maputo 620, Mozambique
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa
| | - Eduardo Gudo
- Instituto Nacional de Saúde (INS), Estrada Nacional N1, Marracuene 3943, Mozambique
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Túlio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7602, South Africa
- Correspondence: (N.I.); (T.d.O.)
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10
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Goodman WR, Scott ER, Keith Z, Singh L, Anderson DT. Upgrade of the helically symmetric experiment Thomson scattering diagnostic suite. Rev Sci Instrum 2022; 93:093518. [PMID: 36182445 DOI: 10.1063/5.0101879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/17/2022] [Indexed: 06/16/2023]
Abstract
The Helically Symmetric eXperiment (HSX) Thomson Scattering (TS) diagnostic is being upgraded to decrease uncertainty in electron temperature and density measurements. Upgrades to the HSX TS diagnostic will consist of a novel redesign of polychromator electronics and digitization of the TS output signal. Here, we also present a study of the benefits of an additional spectral channel that will sample the red-shifted band of the scattered spectrum. To maximize system bandwidth (BW) and gain, while minimizing noise, the existing low-BW polychromator electronics on HSX will be replaced by high-BW, high gain circuitry designed in-house.
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Affiliation(s)
- W R Goodman
- HSX Plasma Laboratory, University of Wisconsin, Madison, Wisconsin 53703, USA
| | - E R Scott
- HSX Plasma Laboratory, University of Wisconsin, Madison, Wisconsin 53703, USA
| | - Z Keith
- HSX Plasma Laboratory, University of Wisconsin, Madison, Wisconsin 53703, USA
| | - L Singh
- HSX Plasma Laboratory, University of Wisconsin, Madison, Wisconsin 53703, USA
| | - D T Anderson
- HSX Plasma Laboratory, University of Wisconsin, Madison, Wisconsin 53703, USA
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11
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Tegally H, Moir M, Everatt J, Giovanetti M, Scheepers C, Wilkinson E, Subramoney K, Makatini Z, Moyo S, Amoako DG, Baxter C, Althaus CL, Anyaneji UJ, Kekana D, Viana R, Giandhari J, Lessells RJ, Maponga T, Maruapula D, Choga W, Matshaba M, Mbulawa MB, Msomi N, Naidoo Y, Pillay S, Sanko TJ, San JE, Scott L, Singh L, Magini NA, Smith-Lawrence P, Stevens W, Dor G, Tshiabuila D, Wolter N, Preiser W, Treurnicht FK, Venter M, Chiloane G, McIntyre C, O'Toole A, Ruis C, Peacock TP, Roemer C, Kosakovsky Pond SL, Williamson C, Pybus OG, Bhiman JN, Glass A, Martin DP, Jackson B, Rambaut A, Laguda-Akingba O, Gaseitsiwe S, von Gottberg A, de Oliveira T. Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. Nat Med 2022; 28:1785-1790. [PMID: 35760080 PMCID: PMC9499863 DOI: 10.1038/s41591-022-01911-2] [Citation(s) in RCA: 358] [Impact Index Per Article: 179.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/21/2022] [Indexed: 11/09/2022]
Abstract
Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa's fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and similar to BA.2 except for the addition of 69-70 deletion (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild-type amino acid at Q493. The two lineages differ only outside of the spike region. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene target failure, on the background of variants not possessing this feature. BA.4 and BA.5 have rapidly replaced BA.2, reaching more than 50% of sequenced cases in South Africa by the first week of April 2022. Using a multinomial logistic regression model, we estimated growth advantages for BA.4 and BA.5 of 0.08 (95% confidence interval (CI): 0.08-0.09) and 0.10 (95% CI: 0.09-0.11) per day, respectively, over BA.2 in South Africa. The continued discovery of genetically diverse Omicron lineages points to the hypothesis that a discrete reservoir, such as human chronic infections and/or animal hosts, is potentially contributing to further evolution and dispersal of the virus.
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Affiliation(s)
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Josie Everatt
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Kathleen Subramoney
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zinhle Makatini
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
| | - Daniel G Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Ugochukwu J Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Dikeledi Kekana
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Wonderful Choga
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | | | - Mpaphi B Mbulawa
- National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Nokukhanya Msomi
- Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu-Natal, Durban, South Africa
| | - Yeshnee Naidoo
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tomasz Janusz Sanko
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - James E San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Lesley Scott
- Department of Molecular Medicine and Haematology, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nonkululeko A Magini
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Wendy Stevens
- Department of Molecular Medicine and Haematology, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- National Priority Program of the National Health Laboratory Service, Johannesburg, South Africa
| | - Graeme Dor
- National Priority Program of the National Health Laboratory Service, Johannesburg, South Africa
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nicole Wolter
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Florette K Treurnicht
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Marietjie Venter
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Georginah Chiloane
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Caitlyn McIntyre
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Aine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | - Carolyn Williamson
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Jinal N Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Allison Glass
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Lancet Laboratories, Johannesburg, South Africa
| | - Darren P Martin
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Ben Jackson
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Oluwakemi Laguda-Akingba
- NHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa
- Faculty of Health Sciences, Walter Sisulu University, Eastern Cape, South Africa
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
- Department of Global Health, University of Washington, Seattle, WA, USA.
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12
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Abud AA, Abi B, Acciarri R, Acero MA, Adames MR, Adamov G, Adamowski M, Adams D, Adinolfi M, Aduszkiewicz A, Aguilar J, Ahmad Z, Ahmed J, Aimard B, Ali-Mohammadzadeh B, Alion T, Allison K, Monsalve SA, AlRashed M, Alt C, Alton A, Alvarez R, Amedo P, Anderson J, Andreopoulos C, Andreotti M, Andrews M, Andrianala F, Andringa S, Anfimov N, Ankowski A, Antoniassi M, Antonova M, Antoshkin A, Antusch S, Aranda-Fernandez A, Arellano L, Arnold LO, Arroyave MA, Asaadi J, Asquith L, Aurisano A, Aushev V, Autiero D, Lara VA, Ayala-Torres M, Azfar F, Back A, Back H, Back JJ, Backhouse C, Bagaturia I, Bagby L, Balashov N, Balasubramanian S, Baldi P, Baller B, Bambah B, Barao F, Barenboim G, Alzas PB, Barker G, Barkhouse W, Barnes C, Barr G, Monarca JB, Barros A, Barros N, Barrow JL, Basharina-Freshville A, Bashyal A, Basque V, Batchelor C, Chagas EBD, Battat JBR, Battisti F, Bay F, Bazetto MCQ, Alba JLLB, Beacom JF, Bechetoille E, Behera B, Beigbeder C, Bellantoni L, Bellettini G, Bellini V, Beltramello O, Benekos N, Montiel CB, Neves FB, Berger J, Berkman S, Bernardini P, Berner RM, Bersani A, Bertolucci S, Betancourt M, Rodríguez AB, Bevan A, Bezawada Y, Bezerra TJC, Bhardwaj A, Bhatnagar V, Bhattacharjee M, Bhattarai D, Bhuller S, Bhuyan B, Biagi S, Bian J, Biassoni M, Biery K, Bilki B, Bishai M, Bitadze A, Blake A, Blaszczyk F, Blazey GC, Blucher E, Boissevain J, Bolognesi S, Bolton T, Bomben L, Bonesini M, Bongrand M, Bonilla-Diaz C, Bonini F, Booth A, Boran F, Bordoni S, Borkum A, Bostan N, Bour P, Bourgeois C, Boyden D, Bracinik J, Braga D, Brailsford D, Branca A, Brandt A, Bremer J, Breton D, Brew C, Brice SJ, Brizzolari C, Bromberg C, Brooke J, Bross A, Brunetti G, Brunetti M, Buchanan N, Budd H, Butorov I, Cagnoli I, Cai T, Caiulo D, Calabrese R, Calafiura P, Calcutt J, Calin M, Calvez S, Calvo E, Caminata A, Campanelli M, Caratelli D, Carber D, Carceller JC, Carini G, Carlus B, Carneiro MF, Carniti P, Terrazas IC, Carranza H, Carroll T, Forero JFC, Castillo A, Castromonte C, Catano-Mur E, Cattadori C, Cavalier F, Cavallaro G, Cavanna F, Centro S, Cerati G, Cervelli A, Villanueva AC, Chalifour M, Chappell A, Chardonnet E, Charitonidis N, Chatterjee A, Chattopadhyay S, Neyra MSSC, Chen H, Chen M, Chen Y, Chen Z, Chen-Wishart Z, Cheon Y, Cherdack D, Chi C, Childress S, Chirco R, Chiriacescu A, Chisnall G, Cho K, Choate S, Chokheli D, Chong PS, Christensen A, Christian D, Christodoulou G, Chukanov A, Chung M, Church E, Cicero V, Clarke P, Cline G, Coan TE, Cocco AG, Coelho JAB, Colton N, Conley E, Conley R, Conrad J, Convery M, Copello S, Cova P, Cremaldi L, Cremonesi L, Crespo-Anadón JI, Crisler M, Cristaldo E, Crnkovic J, Cross R, Cudd A, Cuesta C, Cui Y, Cussans D, Dalager O, da Motta H, Da Silva Peres L, David C, David Q, Davies GS, Davini S, Dawson J, De K, De S, Debbins P, De Bonis I, Decowski MP, De Gouvêa A, De Holanda PC, De Icaza Astiz IL, Deisting A, De Jong P, Delbart A, Delepine D, Delgado M, Dell’Acqua A, Delmonte N, De Lurgio P, de Mello Neto JRT, DeMuth DM, Dennis S, Densham C, Deptuch GW, De Roeck A, De Romeri V, De Souza G, Devi R, Dharmapalan R, Dias M, Diaz F, Díaz JS, Domizio SD, Giulio LD, Ding P, Noto LD, Dirkx G, Distefano C, Diurba R, Diwan M, Djurcic Z, Doering D, Dolan S, Dolek F, Dolinski M, Domine L, Donon Y, Douglas D, Douillet D, Dragone A, Drake G, Drielsma F, Duarte L, Duchesneau D, Duffy K, Dunne P, Dutta B, Duyang H, Dvornikov O, Dwyer D, Dyshkant A, Eads M, Earle A, Edmunds D, Eisch J, Emberger L, Emery S, Englezos P, Ereditato A, Erjavec T, Escobar C, Eurin G, Evans JJ, Ewart E, Ezeribe AC, Fahey K, Falcone A, Fani’ M, Farnese C, Farzan Y, Fedoseev D, Felix J, Feng Y, Fernandez-Martinez E, Menendez PF, Morales MF, Ferraro F, Fields L, Filip P, Filthaut F, Fiorini M, Fischer V, Fitzpatrick RS, Flanagan W, Fleming B, Flight R, Fogarty S, Foreman W, Fowler J, Fox W, Franc J, Francis K, Franco D, Freeman J, Freestone J, Fried J, Friedland A, Robayo FF, Fuess S, Furic IK, Furman K, Furmanski AP, Gabrielli A, Gago A, Gallagher H, Gallas A, Gallego-Ros A, Gallice N, Galymov V, Gamberini E, Gamble T, Ganacim F, Gandhi R, Gandrajula R, Gao F, Gao S, Garcia-Gamez D, García-Peris MÁ, Gardiner S, Gastler D, Gauvreau J, Ge G, Geffroy N, Gelli B, Gendotti A, Gent S, Ghorbani-Moghaddam Z, Giammaria P, Giammaria T, Giangiacomi N, Gibin D, Gil-Botella I, Gilligan S, Girerd C, Giri AK, Gnani D, Gogota O, Gold M, Gollapinni S, Gollwitzer K, Gomes RA, Bermeo LVG, Fajardo LSG, Gonnella F, Gonzalez-Diaz D, Gonzalez-Lopez M, Goodman MC, Goodwin O, Goswami S, Gotti C, Goudzovski E, Grace C, Gran R, Granados E, Granger P, Grant A, Grant C, Gratieri D, Green P, Greenler L, Greer J, Grenard J, Griffith WC, Groh M, Grudzinski J, Grzelak K, Gu W, Guardincerri E, Guarino V, Guarise M, Guenette R, Guerard E, Guerzoni M, Guffanti D, Guglielmi A, Guo B, Gupta A, Gupta V, Guthikonda KK, Gutierrez R, Guzowski P, Guzzo MM, Gwon S, Ha C, Haaf K, Habig A, Hadavand H, Haenni R, Hahn A, Haiston J, Hamacher-Baumann P, Hamernik T, Hamilton P, Han J, Harris DA, Hartnell J, Hartnett T, Harton J, Hasegawa T, Hasnip C, Hatcher R, Hatfield KW, Hatzikoutelis A, Hayes C, Hayrapetyan K, Hays J, Hazen E, He M, Heavey A, Heeger KM, Heise J, Henry S, Morquecho MAH, Herner K, Hewes J, Hilgenberg C, Hill T, Hillier SJ, Himmel A, Hinkle E, Hirsch LR, Ho J, Hoff J, Holin A, Hoppe E, Horton-Smith GA, Hostert M, Hourlier A, Howard B, Howell R, Hoyos J, Hristova I, Hronek MS, Huang J, Hulcher Z, Iles G, Ilic N, Iliescu AM, Illingworth R, Ingratta G, Ioannisian A, Irwin B, Isenhower L, Itay R, Jackson CM, Jain V, James E, Jang W, Jargowsky B, Jediny F, Jena D, Jeong YS, Jesús-Valls C, Ji X, Jiang L, Jiménez S, Jipa A, Johnson R, Johnson W, Johnston N, Jones B, Jones S, Judah M, Jung CK, Junk T, Jwa Y, Kabirnezhad M, Kaboth A, Kadenko I, Kakorin I, Kalitkina A, Kalra D, Kamiya F, Kaneshige N, Kaplan DM, Karagiorgi G, Karaman G, Karcher A, Karolak M, Karyotakis Y, Kasai S, Kasetti SP, Kashur L, Kazaryan N, Kearns E, Keener P, Kelly KJ, Kemp E, Kemularia O, Ketchum W, Kettell SH, Khabibullin M, Khotjantsev A, Khvedelidze A, Kim D, King B, Kirby B, Kirby M, Klein J, Klustova A, Kobilarcik T, Koehler K, Koerner LW, Koh DH, Kohn S, Koller PP, Kolupaeva L, Korablev D, Kordosky M, Kosc T, Kose U, Kostelecký VA, Kothekar K, Kralik R, Kreczko L, Krennrich F, Kreslo I, Kropp W, Kroupova T, Kubota S, Kudenko Y, Kudryavtsev VA, Kulagin S, Kumar J, Kumar P, Kunze P, Kurita N, Kuruppu C, Kus V, Kutter T, Kvasnicka J, Kwak D, Lambert A, Land B, Lane CE, Lang K, Langford T, Langstaff M, Larkin J, Lasorak P, Last D, Laundrie A, Laurenti G, Lawrence A, Lazanu I, LaZur R, Lazzaroni M, Le T, Leardini S, Learned J, LeBrun P, LeCompte T, Lee C, Lee SY, Miotto GL, Lehnert R, de Oliveira MAL, Leitner M, Lepin LM, Li SW, Li Y, Liao H, Lin CS, Lin Q, Lin S, Lineros RA, Ling J, Lister A, Littlejohn BR, Liu J, Liu Y, Lockwitz S, Loew T, Lokajicek M, Lomidze I, Long K, Lord T, LoSecco JM, Louis WC, Lu 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Whittington D, Wilking MJ, Wilkinson A, Wilkinson C, Williams Z, Wilson F, Wilson RJ, Wisniewski W, Wolcott J, Wongjirad T, Wood A, Wood K, Worcester E, Worcester M, Wresilo K, Wret C, Wu W, Wu W, Xiao Y, Xie F, Yaeggy B, Yandel E, Yang G, Yang K, Yang T, Yankelevich A, Yershov N, Yonehara K, Yoon YS, Young T, Yu B, Yu H, Yu H, Yu J, Yu Y, Yuan W, Zaki R, Zalesak J, Zambelli L, Zamorano B, Zani A, Zazueta L, Zeller GP, Zennamo J, Zeug K, Zhang C, Zhang S, Zhang Y, Zhao M, Zhivun E, Zhu G, Zimmerman ED, Zucchelli S, Zuklin J, Zutshi V, Zwaska R. Scintillation light detection in the 6-m drift-length ProtoDUNE Dual Phase liquid argon TPC. Eur Phys J C Part Fields 2022; 82:618. [PMID: 35859696 PMCID: PMC9288420 DOI: 10.1140/epjc/s10052-022-10549-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
DUNE is a dual-site experiment for long-baseline neutrino oscillation studies, neutrino astrophysics and nucleon decay searches. ProtoDUNE Dual Phase (DP) is a 6 × 6 × 6 m 3 liquid argon time-projection-chamber (LArTPC) that recorded cosmic-muon data at the CERN Neutrino Platform in 2019-2020 as a prototype of the DUNE Far Detector. Charged particles propagating through the LArTPC produce ionization and scintillation light. The scintillation light signal in these detectors can provide the trigger for non-beam events. In addition, it adds precise timing capabilities and improves the calorimetry measurements. In ProtoDUNE-DP, scintillation and electroluminescence light produced by cosmic muons in the LArTPC is collected by photomultiplier tubes placed up to 7 m away from the ionizing track. In this paper, the ProtoDUNE-DP photon detection system performance is evaluated with a particular focus on the different wavelength shifters, such as PEN and TPB, and the use of Xe-doped LAr, considering its future use in giant LArTPCs. The scintillation light production and propagation processes are analyzed and a comparison of simulation to data is performed, improving understanding of the liquid argon properties.
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Affiliation(s)
- A. Abed Abud
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
- University of Liverpool, Liverpool, L69 7ZE UK
| | - B. Abi
- University of Oxford, Oxford, OX1 3RH UK
| | - R. Acciarri
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - M. A. Acero
- Universidad del Atlántico, Barranquilla, Atlántico Colombia
| | - M. R. Adames
- Universidade Tecnológica Federal do Paraná, Curitiba, Brazil
| | - G. Adamov
- Georgian Technical University, Tbilisi, Georgia
| | - M. Adamowski
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - D. Adams
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | | | | | - J. Aguilar
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Z. Ahmad
- Variable Energy Cyclotron Centre, Kolkata, West Bengal 700 064 India
| | - J. Ahmed
- University of Warwick, Coventry, CV4 7AL UK
| | - B. Aimard
- Laboratoire d’Annecy de Physique des Particules, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LAPP-IN2P3, 74000 Annecy, France
| | - B. Ali-Mohammadzadeh
- Università di Catania, 2, 95131 Catania, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Catania, 95123 Catania, Italy
| | - T. Alion
- University of Sussex, Brighton, BN1 9RH UK
| | - K. Allison
- University of Colorado Boulder, Boulder, CO 80309 USA
| | - S. Alonso Monsalve
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
- ETH Zurich, Zurich, Switzerland
| | - M. AlRashed
- Kansas State University, Manhattan, KS 66506 USA
| | - C. Alt
- ETH Zurich, Zurich, Switzerland
| | - A. Alton
- Augustana University, Sioux Falls, SD 57197 USA
| | - R. Alvarez
- CIEMAT, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, 28040 Madrid, Spain
| | - P. Amedo
- Instituto Galego de Fisica de Altas Enerxias, A Coruña, Spain
| | - J. Anderson
- Argonne National Laboratory, Argonne, IL 60439 USA
| | - C. Andreopoulos
- University of Liverpool, Liverpool, L69 7ZE UK
- STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX UK
| | - M. Andreotti
- University of Ferrara, Ferrara, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Ferrara, 44122 Ferrara, Italy
| | - M. Andrews
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - F. Andrianala
- University of Antananarivo, 101 Antananarivo, Madagascar
| | - S. Andringa
- Laboratório de Instrumentação e Física Experimental de Partículas, 1649-003 Lisboa, 3004-516 Coimbra, Portugal
| | - N. Anfimov
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | - A. Ankowski
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - M. Antoniassi
- Universidade Tecnológica Federal do Paraná, Curitiba, Brazil
| | - M. Antonova
- Instituto de Física Corpuscular, CSIC and Universitat de València, 46980 Paterna, Valencia Spain
| | - A. Antoshkin
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | - S. Antusch
- University of Basel, 4056 Basel, Switzerland
| | | | - L. Arellano
- University of Manchester, Manchester, M13 9PL UK
| | | | | | - J. Asaadi
- University of Texas at Arlington, Arlington, TX 76019 USA
| | - L. Asquith
- University of Sussex, Brighton, BN1 9RH UK
| | - A. Aurisano
- University of Cincinnati, Cincinnati, OH 45221 USA
| | - V. Aushev
- Taras Shevchenko National University of Kyiv, Kyiv, 01601 Ukraine
| | - D. Autiero
- Institut de Physique des 2 Infinis de Lyon, 69622 Villeurbanne, France
| | | | - M. Ayala-Torres
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Mexico City, Mexico
| | - F. Azfar
- University of Oxford, Oxford, OX1 3RH UK
| | - A. Back
- Indiana University, Bloomington, IN 47405 USA
| | - H. Back
- Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - J. J. Back
- University of Warwick, Coventry, CV4 7AL UK
| | | | | | - L. Bagby
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - N. Balashov
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | | | - P. Baldi
- University of California Irvine, Irvine, CA 92697 USA
| | - B. Baller
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - B. Bambah
- University of Hyderabad, Gachibowli, Hyderabad, 500 046 India
| | - F. Barao
- Instituto Superior Técnico-IST, Universidade de Lisboa, 1049-001 Lisbon, Portugal
- Laboratório de Instrumentação e Física Experimental de Partículas, 1649-003 Lisboa, 3004-516 Coimbra, Portugal
| | - G. Barenboim
- Instituto de Física Corpuscular, CSIC and Universitat de València, 46980 Paterna, Valencia Spain
| | - P. Barham Alzas
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - G. Barker
- University of Warwick, Coventry, CV4 7AL UK
| | - W. Barkhouse
- University of North Dakota, Grand Forks, ND 58202-8357 USA
| | - C. Barnes
- University of Michigan, Ann Arbor, MI 48109 USA
| | - G. Barr
- University of Oxford, Oxford, OX1 3RH UK
| | | | - A. Barros
- Universidade Tecnológica Federal do Paraná, Curitiba, Brazil
| | - N. Barros
- Faculdade de Ciências da Universidade de Lisboa-FCUL, 1749-016 Lisbon, Portugal
- Laboratório de Instrumentação e Física Experimental de Partículas, 1649-003 Lisboa, 3004-516 Coimbra, Portugal
| | - J. L. Barrow
- Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | | | - A. Bashyal
- Argonne National Laboratory, Argonne, IL 60439 USA
| | - V. Basque
- University of Manchester, Manchester, M13 9PL UK
| | | | | | | | | | - F. Bay
- Antalya Bilim University, 07190 Döşemealti/Antalya, Turkey
| | - M. C. Q. Bazetto
- Universidade Estadual de Campinas, Campinas, SP 13083-970 Brazil
| | | | | | - E. Bechetoille
- Institut de Physique des 2 Infinis de Lyon, 69622 Villeurbanne, France
| | - B. Behera
- Colorado State University, Fort Collins, CO 80523 USA
| | - C. Beigbeder
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - L. Bellantoni
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | | | - V. Bellini
- Università di Catania, 2, 95131 Catania, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Catania, 95123 Catania, Italy
| | - O. Beltramello
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - N. Benekos
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | | | - F. Bento Neves
- Laboratório de Instrumentação e Física Experimental de Partículas, 1649-003 Lisboa, 3004-516 Coimbra, Portugal
| | - J. Berger
- Colorado State University, Fort Collins, CO 80523 USA
| | - S. Berkman
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - P. Bernardini
- Istituto Nazionale di Fisica Nucleare Sezione di Lecce, 73100 Lecce, Italy
- Università del Salento, 73100 Lecce, Italy
| | | | - A. Bersani
- Istituto Nazionale di Fisica Nucleare Sezione di Genova, 16146 Genoa, GE Italy
| | - S. Bertolucci
- Università del Bologna, 40127 Bologna, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - M. Betancourt
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | | | - A. Bevan
- Queen Mary University of London, London, E1 4NS UK
| | - Y. Bezawada
- University of California Davis, Davis, CA 95616 USA
| | | | - A. Bhardwaj
- Louisiana State University, Baton Rouge, LA 70803 USA
| | - V. Bhatnagar
- Panjab University, Chandigarh, U.T. 160014 India
| | - M. Bhattacharjee
- Indian Institute of Technology Guwahati, Guwahati, 781 039 India
| | - D. Bhattarai
- University of Mississippi, University, MS 38677 USA
| | - S. Bhuller
- University of Bristol, Bristol, BS8 1TL UK
| | - B. Bhuyan
- Indian Institute of Technology Guwahati, Guwahati, 781 039 India
| | - S. Biagi
- Istituto Nazionale di Fisica Nucleare Laboratori Nazionali del Sud, 95123 Catania, Italy
| | - J. Bian
- University of California Irvine, Irvine, CA 92697 USA
| | - M. Biassoni
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
| | - K. Biery
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - B. Bilki
- Beykent University, Istanbul, Turkey
- University of Iowa, Iowa City, IA 52242 USA
| | - M. Bishai
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - A. Bitadze
- University of Manchester, Manchester, M13 9PL UK
| | - A. Blake
- Lancaster University, Lancaster, LA1 4YB UK
| | - F. Blaszczyk
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - G. C. Blazey
- Northern Illinois University, DeKalb, IL 60115 USA
| | - E. Blucher
- University of Chicago, Chicago, IL 60637 USA
| | - J. Boissevain
- Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - S. Bolognesi
- IRFU, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - T. Bolton
- Kansas State University, Manhattan, KS 66506 USA
| | - L. Bomben
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
- University of Insubria, Via Ravasi, 2, 21100 Varese, VA Italy
| | - M. Bonesini
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
- Università del Milano-Bicocca, 20126 Milan, Italy
| | - M. Bongrand
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | | | - F. Bonini
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - A. Booth
- Queen Mary University of London, London, E1 4NS UK
| | - F. Boran
- Beykent University, Istanbul, Turkey
| | - S. Bordoni
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - A. Borkum
- University of Sussex, Brighton, BN1 9RH UK
| | - N. Bostan
- University of Notre Dame, Notre Dame, IN 46556 USA
| | - P. Bour
- Czech Technical University, 115 19 Prague 1, Czech Republic
| | - C. Bourgeois
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - D. Boyden
- Northern Illinois University, DeKalb, IL 60115 USA
| | - J. Bracinik
- University of Birmingham, Birmingham, B15 2TT UK
| | - D. Braga
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | | | - A. Branca
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
| | - A. Brandt
- University of Texas at Arlington, Arlington, TX 76019 USA
| | - J. Bremer
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - D. Breton
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - C. Brew
- STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX UK
| | - S. J. Brice
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - C. Brizzolari
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
- Università del Milano-Bicocca, 20126 Milan, Italy
| | - C. Bromberg
- Michigan State University, East Lansing, MI 48824 USA
| | - J. Brooke
- University of Bristol, Bristol, BS8 1TL UK
| | - A. Bross
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - G. Brunetti
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
- Università del Milano-Bicocca, 20126 Milan, Italy
| | | | - N. Buchanan
- Colorado State University, Fort Collins, CO 80523 USA
| | - H. Budd
- University of Rochester, Rochester, NY 14627 USA
| | - I. Butorov
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | - I. Cagnoli
- Università del Bologna, 40127 Bologna, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - T. Cai
- York University, Toronto, M3J 1P3 Canada
| | - D. Caiulo
- Institut de Physique des 2 Infinis de Lyon, 69622 Villeurbanne, France
| | - R. Calabrese
- University of Ferrara, Ferrara, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Ferrara, 44122 Ferrara, Italy
| | - P. Calafiura
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - J. Calcutt
- Oregon State University, Corvallis, OR 97331 USA
| | - M. Calin
- University of Bucharest, Bucharest, Romania
| | - S. Calvez
- Colorado State University, Fort Collins, CO 80523 USA
| | - E. Calvo
- CIEMAT, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, 28040 Madrid, Spain
| | - A. Caminata
- Istituto Nazionale di Fisica Nucleare Sezione di Genova, 16146 Genoa, GE Italy
| | | | - D. Caratelli
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - D. Carber
- Colorado State University, Fort Collins, CO 80523 USA
| | | | - G. Carini
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - B. Carlus
- Institut de Physique des 2 Infinis de Lyon, 69622 Villeurbanne, France
| | | | - P. Carniti
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
| | | | - H. Carranza
- University of Texas at Arlington, Arlington, TX 76019 USA
| | - T. Carroll
- University of Wisconsin Madison, Madison, WI 53706 USA
| | | | - A. Castillo
- Universidad Sergio Arboleda, 11022 Bogotá, Colombia
| | | | - E. Catano-Mur
- College of William and Mary, Williamsburg, VA 23187 USA
| | - C. Cattadori
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
| | - F. Cavalier
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - G. Cavallaro
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
| | - F. Cavanna
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - S. Centro
- Istituto Nazionale di Fisica Nucleare Sezione di Padova, 35131 Padua, Italy
- Universtà degli Studi di Padova, 35131 Padua, Italy
| | - G. Cerati
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - A. Cervelli
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - A. Cervera Villanueva
- Instituto de Física Corpuscular, CSIC and Universitat de València, 46980 Paterna, Valencia Spain
| | - M. Chalifour
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | | | - E. Chardonnet
- Université de Paris, CNRS, Astroparticule et Cosmologie, 75006 Paris, France
| | - N. Charitonidis
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | | | - S. Chattopadhyay
- Variable Energy Cyclotron Centre, Kolkata, West Bengal 700 064 India
| | | | - H. Chen
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - M. Chen
- University of California Irvine, Irvine, CA 92697 USA
| | - Y. Chen
- University of Bern, 3012 Bern, Switzerland
| | - Z. Chen
- Stony Brook University, SUNY, Stony Brook, NY 11794 USA
| | | | - Y. Cheon
- Ulsan National Institute of Science and Technology, Ulsan, 689-798 South Korea
| | - D. Cherdack
- University of Houston, Houston, TX 77204 USA
| | - C. Chi
- Columbia University, New York, NY 10027 USA
| | - S. Childress
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - R. Chirco
- Illinois Institute of Technology, Chicago, IL 60616 USA
| | | | | | - K. Cho
- Korea Institute of Science and Technology Information, Daejeon, 34141 South Korea
| | - S. Choate
- Northern Illinois University, DeKalb, IL 60115 USA
| | - D. Chokheli
- Georgian Technical University, Tbilisi, Georgia
| | - P. S. Chong
- University of Pennsylvania, Philadelphia, PA 19104 USA
| | | | - D. Christian
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - G. Christodoulou
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - A. Chukanov
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | - M. Chung
- Ulsan National Institute of Science and Technology, Ulsan, 689-798 South Korea
| | - E. Church
- Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - V. Cicero
- Università del Bologna, 40127 Bologna, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - P. Clarke
- University of Edinburgh, Edinburgh, EH8 9YL UK
| | - G. Cline
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - T. E. Coan
- Southern Methodist University, Dallas, TX 75275 USA
| | - A. G. Cocco
- Istituto Nazionale di Fisica Nucleare Sezione di Napoli, 80126 Naples, Italy
| | - J. A. B. Coelho
- Université de Paris, CNRS, Astroparticule et Cosmologie, 75006 Paris, France
| | - N. Colton
- Colorado State University, Fort Collins, CO 80523 USA
| | - E. Conley
- Duke University, Durham, NC 27708 USA
| | - R. Conley
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - J. Conrad
- Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - M. Convery
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - S. Copello
- Istituto Nazionale di Fisica Nucleare Sezione di Genova, 16146 Genoa, GE Italy
| | - P. Cova
- Istituto Nazionale di Fisica Nucleare Sezione di Milano, 20133 Milan, Italy
- University of Parma, 43121 Parma, PR Italy
| | - L. Cremaldi
- University of Mississippi, University, MS 38677 USA
| | - L. Cremonesi
- Queen Mary University of London, London, E1 4NS UK
| | - J. I. Crespo-Anadón
- CIEMAT, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, 28040 Madrid, Spain
| | - M. Crisler
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - E. Cristaldo
- Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - J. Crnkovic
- University of Mississippi, University, MS 38677 USA
| | - R. Cross
- Lancaster University, Lancaster, LA1 4YB UK
| | - A. Cudd
- University of Colorado Boulder, Boulder, CO 80309 USA
| | - C. Cuesta
- CIEMAT, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, 28040 Madrid, Spain
| | - Y. Cui
- University of California Riverside, Riverside, CA 92521 USA
| | - D. Cussans
- University of Bristol, Bristol, BS8 1TL UK
| | - O. Dalager
- University of California Irvine, Irvine, CA 92697 USA
| | - H. da Motta
- Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro, RJ 22290-180 Brazil
| | - L. Da Silva Peres
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-901 Brazil
| | - C. David
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
- York University, Toronto, M3J 1P3 Canada
| | - Q. David
- Institut de Physique des 2 Infinis de Lyon, 69622 Villeurbanne, France
| | - G. S. Davies
- University of Mississippi, University, MS 38677 USA
| | - S. Davini
- Istituto Nazionale di Fisica Nucleare Sezione di Genova, 16146 Genoa, GE Italy
| | - J. Dawson
- Université de Paris, CNRS, Astroparticule et Cosmologie, 75006 Paris, France
| | - K. De
- University of Texas at Arlington, Arlington, TX 76019 USA
| | - S. De
- University of Albany, SUNY, Albany, NY 12222 USA
| | - P. Debbins
- University of Iowa, Iowa City, IA 52242 USA
| | - I. De Bonis
- Laboratoire d’Annecy de Physique des Particules, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LAPP-IN2P3, 74000 Annecy, France
| | - M. P. Decowski
- University of Amsterdam, 1098 XG Amsterdam, The Netherlands
- Nikhef National Institute of Subatomic Physics, 1098 XG Amsterdam, The Netherlands
| | | | - P. C. De Holanda
- Universidade Estadual de Campinas, Campinas, SP 13083-970 Brazil
| | | | | | - P. De Jong
- University of Amsterdam, 1098 XG Amsterdam, The Netherlands
- Nikhef National Institute of Subatomic Physics, 1098 XG Amsterdam, The Netherlands
| | - A. Delbart
- IRFU, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - D. Delepine
- Universidad de Guanajuato, C.P. 37000 Guanajuato, Mexico
| | - M. Delgado
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
- Università del Milano-Bicocca, 20126 Milan, Italy
| | - A. Dell’Acqua
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - N. Delmonte
- Istituto Nazionale di Fisica Nucleare Sezione di Milano, 20133 Milan, Italy
- University of Parma, 43121 Parma, PR Italy
| | - P. De Lurgio
- Argonne National Laboratory, Argonne, IL 60439 USA
| | | | - D. M. DeMuth
- Valley City State University, Valley City, ND 58072 USA
| | - S. Dennis
- University of Cambridge, Cambridge, CB3 0HE UK
| | - C. Densham
- STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX UK
| | | | - A. De Roeck
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - V. De Romeri
- Instituto de Física Corpuscular, CSIC and Universitat de València, 46980 Paterna, Valencia Spain
| | - G. De Souza
- Universidade Estadual de Campinas, Campinas, SP 13083-970 Brazil
| | - R. Devi
- University of Jammu, Jammu, 180006 India
| | | | - M. Dias
- Universidade Federal de São Paulo, São Paulo, 09913-030 Brazil
| | - F. Diaz
- Pontificia Universidad Católica del Perú, Lima, Peru
| | - J. S. Díaz
- Indiana University, Bloomington, IN 47405 USA
| | - S. Di Domizio
- Università degli Studi di Genova, Genoa, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Genova, 16146 Genoa, GE Italy
| | - L. Di Giulio
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - P. Ding
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - L. Di Noto
- Università degli Studi di Genova, Genoa, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Genova, 16146 Genoa, GE Italy
| | - G. Dirkx
- Imperial College of Science Technology and Medicine, London, SW7 2BZ UK
| | - C. Distefano
- Istituto Nazionale di Fisica Nucleare Laboratori Nazionali del Sud, 95123 Catania, Italy
| | - R. Diurba
- University of Minnesota Twin Cities, Minneapolis, MN 55455 USA
| | - M. Diwan
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - Z. Djurcic
- Argonne National Laboratory, Argonne, IL 60439 USA
| | - D. Doering
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - S. Dolan
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - F. Dolek
- Beykent University, Istanbul, Turkey
| | - M. Dolinski
- Drexel University, Philadelphia, PA 19104 USA
| | - L. Domine
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Y. Donon
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - D. Douglas
- Michigan State University, East Lansing, MI 48824 USA
| | - D. Douillet
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - A. Dragone
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - G. Drake
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - F. Drielsma
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - L. Duarte
- Universidade Federal de São Paulo, São Paulo, 09913-030 Brazil
| | - D. Duchesneau
- Laboratoire d’Annecy de Physique des Particules, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LAPP-IN2P3, 74000 Annecy, France
| | - K. Duffy
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - P. Dunne
- Imperial College of Science Technology and Medicine, London, SW7 2BZ UK
| | - B. Dutta
- Texas A &M University, College Station, 77840 USA
| | - H. Duyang
- University of South Carolina, Columbia, SC 29208 USA
| | | | - D. Dwyer
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - A. Dyshkant
- Northern Illinois University, DeKalb, IL 60115 USA
| | - M. Eads
- Northern Illinois University, DeKalb, IL 60115 USA
| | - A. Earle
- University of Sussex, Brighton, BN1 9RH UK
| | - D. Edmunds
- Michigan State University, East Lansing, MI 48824 USA
| | - J. Eisch
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - L. Emberger
- University of Manchester, Manchester, M13 9PL UK
- Max-Planck-Institut, 80805 Munich, Germany
| | - S. Emery
- IRFU, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - P. Englezos
- Rutgers University, Piscataway, NJ 08854 USA
| | | | - T. Erjavec
- University of California Davis, Davis, CA 95616 USA
| | - C. Escobar
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - G. Eurin
- IRFU, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - J. J. Evans
- University of Manchester, Manchester, M13 9PL UK
| | - E. Ewart
- Indiana University, Bloomington, IN 47405 USA
| | | | - K. Fahey
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - A. Falcone
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
- Università del Milano-Bicocca, 20126 Milan, Italy
| | - M. Fani’
- Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - C. Farnese
- Istituto Nazionale di Fisica Nucleare Sezione di Padova, 35131 Padua, Italy
| | - Y. Farzan
- Institute for Research in Fundamental Sciences, Tehran, Iran
| | - D. Fedoseev
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | - J. Felix
- Universidad de Guanajuato, C.P. 37000 Guanajuato, Mexico
| | - Y. Feng
- Iowa State University, Ames, IA 50011 USA
| | | | - P. Fernandez Menendez
- Instituto de Física Corpuscular, CSIC and Universitat de València, 46980 Paterna, Valencia Spain
| | | | - F. Ferraro
- Università degli Studi di Genova, Genoa, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Genova, 16146 Genoa, GE Italy
| | - L. Fields
- University of Notre Dame, Notre Dame, IN 46556 USA
| | - P. Filip
- Institute of Physics, Czech Academy of Sciences, 182 00 Prague 8, Czech Republic
| | - F. Filthaut
- Nikhef National Institute of Subatomic Physics, 1098 XG Amsterdam, The Netherlands
- Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - M. Fiorini
- University of Ferrara, Ferrara, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Ferrara, 44122 Ferrara, Italy
| | - V. Fischer
- Iowa State University, Ames, IA 50011 USA
| | | | - W. Flanagan
- University of Dallas, Irving, TX 75062-4736 USA
| | - B. Fleming
- Yale University, New Haven, CT 06520 USA
| | - R. Flight
- University of Rochester, Rochester, NY 14627 USA
| | - S. Fogarty
- Colorado State University, Fort Collins, CO 80523 USA
| | - W. Foreman
- Illinois Institute of Technology, Chicago, IL 60616 USA
| | - J. Fowler
- Duke University, Durham, NC 27708 USA
| | - W. Fox
- Indiana University, Bloomington, IN 47405 USA
| | - J. Franc
- Czech Technical University, 115 19 Prague 1, Czech Republic
| | - K. Francis
- Northern Illinois University, DeKalb, IL 60115 USA
| | - D. Franco
- Yale University, New Haven, CT 06520 USA
| | - J. Freeman
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - J. Freestone
- University of Manchester, Manchester, M13 9PL UK
| | - J. Fried
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - A. Friedland
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | | | - S. Fuess
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - I. K. Furic
- University of Florida, Gainesville, FL 32611-8440 USA
| | - K. Furman
- Queen Mary University of London, London, E1 4NS UK
| | - A. P. Furmanski
- University of Minnesota Twin Cities, Minneapolis, MN 55455 USA
| | - A. Gabrielli
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - A. Gago
- Pontificia Universidad Católica del Perú, Lima, Peru
| | | | - A. Gallas
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - A. Gallego-Ros
- CIEMAT, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, 28040 Madrid, Spain
| | - N. Gallice
- Istituto Nazionale di Fisica Nucleare Sezione di Milano, 20133 Milan, Italy
- Università degli Studi di Milano, 20133 Milan, Italy
| | - V. Galymov
- Institut de Physique des 2 Infinis de Lyon, 69622 Villeurbanne, France
| | - E. Gamberini
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - T. Gamble
- University of Sheffield, Sheffield, S3 7RH UK
| | - F. Ganacim
- Universidade Tecnológica Federal do Paraná, Curitiba, Brazil
| | - R. Gandhi
- Harish-Chandra Research Institute, Jhunsi, Allahabad, 211 019 India
| | - R. Gandrajula
- Michigan State University, East Lansing, MI 48824 USA
| | - F. Gao
- University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - S. Gao
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | | | - M. Á. García-Peris
- Instituto de Física Corpuscular, CSIC and Universitat de València, 46980 Paterna, Valencia Spain
| | - S. Gardiner
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | | | - J. Gauvreau
- Occidental College, Los Angeles, CA 90041 USA
| | - G. Ge
- Columbia University, New York, NY 10027 USA
| | - N. Geffroy
- Laboratoire d’Annecy de Physique des Particules, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LAPP-IN2P3, 74000 Annecy, France
| | - B. Gelli
- Universidade Estadual de Campinas, Campinas, SP 13083-970 Brazil
| | | | - S. Gent
- South Dakota State University, Brookings, SD 57007 USA
| | | | - P. Giammaria
- Universidade Estadual de Campinas, Campinas, SP 13083-970 Brazil
| | - T. Giammaria
- University of Ferrara, Ferrara, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Ferrara, 44122 Ferrara, Italy
| | | | - D. Gibin
- Istituto Nazionale di Fisica Nucleare Sezione di Padova, 35131 Padua, Italy
- Universtà degli Studi di Padova, 35131 Padua, Italy
| | - I. Gil-Botella
- CIEMAT, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, 28040 Madrid, Spain
| | - S. Gilligan
- Oregon State University, Corvallis, OR 97331 USA
| | - C. Girerd
- Institut de Physique des 2 Infinis de Lyon, 69622 Villeurbanne, France
| | - A. K. Giri
- Indian Institute of Technology Hyderabad, Hyderabad, 502285 India
| | - D. Gnani
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - O. Gogota
- Taras Shevchenko National University of Kyiv, Kyiv, 01601 Ukraine
| | - M. Gold
- University of New Mexico, Albuquerque, NM 87131 USA
| | - S. Gollapinni
- Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - K. Gollwitzer
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - R. A. Gomes
- Universidade Federal de Goias, Goiania, GO 74690-900 Brazil
| | | | | | - F. Gonnella
- University of Birmingham, Birmingham, B15 2TT UK
| | | | | | | | - O. Goodwin
- University of Manchester, Manchester, M13 9PL UK
| | - S. Goswami
- Physical Research Laboratory, Ahmedabad, 380 009 India
| | - C. Gotti
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
| | | | - C. Grace
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - R. Gran
- University of Minnesota Duluth, Duluth, MN 55812 USA
| | - E. Granados
- Universidad de Guanajuato, C.P. 37000 Guanajuato, Mexico
| | - P. Granger
- IRFU, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - A. Grant
- Daresbury Laboratory, Cheshire, WA4 4AD UK
| | - C. Grant
- Boston University, Boston, MA 02215 USA
| | - D. Gratieri
- Fluminense Federal University, 9 Icaraí, Niterói, RJ 24220-900 Brazil
| | - P. Green
- University of Manchester, Manchester, M13 9PL UK
| | - L. Greenler
- University of Wisconsin Madison, Madison, WI 53706 USA
| | - J. Greer
- University of Bristol, Bristol, BS8 1TL UK
| | - J. Grenard
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | | | - M. Groh
- Colorado State University, Fort Collins, CO 80523 USA
| | | | - K. Grzelak
- University of Warsaw, 02-093 Warsaw, Poland
| | - W. Gu
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | | | - V. Guarino
- Argonne National Laboratory, Argonne, IL 60439 USA
| | - M. Guarise
- University of Ferrara, Ferrara, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Ferrara, 44122 Ferrara, Italy
| | | | - E. Guerard
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - M. Guerzoni
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - D. Guffanti
- Istituto Nazionale di Fisica Nucleare Sezione di Milano, 20133 Milan, Italy
| | - A. Guglielmi
- Istituto Nazionale di Fisica Nucleare Sezione di Padova, 35131 Padua, Italy
| | - B. Guo
- University of South Carolina, Columbia, SC 29208 USA
| | - A. Gupta
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - V. Gupta
- Nikhef National Institute of Subatomic Physics, 1098 XG Amsterdam, The Netherlands
| | | | | | - P. Guzowski
- University of Manchester, Manchester, M13 9PL UK
| | - M. M. Guzzo
- Universidade Estadual de Campinas, Campinas, SP 13083-970 Brazil
| | - S. Gwon
- Chung-Ang University, Seoul, 06974 South Korea
| | - C. Ha
- Chung-Ang University, Seoul, 06974 South Korea
| | - K. Haaf
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - A. Habig
- University of Minnesota Duluth, Duluth, MN 55812 USA
| | - H. Hadavand
- University of Texas at Arlington, Arlington, TX 76019 USA
| | - R. Haenni
- University of Bern, 3012 Bern, Switzerland
| | - A. Hahn
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - J. Haiston
- South Dakota School of Mines and Technology, Rapid City, SD 57701 USA
| | | | - T. Hamernik
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - P. Hamilton
- Imperial College of Science Technology and Medicine, London, SW7 2BZ UK
| | - J. Han
- University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - D. A. Harris
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
- York University, Toronto, M3J 1P3 Canada
| | | | - T. Hartnett
- STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX UK
| | - J. Harton
- Colorado State University, Fort Collins, CO 80523 USA
| | - T. Hasegawa
- High Energy Accelerator Research Organization (KEK), Ibaraki, 305-0801 Japan
| | - C. Hasnip
- University of Oxford, Oxford, OX1 3RH UK
| | - R. Hatcher
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | | | | | - C. Hayes
- Indiana University, Bloomington, IN 47405 USA
| | | | - J. Hays
- Queen Mary University of London, London, E1 4NS UK
| | - E. Hazen
- Boston University, Boston, MA 02215 USA
| | - M. He
- University of Houston, Houston, TX 77204 USA
| | - A. Heavey
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | | | - J. Heise
- Sanford Underground Research Facility, Lead, SD 57754 USA
| | - S. Henry
- University of Rochester, Rochester, NY 14627 USA
| | | | - K. Herner
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - J. Hewes
- University of Cincinnati, Cincinnati, OH 45221 USA
| | - C. Hilgenberg
- University of Minnesota Twin Cities, Minneapolis, MN 55455 USA
| | - T. Hill
- Idaho State University, Pocatello, ID 83209 USA
| | | | - A. Himmel
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - E. Hinkle
- University of Chicago, Chicago, IL 60637 USA
| | - L. R. Hirsch
- Universidade Tecnológica Federal do Paraná, Curitiba, Brazil
| | - J. Ho
- Harvard University, Cambridge, MA 02138 USA
| | - J. Hoff
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - A. Holin
- STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX UK
| | - E. Hoppe
- Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | | | - M. Hostert
- University of Minnesota Twin Cities, Minneapolis, MN 55455 USA
| | - A. Hourlier
- Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - B. Howard
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - R. Howell
- University of Rochester, Rochester, NY 14627 USA
| | - J. Hoyos
- University of Medellín, Medellín, 050026 Colombia
| | - I. Hristova
- STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX UK
| | - M. S. Hronek
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - J. Huang
- University of California Davis, Davis, CA 95616 USA
| | - Z. Hulcher
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - G. Iles
- Imperial College of Science Technology and Medicine, London, SW7 2BZ UK
| | - N. Ilic
- University of Toronto, Toronto, ON M5S 1A1 Canada
| | - A. M. Iliescu
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - R. Illingworth
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - G. Ingratta
- Università del Bologna, 40127 Bologna, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - A. Ioannisian
- Yerevan Institute for Theoretical Physics and Modeling, Yerevan, 0036 Armenia
| | - B. Irwin
- University of Minnesota Twin Cities, Minneapolis, MN 55455 USA
| | - L. Isenhower
- Abilene Christian University, Abilene, TX 79601 USA
| | - R. Itay
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - C. M. Jackson
- Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - V. Jain
- University of Albany, SUNY, Albany, NY 12222 USA
| | - E. James
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - W. Jang
- University of Texas at Arlington, Arlington, TX 76019 USA
| | - B. Jargowsky
- University of California Irvine, Irvine, CA 92697 USA
| | - F. Jediny
- Czech Technical University, 115 19 Prague 1, Czech Republic
| | - D. Jena
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - Y. S. Jeong
- Chung-Ang University, Seoul, 06974 South Korea
- University of Iowa, Iowa City, IA 52242 USA
| | - C. Jesús-Valls
- Institut de Física d’Altes Energies (IFAE)-Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - X. Ji
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - L. Jiang
- Virginia Tech, Blacksburg, VA 24060 USA
| | - S. Jiménez
- CIEMAT, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, 28040 Madrid, Spain
| | - A. Jipa
- University of Bucharest, Bucharest, Romania
| | - R. Johnson
- University of Cincinnati, Cincinnati, OH 45221 USA
| | - W. Johnson
- South Dakota School of Mines and Technology, Rapid City, SD 57701 USA
| | - N. Johnston
- Indiana University, Bloomington, IN 47405 USA
| | - B. Jones
- University of Texas at Arlington, Arlington, TX 76019 USA
| | - S. Jones
- University College London, London, WC1E 6BT UK
| | - M. Judah
- University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - C. K. Jung
- Stony Brook University, SUNY, Stony Brook, NY 11794 USA
| | - T. Junk
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - Y. Jwa
- Columbia University, New York, NY 10027 USA
| | | | - A. Kaboth
- Royal Holloway College, London, TW20 0EX UK
- STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX UK
| | - I. Kadenko
- Taras Shevchenko National University of Kyiv, Kyiv, 01601 Ukraine
| | - I. Kakorin
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | - A. Kalitkina
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | - D. Kalra
- Columbia University, New York, NY 10027 USA
| | - F. Kamiya
- Universidade Federal do ABC, Santo André, SP 09210-580 Brazil
| | - N. Kaneshige
- University of California Santa Barbara, Santa Barbara, CA 93106 USA
| | - D. M. Kaplan
- Illinois Institute of Technology, Chicago, IL 60616 USA
| | | | - G. Karaman
- University of Iowa, Iowa City, IA 52242 USA
| | - A. Karcher
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - M. Karolak
- IRFU, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Y. Karyotakis
- Laboratoire d’Annecy de Physique des Particules, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LAPP-IN2P3, 74000 Annecy, France
| | - S. Kasai
- National Institute of Technology, Kure College, Hiroshima, 737-8506 Japan
| | - S. P. Kasetti
- Louisiana State University, Baton Rouge, LA 70803 USA
| | - L. Kashur
- Colorado State University, Fort Collins, CO 80523 USA
| | - N. Kazaryan
- Yerevan Institute for Theoretical Physics and Modeling, Yerevan, 0036 Armenia
| | - E. Kearns
- Boston University, Boston, MA 02215 USA
| | - P. Keener
- University of Pennsylvania, Philadelphia, PA 19104 USA
| | - K. J. Kelly
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - E. Kemp
- Universidade Estadual de Campinas, Campinas, SP 13083-970 Brazil
| | | | - W. Ketchum
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | | | - M. Khabibullin
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow, 117312 Russia
| | - A. Khotjantsev
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow, 117312 Russia
| | | | - D. Kim
- Texas A &M University, College Station, 77840 USA
| | - B. King
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - B. Kirby
- Columbia University, New York, NY 10027 USA
| | - M. Kirby
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - J. Klein
- University of Pennsylvania, Philadelphia, PA 19104 USA
| | - A. Klustova
- Imperial College of Science Technology and Medicine, London, SW7 2BZ UK
| | - T. Kobilarcik
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - K. Koehler
- University of Wisconsin Madison, Madison, WI 53706 USA
| | | | - D. H. Koh
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - S. Kohn
- University of California Berkeley, Berkeley, CA 94720 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | | | - L. Kolupaeva
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | - D. Korablev
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | - M. Kordosky
- College of William and Mary, Williamsburg, VA 23187 USA
| | - T. Kosc
- University Grenoble Alpes, CNRS, Grenoble INP, LPSC-IN2P3, 38000 Grenoble, France
| | - U. Kose
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | | | | | - R. Kralik
- University of Sussex, Brighton, BN1 9RH UK
| | - L. Kreczko
- University of Bristol, Bristol, BS8 1TL UK
| | | | - I. Kreslo
- University of Bern, 3012 Bern, Switzerland
| | - W. Kropp
- University of California Irvine, Irvine, CA 92697 USA
| | - T. Kroupova
- University of Pennsylvania, Philadelphia, PA 19104 USA
| | - S. Kubota
- Harvard University, Cambridge, MA 02138 USA
| | - Y. Kudenko
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow, 117312 Russia
| | | | - S. Kulagin
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow, 117312 Russia
| | - J. Kumar
- University of Hawaii, Honolulu, HI 96822 USA
| | - P. Kumar
- University of Sheffield, Sheffield, S3 7RH UK
| | - P. Kunze
- Laboratoire d’Annecy de Physique des Particules, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LAPP-IN2P3, 74000 Annecy, France
| | - N. Kurita
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - C. Kuruppu
- University of South Carolina, Columbia, SC 29208 USA
| | - V. Kus
- Czech Technical University, 115 19 Prague 1, Czech Republic
| | - T. Kutter
- Louisiana State University, Baton Rouge, LA 70803 USA
| | - J. Kvasnicka
- Institute of Physics, Czech Academy of Sciences, 182 00 Prague 8, Czech Republic
| | - D. Kwak
- Ulsan National Institute of Science and Technology, Ulsan, 689-798 South Korea
| | - A. Lambert
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - B. Land
- University of Pennsylvania, Philadelphia, PA 19104 USA
| | - C. E. Lane
- Drexel University, Philadelphia, PA 19104 USA
| | - K. Lang
- University of Texas at Austin, Austin, TX 78712 USA
| | | | - M. Langstaff
- University of Manchester, Manchester, M13 9PL UK
| | - J. Larkin
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - P. Lasorak
- University of Sussex, Brighton, BN1 9RH UK
| | - D. Last
- University of Pennsylvania, Philadelphia, PA 19104 USA
| | - A. Laundrie
- University of Wisconsin Madison, Madison, WI 53706 USA
| | - G. Laurenti
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - A. Lawrence
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - I. Lazanu
- University of Bucharest, Bucharest, Romania
| | - R. LaZur
- Colorado State University, Fort Collins, CO 80523 USA
| | - M. Lazzaroni
- Istituto Nazionale di Fisica Nucleare Sezione di Milano, 20133 Milan, Italy
- Università degli Studi di Milano, 20133 Milan, Italy
| | - T. Le
- Tufts University, Medford, MA 02155 USA
| | - S. Leardini
- Instituto Galego de Fisica de Altas Enerxias, A Coruña, Spain
| | - J. Learned
- University of Hawaii, Honolulu, HI 96822 USA
| | - P. LeBrun
- Institut de Physique des 2 Infinis de Lyon, 69622 Villeurbanne, France
| | - T. LeCompte
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - C. Lee
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - S. Y. Lee
- Jeonbuk National University, Jeonrabuk-do, 54896 South Korea
| | - G. Lehmann Miotto
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - R. Lehnert
- Indiana University, Bloomington, IN 47405 USA
| | | | - M. Leitner
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - L. M. Lepin
- University of Manchester, Manchester, M13 9PL UK
| | - S. W. Li
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - Y. Li
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - H. Liao
- Kansas State University, Manhattan, KS 66506 USA
| | - C. S. Lin
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Q. Lin
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - S. Lin
- Louisiana State University, Baton Rouge, LA 70803 USA
| | | | - J. Ling
- Sun Yat-Sen University, Guangzhou, 510275 China
| | - A. Lister
- University of Wisconsin Madison, Madison, WI 53706 USA
| | | | - J. Liu
- University of California Irvine, Irvine, CA 92697 USA
| | - Y. Liu
- University of Chicago, Chicago, IL 60637 USA
| | - S. Lockwitz
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - T. Loew
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - M. Lokajicek
- Institute of Physics, Czech Academy of Sciences, 182 00 Prague 8, Czech Republic
| | - I. Lomidze
- Georgian Technical University, Tbilisi, Georgia
| | - K. Long
- Imperial College of Science Technology and Medicine, London, SW7 2BZ UK
| | - T. Lord
- University of Warwick, Coventry, CV4 7AL UK
| | | | - W. C. Louis
- Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - X.-G. Lu
- University of Warwick, Coventry, CV4 7AL UK
| | - K. B. Luk
- University of California Berkeley, Berkeley, CA 94720 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - B. Lunday
- University of Pennsylvania, Philadelphia, PA 19104 USA
| | - X. Luo
- University of California Santa Barbara, Santa Barbara, CA 93106 USA
| | - E. Luppi
- University of Ferrara, Ferrara, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Ferrara, 44122 Ferrara, Italy
| | - T. Lux
- Institut de Física d’Altes Energies (IFAE)-Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - V. P. Luzio
- Universidade Federal do ABC, Santo André, SP 09210-580 Brazil
| | - J. Maalmi
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - D. MacFarlane
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - A. A. Machado
- Universidade Estadual de Campinas, Campinas, SP 13083-970 Brazil
| | - P. Machado
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | | | - J. R. Macier
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - A. Maddalena
- Laboratori Nazionali del Gran Sasso, L’Aquila, AQ Italy
| | - A. Madera
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - P. Madigan
- University of California Berkeley, Berkeley, CA 94720 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - S. Magill
- Argonne National Laboratory, Argonne, IL 60439 USA
| | - K. Mahn
- Michigan State University, East Lansing, MI 48824 USA
| | - A. Maio
- Faculdade de Ciências da Universidade de Lisboa-FCUL, 1749-016 Lisbon, Portugal
- Laboratório de Instrumentação e Física Experimental de Partículas, 1649-003 Lisboa, 3004-516 Coimbra, Portugal
| | - A. Major
- Duke University, Durham, NC 27708 USA
| | | | - G. Mandrioli
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | | | - J. Maneira
- Faculdade de Ciências da Universidade de Lisboa-FCUL, 1749-016 Lisbon, Portugal
- Laboratório de Instrumentação e Física Experimental de Partículas, 1649-003 Lisboa, 3004-516 Coimbra, Portugal
| | - L. Manenti
- University College London, London, WC1E 6BT UK
| | - S. Manly
- University of Rochester, Rochester, NY 14627 USA
| | - A. Mann
- Tufts University, Medford, MA 02155 USA
| | | | | | - V. N. Manyam
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - L. Manzanillas
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - M. Marchan
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - A. Marchionni
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - W. Marciano
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - D. Marfatia
- University of Hawaii, Honolulu, HI 96822 USA
| | | | - J. Maricic
- University of Hawaii, Honolulu, HI 96822 USA
| | - R. Marie
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - F. Marinho
- Universidade Federal de São Carlos, Araras, SP 13604-900 Brazil
| | - A. D. Marino
- University of Colorado Boulder, Boulder, CO 80309 USA
| | - D. Marsden
- University of Manchester, Manchester, M13 9PL UK
| | - M. Marshak
- University of Minnesota Twin Cities, Minneapolis, MN 55455 USA
| | - C. Marshall
- University of Rochester, Rochester, NY 14627 USA
| | | | - J. Marteau
- Institut de Physique des 2 Infinis de Lyon, 69622 Villeurbanne, France
| | - J. Martín-Albo
- Instituto de Física Corpuscular, CSIC and Universitat de València, 46980 Paterna, Valencia Spain
| | - N. Martinez
- Kansas State University, Manhattan, KS 66506 USA
| | | | - P. Martínez Miravé
- Instituto de Física Corpuscular, CSIC and Universitat de València, 46980 Paterna, Valencia Spain
| | - S. Martynenko
- Stony Brook University, SUNY, Stony Brook, NY 11794 USA
| | - V. Mascagna
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
- University of Insubria, Via Ravasi, 2, 21100 Varese, VA Italy
| | - K. Mason
- Tufts University, Medford, MA 02155 USA
| | - A. Mastbaum
- Rutgers University, Piscataway, NJ 08854 USA
| | - F. Matichard
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - S. Matsuno
- University of Hawaii, Honolulu, HI 96822 USA
| | - J. Matthews
- Louisiana State University, Baton Rouge, LA 70803 USA
| | - C. Mauger
- University of Pennsylvania, Philadelphia, PA 19104 USA
| | - N. Mauri
- Università del Bologna, 40127 Bologna, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | | | - I. Mawby
- University of Warwick, Coventry, CV4 7AL UK
| | - R. Mazza
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
| | - A. Mazzacane
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - E. Mazzucato
- IRFU, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | | | - E. McCluskey
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - N. McConkey
- University of Manchester, Manchester, M13 9PL UK
| | | | - C. McGrew
- Stony Brook University, SUNY, Stony Brook, NY 11794 USA
| | - A. McNab
- University of Manchester, Manchester, M13 9PL UK
| | - A. Mefodiev
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow, 117312 Russia
| | - P. Mehta
- Jawaharlal Nehru University, New Delhi, 110067 India
| | - P. Melas
- University of Athens, 157 84 Zografou, Greece
| | - O. Mena
- Instituto de Física Corpuscular, CSIC and Universitat de València, 46980 Paterna, Valencia Spain
| | - H. Mendez
- University of Puerto Rico, Mayaguez, PR 00681 USA
| | - P. Mendez
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - D. P. Méndez
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - A. Menegolli
- Istituto Nazionale di Fisica Nucleare Sezione di Pavia, 27100 Pavia, Italy
- Università degli Studi di Pavia, 27100 Pavia, PV Italy
| | - G. Meng
- Istituto Nazionale di Fisica Nucleare Sezione di Padova, 35131 Padua, Italy
| | | | - W. Metcalf
- Louisiana State University, Baton Rouge, LA 70803 USA
| | - T. Mettler
- University of Bern, 3012 Bern, Switzerland
| | - M. Mewes
- Indiana University, Bloomington, IN 47405 USA
| | - H. Meyer
- Wichita State University, Wichita, KS 67260 USA
| | - T. Miao
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - G. Michna
- South Dakota State University, Brookings, SD 57007 USA
| | - T. Miedema
- Nikhef National Institute of Subatomic Physics, 1098 XG Amsterdam, The Netherlands
- Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - V. Mikola
- University College London, London, WC1E 6BT UK
| | - R. Milincic
- University of Hawaii, Honolulu, HI 96822 USA
| | - G. Miller
- University of Manchester, Manchester, M13 9PL UK
| | - W. Miller
- University of Minnesota Twin Cities, Minneapolis, MN 55455 USA
| | - J. Mills
- Tufts University, Medford, MA 02155 USA
| | - O. Mineev
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow, 117312 Russia
| | - A. Minotti
- Istituto Nazionale di Fisica Nucleare Sezione di Milano, 20133 Milan, Italy
- Università del Milano-Bicocca, 20126 Milan, Italy
| | - O. G. Miranda
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Mexico City, Mexico
| | - S. Miryala
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - C. S. Mishra
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - S. R. Mishra
- University of South Carolina, Columbia, SC 29208 USA
| | - A. Mislivec
- University of Minnesota Twin Cities, Minneapolis, MN 55455 USA
| | - M. Mitchell
- Louisiana State University, Baton Rouge, LA 70803 USA
| | - D. Mladenov
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - I. Mocioiu
- Pennsylvania State University, University Park, PA 16802 USA
| | - K. Moffat
- Durham University, Durham, DH1 3LE UK
| | - N. Moggi
- Università del Bologna, 40127 Bologna, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - R. Mohanta
- University of Hyderabad, Gachibowli, Hyderabad, 500 046 India
| | - T. A. Mohayai
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - N. Mokhov
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - J. Molina
- Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - L. Molina Bueno
- Instituto de Física Corpuscular, CSIC and Universitat de València, 46980 Paterna, Valencia Spain
| | - E. Montagna
- Università del Bologna, 40127 Bologna, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - A. Montanari
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - C. Montanari
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
- Istituto Nazionale di Fisica Nucleare Sezione di Pavia, 27100 Pavia, Italy
- Università degli Studi di Pavia, 27100 Pavia, PV Italy
| | - D. Montanari
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - L. M. Montañno Zetina
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Mexico City, Mexico
| | - S. H. Moon
- Ulsan National Institute of Science and Technology, Ulsan, 689-798 South Korea
| | - M. Mooney
- Colorado State University, Fort Collins, CO 80523 USA
| | - A. F. Moor
- University of Cambridge, Cambridge, CB3 0HE UK
| | - D. Moreno
- Universidad Antonio Nariño, Bogotá, Colombia
| | - D. Moretti
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
| | - C. Morris
- University of Houston, Houston, TX 77204 USA
| | - C. Mossey
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - M. Mote
- Louisiana State University, Baton Rouge, LA 70803 USA
| | - E. Motuk
- University College London, London, WC1E 6BT UK
| | - C. A. Moura
- Universidade Federal do ABC, Santo André, SP 09210-580 Brazil
| | - J. Mousseau
- University of Michigan, Ann Arbor, MI 48109 USA
| | - G. Mouster
- Lancaster University, Lancaster, LA1 4YB UK
| | - W. Mu
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - L. Mualem
- California Institute of Technology, Pasadena, CA 91125 USA
| | - J. Mueller
- Colorado State University, Fort Collins, CO 80523 USA
| | - M. Muether
- Wichita State University, Wichita, KS 67260 USA
| | - S. Mufson
- Indiana University, Bloomington, IN 47405 USA
| | - F. Muheim
- University of Edinburgh, Edinburgh, EH8 9YL UK
| | - A. Muir
- Daresbury Laboratory, Cheshire, WA4 4AD UK
| | - M. Mulhearn
- University of California Davis, Davis, CA 95616 USA
| | - D. Munford
- University of Houston, Houston, TX 77204 USA
| | - H. Muramatsu
- University of Minnesota Twin Cities, Minneapolis, MN 55455 USA
| | | | - J. Musser
- Indiana University, Bloomington, IN 47405 USA
| | | | - S. Nagu
- University of Lucknow, Lucknow, Uttar Pradesh 226007 India
| | - M. Nalbandyan
- Yerevan Institute for Theoretical Physics and Modeling, Yerevan, 0036 Armenia
| | - R. Nandakumar
- STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX UK
| | - D. Naples
- University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - S. Narita
- Iwate University, Morioka, Iwate 020-8551 Japan
| | - A. Nath
- Indian Institute of Technology Guwahati, Guwahati, 781 039 India
| | | | - N. Nayak
- University of California Irvine, Irvine, CA 92697 USA
| | | | - K. Negishi
- Iwate University, Morioka, Iwate 020-8551 Japan
| | - J. K. Nelson
- College of William and Mary, Williamsburg, VA 23187 USA
| | - J. Nesbit
- University of Wisconsin Madison, Madison, WI 53706 USA
| | - M. Nessi
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - D. Newbold
- STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX UK
| | - M. Newcomer
- University of Pennsylvania, Philadelphia, PA 19104 USA
| | - H. Newton
- Daresbury Laboratory, Cheshire, WA4 4AD UK
| | - R. Nichol
- University College London, London, WC1E 6BT UK
| | | | - A. Nikolica
- University of Pennsylvania, Philadelphia, PA 19104 USA
| | - E. Niner
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | | | - A. Norman
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - A. Norrick
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - R. Northrop
- University of Chicago, Chicago, IL 60637 USA
| | - P. Novella
- Instituto de Física Corpuscular, CSIC and Universitat de València, 46980 Paterna, Valencia Spain
| | | | - M. Oberling
- Argonne National Laboratory, Argonne, IL 60439 USA
| | | | - A. Olivier
- University of Rochester, Rochester, NY 14627 USA
| | - A. Olshevskiy
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | - Y. Onel
- University of Iowa, Iowa City, IA 52242 USA
| | - Y. Onishchuk
- Taras Shevchenko National University of Kyiv, Kyiv, 01601 Ukraine
| | - J. Ott
- University of California Irvine, Irvine, CA 92697 USA
| | - L. Pagani
- University of California Davis, Davis, CA 95616 USA
| | - G. Palacio
- Universidad EIA, Envigado, Antioquia, Colombia
| | - O. Palamara
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - S. Palestini
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - J. M. Paley
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - M. Pallavicini
- Università degli Studi di Genova, Genoa, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Genova, 16146 Genoa, GE Italy
| | - C. Palomares
- CIEMAT, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, 28040 Madrid, Spain
| | | | - E. Pantic
- University of California Davis, Davis, CA 95616 USA
| | - V. Paolone
- University of Pittsburgh, Pittsburgh, PA 15260 USA
| | | | - R. Papaleo
- Istituto Nazionale di Fisica Nucleare Laboratori Nazionali del Sud, 95123 Catania, Italy
| | - A. Papanestis
- STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX UK
| | | | - S. Parke
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - E. Parozzi
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
- Università del Milano-Bicocca, 20126 Milan, Italy
| | - Z. Parsa
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - M. Parvu
- University of Bucharest, Bucharest, Romania
| | - S. Pascoli
- Università del Bologna, 40127 Bologna, Italy
- Durham University, Durham, DH1 3LE UK
| | - L. Pasqualini
- Università del Bologna, 40127 Bologna, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - J. Pasternak
- Imperial College of Science Technology and Medicine, London, SW7 2BZ UK
| | - J. Pater
- University of Manchester, Manchester, M13 9PL UK
| | - C. Patrick
- University College London, London, WC1E 6BT UK
| | - L. Patrizii
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | | | - S. J. Patton
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - T. Patzak
- Université de Paris, CNRS, Astroparticule et Cosmologie, 75006 Paris, France
| | - A. Paudel
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - B. Paulos
- University of Wisconsin Madison, Madison, WI 53706 USA
| | - L. Paulucci
- Universidade Federal do ABC, Santo André, SP 09210-580 Brazil
| | - Z. Pavlovic
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - G. Pawloski
- University of Minnesota Twin Cities, Minneapolis, MN 55455 USA
| | - D. Payne
- University of Liverpool, Liverpool, L69 7ZE UK
| | - V. Pec
- Institute of Physics, Czech Academy of Sciences, 182 00 Prague 8, Czech Republic
| | | | - A. Pena Perez
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - E. Pennacchio
- Institut de Physique des 2 Infinis de Lyon, 69622 Villeurbanne, France
| | - A. Penzo
- University of Iowa, Iowa City, IA 52242 USA
| | - O. L. G. Peres
- Universidade Estadual de Campinas, Campinas, SP 13083-970 Brazil
| | - J. Perry
- University of Edinburgh, Edinburgh, EH8 9YL UK
| | | | - G. Pessina
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
| | - G. Petrillo
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - C. Petta
- Università di Catania, 2, 95131 Catania, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Catania, 95123 Catania, Italy
| | - R. Petti
- University of South Carolina, Columbia, SC 29208 USA
| | - V. Pia
- Università del Bologna, 40127 Bologna, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - F. Piastra
- University of Bern, 3012 Bern, Switzerland
| | - L. Pickering
- Michigan State University, East Lansing, MI 48824 USA
| | - F. Pietropaolo
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
- Istituto Nazionale di Fisica Nucleare Sezione di Padova, 35131 Padua, Italy
| | - V. L. Pimentel
- Universidade Estadual de Campinas, Campinas, SP 13083-970 Brazil
- Centro de Tecnologia da Informacao Renato Archer, Amarais, Campinas, SP CEP 13069-901 Brazil
| | - G. Pinaroli
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - K. Plows
- University of Oxford, Oxford, OX1 3RH UK
| | - R. Plunkett
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - R. Poling
- University of Minnesota Twin Cities, Minneapolis, MN 55455 USA
| | - F. Pompa
- Instituto de Física Corpuscular, CSIC and Universitat de València, 46980 Paterna, Valencia Spain
| | - X. Pons
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | | | - F. Poppi
- Università del Bologna, 40127 Bologna, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - S. Pordes
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - J. Porter
- University of Sussex, Brighton, BN1 9RH UK
| | - M. Potekhin
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - R. Potenza
- Università di Catania, 2, 95131 Catania, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Catania, 95123 Catania, Italy
| | | | - J. Pozimski
- Imperial College of Science Technology and Medicine, London, SW7 2BZ UK
| | - M. Pozzato
- Università del Bologna, 40127 Bologna, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - S. Prakash
- Universidade Estadual de Campinas, Campinas, SP 13083-970 Brazil
| | - T. Prakash
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - M. Prest
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
| | - S. Prince
- Harvard University, Cambridge, MA 02138 USA
| | - F. Psihas
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - D. Pugnere
- Institut de Physique des 2 Infinis de Lyon, 69622 Villeurbanne, France
| | - X. Qian
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - J. L. Raaf
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - V. Radeka
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | | | | | - A. Rafique
- Argonne National Laboratory, Argonne, IL 60439 USA
| | - E. Raguzin
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - M. Rai
- University of Warwick, Coventry, CV4 7AL UK
| | | | - I. Rakhno
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | | | | | - R. Rameika
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | | | - B. Ramson
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - A. Rappoldi
- Istituto Nazionale di Fisica Nucleare Sezione di Pavia, 27100 Pavia, Italy
- Università degli Studi di Pavia, 27100 Pavia, PV Italy
| | - G. Raselli
- Istituto Nazionale di Fisica Nucleare Sezione di Pavia, 27100 Pavia, Italy
- Università degli Studi di Pavia, 27100 Pavia, PV Italy
| | - P. Ratoff
- Lancaster University, Lancaster, LA1 4YB UK
| | - S. Raut
- Stony Brook University, SUNY, Stony Brook, NY 11794 USA
| | | | - E. M. Rea
- University of Minnesota Twin Cities, Minneapolis, MN 55455 USA
| | - J. S. Real
- University Grenoble Alpes, CNRS, Grenoble INP, LPSC-IN2P3, 38000 Grenoble, France
| | - B. Rebel
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
- University of Wisconsin Madison, Madison, WI 53706 USA
| | - R. Rechenmacher
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | | | - J. Reichenbacher
- South Dakota School of Mines and Technology, Rapid City, SD 57701 USA
| | - S. D. Reitzner
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - H. Rejeb Sfar
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - A. Renshaw
- University of Houston, Houston, TX 77204 USA
| | - S. Rescia
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - F. Resnati
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - M. Ribas
- Universidade Tecnológica Federal do Paraná, Curitiba, Brazil
| | - S. Riboldi
- Istituto Nazionale di Fisica Nucleare Sezione di Milano, 20133 Milan, Italy
| | - C. Riccio
- Stony Brook University, SUNY, Stony Brook, NY 11794 USA
| | - G. Riccobene
- Istituto Nazionale di Fisica Nucleare Laboratori Nazionali del Sud, 95123 Catania, Italy
| | | | - J. S. Ricol
- University Grenoble Alpes, CNRS, Grenoble INP, LPSC-IN2P3, 38000 Grenoble, France
| | - A. Rigamonti
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | | | | | | | - D. Rivera
- Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - A. Robert
- University Grenoble Alpes, CNRS, Grenoble INP, LPSC-IN2P3, 38000 Grenoble, France
| | - L. Rochester
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - M. Roda
- University of Liverpool, Liverpool, L69 7ZE UK
| | | | | | | | | | | | - M. Rosenberg
- University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - P. Rosier
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - B. Roskovec
- University of California Irvine, Irvine, CA 92697 USA
| | - M. Rossella
- Istituto Nazionale di Fisica Nucleare Sezione di Pavia, 27100 Pavia, Italy
- Università degli Studi di Pavia, 27100 Pavia, PV Italy
| | - M. Rossi
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - J. Rout
- Jawaharlal Nehru University, New Delhi, 110067 India
| | - P. Roy
- Wichita State University, Wichita, KS 67260 USA
| | | | - C. Rubbia
- Gran Sasso Science Institute, L’Aquila, Italy
| | - B. Russell
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | | | - A. Rybnikov
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | | | - R. Saakyan
- University College London, London, WC1E 6BT UK
| | - S. Sacerdoti
- Université de Paris, CNRS, Astroparticule et Cosmologie, 75006 Paris, France
| | - T. Safford
- Michigan State University, East Lansing, MI 48824 USA
| | - N. Sahu
- Indian Institute of Technology Hyderabad, Hyderabad, 502285 India
| | - K. Sakashita
- High Energy Accelerator Research Organization (KEK), Ibaraki, 305-0801 Japan
| | - P. Sala
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
- Istituto Nazionale di Fisica Nucleare Sezione di Milano, 20133 Milan, Italy
| | - N. Samios
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - O. Samoylov
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | | | - V. Sandberg
- Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | | | - D. Sankey
- STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX UK
| | - S. Santana
- University of Puerto Rico, Mayaguez, PR 00681 USA
| | | | | | - P. Sapienza
- Istituto Nazionale di Fisica Nucleare Laboratori Nazionali del Sud, 95123 Catania, Italy
| | - C. Sarasty
- University of Cincinnati, Cincinnati, OH 45221 USA
| | | | - G. Savage
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - V. Savinov
- University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - A. Scaramelli
- Istituto Nazionale di Fisica Nucleare Sezione di Pavia, 27100 Pavia, Italy
| | - A. Scarff
- University of Sheffield, Sheffield, S3 7RH UK
| | - A. Scarpelli
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - T. Schefke
- Louisiana State University, Baton Rouge, LA 70803 USA
| | - H. Schellman
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
- Oregon State University, Corvallis, OR 97331 USA
| | - S. Schifano
- University of Ferrara, Ferrara, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Ferrara, 44122 Ferrara, Italy
| | - P. Schlabach
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - D. Schmitz
- University of Chicago, Chicago, IL 60637 USA
| | - A. W. Schneider
- Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | | | - A. Schukraft
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - E. Segreto
- Universidade Estadual de Campinas, Campinas, SP 13083-970 Brazil
| | - A. Selyunin
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | - C. R. Senise
- Universidade Federal de São Paulo, São Paulo, 09913-030 Brazil
| | - J. Sensenig
- University of Pennsylvania, Philadelphia, PA 19104 USA
| | - A. Sergi
- University of Birmingham, Birmingham, B15 2TT UK
| | | | | | - S. Shafaq
- Jawaharlal Nehru University, New Delhi, 110067 India
| | - F. Shaker
- York University, Toronto, M3J 1P3 Canada
| | - M. Shamma
- University of California Riverside, Riverside, CA 92521 USA
| | | | | | - R. Sharma
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - R. K. Sharma
- Punjab Agricultural University, Ludhiana, 141004 India
| | - T. Shaw
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - K. Shchablo
- Institut de Physique des 2 Infinis de Lyon, 69622 Villeurbanne, France
| | | | - A. Sheshukov
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | - S. Shin
- Jeonbuk National University, Jeonrabuk-do, 54896 South Korea
| | | | - D. Shooltz
- Michigan State University, East Lansing, MI 48824 USA
| | - R. Shrock
- Stony Brook University, SUNY, Stony Brook, NY 11794 USA
| | - H. Siegel
- Columbia University, New York, NY 10027 USA
| | - L. Simard
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - J. Sinclair
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - G. Sinev
- South Dakota School of Mines and Technology, Rapid City, SD 57701 USA
| | - J. Singh
- University of Lucknow, Lucknow, Uttar Pradesh 226007 India
| | - J. Singh
- University of Lucknow, Lucknow, Uttar Pradesh 226007 India
| | - L. Singh
- Central University of South Bihar, Gaya, 824236 India
| | - P. Singh
- Queen Mary University of London, London, E1 4NS UK
| | - V. Singh
- Banaras Hindu University, Varanasi, 221 005 India
- Central University of South Bihar, Gaya, 824236 India
| | - R. Sipos
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | | | - G. Sirri
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - A. Sitraka
- South Dakota School of Mines and Technology, Rapid City, SD 57701 USA
| | - K. Siyeon
- Chung-Ang University, Seoul, 06974 South Korea
| | - K. Skarpaas
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - A. Smith
- University of Cambridge, Cambridge, CB3 0HE UK
| | - E. Smith
- Indiana University, Bloomington, IN 47405 USA
| | - P. Smith
- Indiana University, Bloomington, IN 47405 USA
| | - J. Smolik
- Czech Technical University, 115 19 Prague 1, Czech Republic
| | - M. Smy
- University of California Irvine, Irvine, CA 92697 USA
| | - E. Snider
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - P. Snopok
- Illinois Institute of Technology, Chicago, IL 60616 USA
| | | | | | - H. Sobel
- University of California Irvine, Irvine, CA 92697 USA
| | | | - S. Sokolov
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | | | | | - S. R. Soleti
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - N. Solomey
- Wichita State University, Wichita, KS 67260 USA
| | - V. Solovov
- Laboratório de Instrumentação e Física Experimental de Partículas, 1649-003 Lisboa, 3004-516 Coimbra, Portugal
| | - W. E. Sondheim
- Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - M. Sorel
- Instituto de Física Corpuscular, CSIC and Universitat de València, 46980 Paterna, Valencia Spain
| | - A. Sotnikov
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | - J. Soto-Oton
- CIEMAT, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, 28040 Madrid, Spain
| | | | - A. Sousa
- University of Cincinnati, Cincinnati, OH 45221 USA
| | - K. Soustruznik
- Institute of Particle and Nuclear Physics of the Faculty of Mathematics and Physics of the Charles University, 180 00 Prague 8, Czech Republic
| | | | - M. Spanu
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
- Università del Milano-Bicocca, 20126 Milan, Italy
| | - J. Spitz
- University of Michigan, Ann Arbor, MI 48109 USA
| | | | | | - M. Stancari
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - L. Stanco
- Istituto Nazionale di Fisica Nucleare Sezione di Padova, 35131 Padua, Italy
- Universtà degli Studi di Padova, 35131 Padua, Italy
| | | | - R. Stein
- University of Bristol, Bristol, BS8 1TL UK
| | - H. M. Steiner
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | | | - J. Stewart
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | | | - J. Stock
- South Dakota School of Mines and Technology, Rapid City, SD 57701 USA
| | - F. Stocker
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - T. Stokes
- Louisiana State University, Baton Rouge, LA 70803 USA
| | - M. Strait
- University of Minnesota Twin Cities, Minneapolis, MN 55455 USA
| | - T. Strauss
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - L. Strigari
- Texas A &M University, College Station, 77840 USA
| | - A. Stuart
- Universidad de Colima, Colima, Mexico
| | | | | | - H. Sullivan
- University of Texas at Arlington, Arlington, TX 76019 USA
| | - D. Summers
- University of Mississippi, University, MS 38677 USA
| | - A. Surdo
- Istituto Nazionale di Fisica Nucleare Sezione di Lecce, 73100 Lecce, Italy
| | - V. Susic
- University of Basel, 4056 Basel, Switzerland
| | - L. Suter
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - C. M. Sutera
- Università di Catania, 2, 95131 Catania, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Catania, 95123 Catania, Italy
| | - R. Svoboda
- University of California Davis, Davis, CA 95616 USA
| | - B. Szczerbinska
- Texas A &M University-Corpus Christi, Corpus Christi, TX 78412 USA
| | - A. M. Szelc
- University of Edinburgh, Edinburgh, EH8 9YL UK
| | - H. Tanaka
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - S. Tang
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - A. Tapia
- University of Medellín, Medellín, 050026 Colombia
| | | | - A. Tapper
- Imperial College of Science Technology and Medicine, London, SW7 2BZ UK
| | - S. Tariq
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - E. Tarpara
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - N. Tata
- Harvard University, Cambridge, MA 02138 USA
| | - E. Tatar
- Idaho State University, Pocatello, ID 83209 USA
| | - R. Tayloe
- Indiana University, Bloomington, IN 47405 USA
| | - A. M. Teklu
- Stony Brook University, SUNY, Stony Brook, NY 11794 USA
| | - P. Tennessen
- Antalya Bilim University, 07190 Döşemealti/Antalya, Turkey
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - M. Tenti
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - K. Terao
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - C. A. Ternes
- Instituto de Física Corpuscular, CSIC and Universitat de València, 46980 Paterna, Valencia Spain
| | - F. Terranova
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
- Università del Milano-Bicocca, 20126 Milan, Italy
| | - G. Testera
- Istituto Nazionale di Fisica Nucleare Sezione di Genova, 16146 Genoa, GE Italy
| | - T. Thakore
- University of Cincinnati, Cincinnati, OH 45221 USA
| | - A. Thea
- STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX UK
| | | | - C. Thorn
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - S. C. Timm
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | | | - L. Tomassetti
- University of Ferrara, Ferrara, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Ferrara, 44122 Ferrara, Italy
| | - A. Tonazzo
- Université de Paris, CNRS, Astroparticule et Cosmologie, 75006 Paris, France
| | - D. Torbunov
- University of Minnesota Twin Cities, Minneapolis, MN 55455 USA
| | - M. Torti
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
- Università del Milano-Bicocca, 20126 Milan, Italy
| | - M. Tortola
- Instituto de Física Corpuscular, CSIC and Universitat de València, 46980 Paterna, Valencia Spain
| | - F. Tortorici
- Università di Catania, 2, 95131 Catania, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Catania, 95123 Catania, Italy
| | - N. Tosi
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - D. Totani
- University of California Santa Barbara, Santa Barbara, CA 93106 USA
| | - M. Toups
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | | | - R. Travaglini
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - J. Trevor
- California Institute of Technology, Pasadena, CA 91125 USA
| | - S. Trilov
- University of Bristol, Bristol, BS8 1TL UK
| | | | - Y. Tsai
- University of California Irvine, Irvine, CA 92697 USA
| | - Y.-T. Tsai
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | | | - K. V. Tsang
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - N. Tsverava
- Georgian Technical University, Tbilisi, Georgia
| | - S. Tufanli
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - C. Tull
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - E. Tyley
- University of Sheffield, Sheffield, S3 7RH UK
| | - M. Tzanov
- Louisiana State University, Baton Rouge, LA 70803 USA
| | - L. Uboldi
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | | | - J. Urheim
- Indiana University, Bloomington, IN 47405 USA
| | - T. Usher
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | - S. Uzunyan
- Northern Illinois University, DeKalb, IL 60115 USA
| | - M. R. Vagins
- Kavli Institute for the Physics and Mathematics of the Universe, Kashiwa, Chiba 277-8583 Japan
| | - P. Vahle
- College of William and Mary, Williamsburg, VA 23187 USA
| | - S. Valder
- University of Sussex, Brighton, BN1 9RH UK
| | | | - E. Valencia
- Universidad de Guanajuato, C.P. 37000 Guanajuato, Mexico
| | - R. Valentim
- Universidade Federal de São Paulo, São Paulo, 09913-030 Brazil
| | - Z. Vallari
- California Institute of Technology, Pasadena, CA 91125 USA
| | - E. Vallazza
- Istituto Nazionale di Fisica Nucleare Sezione di Milano Bicocca, 3, 20126 Milan, Italy
| | - J. W. F. Valle
- Instituto de Física Corpuscular, CSIC and Universitat de València, 46980 Paterna, Valencia Spain
| | - S. Vallecorsa
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - R. Van Berg
- University of Pennsylvania, Philadelphia, PA 19104 USA
| | | | | | - D. Vannerom
- Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - F. Varanini
- Istituto Nazionale di Fisica Nucleare Sezione di Padova, 35131 Padua, Italy
| | - D. Vargas Oliva
- Institut de Física d’Altes Energies (IFAE)-Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - G. Varner
- University of Hawaii, Honolulu, HI 96822 USA
| | - J. Vasel
- Indiana University, Bloomington, IN 47405 USA
| | - S. Vasina
- Joint Institute for Nuclear Research, Dzhelepov Laboratory of Nuclear Problems 6 Joliot-Curie, Dubna, Moscow Region 141980 Russia
| | - G. Vasseur
- IRFU, CEA, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - N. Vaughan
- Oregon State University, Corvallis, OR 97331 USA
| | - K. Vaziri
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - S. Ventura
- Istituto Nazionale di Fisica Nucleare Sezione di Padova, 35131 Padua, Italy
| | - A. Verdugo
- CIEMAT, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas, 28040 Madrid, Spain
| | - S. Vergani
- University of Cambridge, Cambridge, CB3 0HE UK
| | - M. A. Vermeulen
- Nikhef National Institute of Subatomic Physics, 1098 XG Amsterdam, The Netherlands
| | - M. Verzocchi
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - M. Vicenzi
- Università degli Studi di Genova, Genoa, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Genova, 16146 Genoa, GE Italy
| | - H. Vieira de Souza
- Université de Paris, CNRS, Astroparticule et Cosmologie, 75006 Paris, France
| | - C. Vignoli
- Laboratori Nazionali del Gran Sasso, L’Aquila, AQ Italy
| | - C. Vilela
- CERN, The European Organization for Nuclear Research, 1211 Meyrin, Switzerland
| | - B. Viren
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - T. Vrba
- Czech Technical University, 115 19 Prague 1, Czech Republic
| | - T. Wachala
- H. Niewodniczański Institute of Nuclear Physics, Polish Academy of Sciences, Kraków, Poland
| | - A. V. Waldron
- Imperial College of Science Technology and Medicine, London, SW7 2BZ UK
| | - M. Wallbank
- University of Cincinnati, Cincinnati, OH 45221 USA
| | - C. Wallis
- Colorado State University, Fort Collins, CO 80523 USA
| | - H. Wang
- University of California Los Angeles, Los Angeles, CA 90095 USA
| | - J. Wang
- South Dakota School of Mines and Technology, Rapid City, SD 57701 USA
| | - L. Wang
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | | | - X. Wang
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - Y. Wang
- University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Y. Wang
- Stony Brook University, SUNY, Stony Brook, NY 11794 USA
| | | | - D. Warner
- Colorado State University, Fort Collins, CO 80523 USA
| | - M. O. Wascko
- Imperial College of Science Technology and Medicine, London, SW7 2BZ UK
| | - D. Waters
- University College London, London, WC1E 6BT UK
| | - A. Watson
- University of Birmingham, Birmingham, B15 2TT UK
| | - K. Wawrowska
- STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX UK
- University of Sussex, Brighton, BN1 9RH UK
| | | | - A. Weber
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
- Johannes Gutenberg-Universität Mainz, 55122 Mainz, Germany
| | - M. Weber
- University of Bern, 3012 Bern, Switzerland
| | - H. Wei
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | | | - D. Wenman
- University of Wisconsin Madison, Madison, WI 53706 USA
| | | | - A. White
- University of Texas at Arlington, Arlington, TX 76019 USA
| | | | | | - M. J. Wilking
- Stony Brook University, SUNY, Stony Brook, NY 11794 USA
| | | | - C. Wilkinson
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Z. Williams
- University of Texas at Arlington, Arlington, TX 76019 USA
| | - F. Wilson
- STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX UK
| | - R. J. Wilson
- Colorado State University, Fort Collins, CO 80523 USA
| | - W. Wisniewski
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
| | | | | | - A. Wood
- University of Houston, Houston, TX 77204 USA
| | - K. Wood
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - E. Worcester
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - M. Worcester
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - K. Wresilo
- University of Cambridge, Cambridge, CB3 0HE UK
| | - C. Wret
- University of Rochester, Rochester, NY 14627 USA
| | - W. Wu
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - W. Wu
- University of California Irvine, Irvine, CA 92697 USA
| | - Y. Xiao
- University of California Irvine, Irvine, CA 92697 USA
| | - F. Xie
- University of Sussex, Brighton, BN1 9RH UK
| | - B. Yaeggy
- University of Cincinnati, Cincinnati, OH 45221 USA
| | - E. Yandel
- University of California Santa Barbara, Santa Barbara, CA 93106 USA
| | - G. Yang
- Stony Brook University, SUNY, Stony Brook, NY 11794 USA
| | - K. Yang
- University of Oxford, Oxford, OX1 3RH UK
| | - T. Yang
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | | | - N. Yershov
- Institute for Nuclear Research of the Russian Academy of Sciences, Moscow, 117312 Russia
| | - K. Yonehara
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - Y. S. Yoon
- Chung-Ang University, Seoul, 06974 South Korea
| | - T. Young
- University of North Dakota, Grand Forks, ND 58202-8357 USA
| | - B. Yu
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - H. Yu
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - H. Yu
- Sun Yat-Sen University, Guangzhou, 510275 China
| | - J. Yu
- University of Texas at Arlington, Arlington, TX 76019 USA
| | - Y. Yu
- Illinois Institute of Technology, Chicago, IL 60616 USA
| | - W. Yuan
- University of Edinburgh, Edinburgh, EH8 9YL UK
| | - R. Zaki
- York University, Toronto, M3J 1P3 Canada
| | - J. Zalesak
- Institute of Physics, Czech Academy of Sciences, 182 00 Prague 8, Czech Republic
| | - L. Zambelli
- Laboratoire d’Annecy de Physique des Particules, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LAPP-IN2P3, 74000 Annecy, France
| | - B. Zamorano
- University of Granada & CAFPE, 18002 Granada, Spain
| | - A. Zani
- Istituto Nazionale di Fisica Nucleare Sezione di Milano, 20133 Milan, Italy
| | - L. Zazueta
- College of William and Mary, Williamsburg, VA 23187 USA
| | - G. P. Zeller
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - J. Zennamo
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
| | - K. Zeug
- University of Wisconsin Madison, Madison, WI 53706 USA
| | - C. Zhang
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - S. Zhang
- Indiana University, Bloomington, IN 47405 USA
| | - Y. Zhang
- University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - M. Zhao
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - E. Zhivun
- Brookhaven National Laboratory, Upton, NY 11973 USA
| | - G. Zhu
- Ohio State University, Columbus, OH 43210 USA
| | | | - S. Zucchelli
- Università del Bologna, 40127 Bologna, Italy
- Istituto Nazionale di Fisica Nucleare Sezione di Bologna, 40127 Bologna, BO Italy
| | - J. Zuklin
- Institute of Physics, Czech Academy of Sciences, 182 00 Prague 8, Czech Republic
| | - V. Zutshi
- Northern Illinois University, DeKalb, IL 60115 USA
| | - R. Zwaska
- Fermi National Accelerator Laboratory, Batavia, IL 60510 USA
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13
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Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, Anyaneji UJ, Bester PA, Boni MF, Chand M, Choga WT, Colquhoun R, Davids M, Deforche K, Doolabh D, du Plessis L, Engelbrecht S, Everatt J, Giandhari J, Giovanetti M, Hardie D, Hill V, Hsiao NY, Iranzadeh A, Ismail A, Joseph C, Joseph R, Koopile L, Kosakovsky Pond SL, Kraemer MUG, Kuate-Lere L, Laguda-Akingba O, Lesetedi-Mafoko O, Lessells RJ, Lockman S, Lucaci AG, Maharaj A, Mahlangu B, Maponga T, Mahlakwane K, Makatini Z, Marais G, Maruapula D, Masupu K, Matshaba M, Mayaphi S, Mbhele N, Mbulawa MB, Mendes A, Mlisana K, Mnguni A, Mohale T, Moir M, Moruisi K, Mosepele M, Motsatsi G, Motswaledi MS, Mphoyakgosi T, Msomi N, Mwangi PN, Naidoo Y, Ntuli N, Nyaga M, Olubayo L, Pillay S, Radibe B, Ramphal Y, Ramphal U, San JE, Scott L, Shapiro R, Singh L, Smith-Lawrence P, Stevens W, Strydom A, Subramoney K, Tebeila N, Tshiabuila D, Tsui J, van Wyk S, Weaver S, Wibmer CK, Wilkinson E, Wolter N, Zarebski AE, Zuze B, Goedhals D, Preiser W, Treurnicht F, Venter M, Williamson C, Pybus OG, Bhiman J, Glass A, Martin DP, Rambaut A, Gaseitsiwe S, von Gottberg A, de Oliveira T. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature 2022; 603:679-686. [PMID: 35042229 PMCID: PMC8942855 DOI: 10.1038/s41586-022-04411-y] [Citation(s) in RCA: 918] [Impact Index Per Article: 459.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 01/07/2022] [Indexed: 01/02/2023]
Abstract
The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) variants, respectively1-3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron, B.1.1.529) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function4. Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.
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Affiliation(s)
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
| | - Daniel G Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Ugochukwu J Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Phillip A Bester
- Division of Virology, National Health Laboratory Service, Bloemfontein, South Africa
- Division of Virology, University of the Free State, Bloemfontein, South Africa
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Rachel Colquhoun
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Michaela Davids
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | | | - Deelan Doolabh
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Louis du Plessis
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Josie Everatt
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Diana Hardie
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Nei-Yuan Hsiao
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
| | - Arash Iranzadeh
- Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Arshad Ismail
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Rageema Joseph
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Legodile Koopile
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | | | - Lesego Kuate-Lere
- Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Oluwakemi Laguda-Akingba
- NHLS Port Elizabeth Laboratory, Port Elizabeth, South Africa
- Faculty of Health Sciences, Walter Sisulu University, Mthatha, South Africa
| | - Onalethatha Lesetedi-Mafoko
- Public Health Department, Integrated Disease Surveillance and Response, Ministry of Health and Wellness, Gaborone, Botswana
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alexander G Lucaci
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | - Arisha Maharaj
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Boitshoko Mahlangu
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Tongai Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Kamela Mahlakwane
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- NHLS Tygerberg Laboratory, Tygerberg Hospital, Cape Town, South Africa
| | - Zinhle Makatini
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Gert Marais
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Kereng Masupu
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
| | - Mogomotsi Matshaba
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
- Baylor College of Medicine, Houston, TX, USA
| | - Simnikiwe Mayaphi
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Nokuzola Mbhele
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mpaphi B Mbulawa
- National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Adriano Mendes
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Koleka Mlisana
- National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Anele Mnguni
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Thabo Mohale
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Kgomotso Moruisi
- Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Mosepele Mosepele
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
- Department of Medicine, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Gerald Motsatsi
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Modisa S Motswaledi
- Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana
- Department of Medical Laboratory Sciences, School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Thongbotho Mphoyakgosi
- National Health Laboratory, Health Services Management, Ministry of Health and Wellness, Gaborone, Botswana
| | - Nokukhanya Msomi
- Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu-Natal, Durban, South Africa
| | - Peter N Mwangi
- Division of Virology, University of the Free State, Bloemfontein, South Africa
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Noxolo Ntuli
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Martin Nyaga
- Division of Virology, University of the Free State, Bloemfontein, South Africa
- Next Generation Sequencing Unit, Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Lucier Olubayo
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Botshelo Radibe
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Yajna Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James E San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Lesley Scott
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Wendy Stevens
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Amy Strydom
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Kathleen Subramoney
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Naume Tebeila
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Joseph Tsui
- Department of Zoology, University of Oxford, Oxford, UK
| | - Stephanie van Wyk
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Steven Weaver
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | - Constantinos K Wibmer
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Nicole Wolter
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Boitumelo Zuze
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Dominique Goedhals
- Division of Virology, University of the Free State, Bloemfontein, South Africa
- PathCare Vermaak, Pretoria, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- NHLS Tygerberg Laboratory, Tygerberg Hospital, Cape Town, South Africa
| | - Florette Treurnicht
- Department of Virology, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Marietje Venter
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Carolyn Williamson
- Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Virology, NHLS Groote Schuur Laboratory, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Jinal Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Allison Glass
- Lancet Laboratories, Johannesburg, South Africa
- Department of Molecular Pathology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Darren P Martin
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
- Department of Global Health, University of Washington, Seattle, WA, USA.
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14
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Singh L, San JE, Tegally H, Brzoska PM, Anyaneji UJ, Wilkinson E, Clark L, Giandhari J, Pillay S, Lessells RJ, Martin DP, Furtado M, Kiran AM, de Oliveira T. Targeted Sanger sequencing to recover key mutations in SARS-CoV-2 variant genome assemblies produced by next-generation sequencing. Microb Genom 2022; 8:000774. [PMID: 35294336 PMCID: PMC9176282 DOI: 10.1099/mgen.0.000774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/06/2022] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is adaptively evolving to ensure its persistence within human hosts. It is therefore necessary to continuously monitor the emergence and prevalence of novel variants that arise. Importantly, some mutations have been associated with both molecular diagnostic failures and reduced or abrogated next-generation sequencing (NGS) read coverage in some genomic regions. Such impacts are particularly problematic when they occur in genomic regions such as those that encode the spike (S) protein, which are crucial for identifying and tracking the prevalence and dissemination dynamics of concerning viral variants. Targeted Sanger sequencing presents a fast and cost-effective means to accurately extend the coverage of whole-genome sequences. We designed a custom set of primers to amplify a 401 bp segment of the receptor-binding domain (RBD) (between positions 22698 and 23098 relative to the Wuhan-Hu-1 reference). We then designed a Sanger sequencing wet-laboratory protocol. We applied the primer set and wet-laboratory protocol to sequence 222 samples that were missing positions with key mutations K417N, E484K, and N501Y due to poor coverage after NGS sequencing. Finally, we developed SeqPatcher, a Python-based computational tool to analyse the trace files yielded by Sanger sequencing to generate consensus sequences, or take preanalysed consensus sequences in fasta format, and merge them with their corresponding whole-genome assemblies. We successfully sequenced 153 samples of 222 (69 %) using Sanger sequencing and confirmed the occurrence of key beta variant mutations (K417N, E484K, N501Y) in the S genes of 142 of 153 (93 %) samples. Additionally, one sample had the Y508F mutation and four samples the S477N. Samples with RT-PCR Ct scores ranging from 13.85 to 37.47 (mean=25.70) could be Sanger sequenced efficiently. These results show that our method and pipeline can be used to improve the quality of whole-genome assemblies produced using NGS and can be used with any pairs of the most used NGS and Sanger sequencing platforms.
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Affiliation(s)
- Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - James E. San
- KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | | | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Lindsay Clark
- HPCBio, Roy J. Carver Biotechnology Center, University of Illinois, IL, USA
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - Darren Patrick Martin
- Institute of Infectious Diseases and Molecular Medicine, Division of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7701, South Africa
| | | | - Anmol M. Kiran
- Malawi-Liverpool-Wellcome Trust, Chichiri, Blantyre 3, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool CH64 7TE, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, 7600, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
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15
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Cele S, Karim F, Lustig G, San JE, Hermanus T, Tegally H, Snyman J, Moyo-Gwete T, Wilkinson E, Bernstein M, Khan K, Hwa SH, Tilles SW, Singh L, Giandhari J, Mthabela N, Mazibuko M, Ganga Y, Gosnell BI, Karim SSA, Hanekom W, Van Voorhis WC, Ndung'u T, Lessells RJ, Moore PL, Moosa MYS, de Oliveira T, Sigal A. SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape. Cell Host Microbe 2022; 30:154-162.e5. [PMID: 35120605 PMCID: PMC8758318 DOI: 10.1016/j.chom.2022.01.005] [Citation(s) in RCA: 130] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/05/2021] [Accepted: 01/12/2022] [Indexed: 11/25/2022]
Abstract
Characterizing SARS-CoV-2 evolution in specific geographies may help predict properties of the variants that come from these regions. We mapped neutralization of a SARS-CoV-2 strain that evolved over 6 months from ancestral virus in a person with advanced HIV disease in South Africa; this person was infected prior to emergence of the Beta and Delta variants. We longitudinally tracked the evolved virus and tested it against self-plasma and convalescent plasma from ancestral, Beta, and Delta infections. Early virus was similar to ancestral, but it evolved a multitude of mutations found in Omicron and other variants. It showed substantial but incomplete Pfizer BNT162b2 escape, weak neutralization by self-plasma, and despite pre-dating Delta, it also showed extensive escape of Delta infection-elicited neutralization. This example is consistent with the notion that SARS-CoV-2 evolving in individual immune-compromised hosts, including those with advanced HIV disease, may gain immune escape of vaccines and enhanced escape of Delta immunity, and this has implications for vaccine breakthrough and reinfections.
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Affiliation(s)
- Sandile Cele
- Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Farina Karim
- Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Tandile Hermanus
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa; Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Jumari Snyman
- Africa Health Research Institute, Durban, South Africa; HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
| | - Thandeka Moyo-Gwete
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa; Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | | | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Shi-Hsia Hwa
- Africa Health Research Institute, Durban, South Africa; Division of Infection and Immunity, University College London, London, UK
| | - Sasha W Tilles
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | | | | | - Yashica Ganga
- Africa Health Research Institute, Durban, South Africa
| | - Bernadett I Gosnell
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Willem Hanekom
- Africa Health Research Institute, Durban, South Africa; Division of Infection and Immunity, University College London, London, UK
| | - Wesley C Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Thumbi Ndung'u
- Africa Health Research Institute, Durban, South Africa; HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J Lessells
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa, Durban, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Penny L Moore
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa; National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa, Durban, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa; Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; Department of Global Health, University of Washington, Seattle, WA, USA
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Max Planck Institute for Infection Biology, Berlin, Germany.
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16
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Rodgers MA, Olivo A, Harris BJ, Lark C, Luo X, Berg MG, Meyer TV, Mohaimani A, Orf GS, Goldstein Y, Fox AS, Hirschhorn J, Glen WB, Nolte F, Landay A, Jennings C, Moy J, Servellita V, Chiu C, Batra R, Snell LB, Nebbia G, Douthwaite S, Tanuri A, Singh L, de Oliveira T, Ahouidi A, Mboup S, Cloherty GA. Detection of SARS-CoV-2 variants by Abbott molecular, antigen, and serological tests. J Clin Virol 2022; 147:105080. [PMID: 35086043 PMCID: PMC8770247 DOI: 10.1016/j.jcv.2022.105080] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 12/21/2021] [Accepted: 01/19/2022] [Indexed: 01/31/2023]
Abstract
Background : Viral diversity presents an ongoing challenge for diagnostic tests, which need to accurately detect all circulating variants. The Abbott Global Surveillance program monitors severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants and their impact on diagnostic test performance. Objectives : To evaluate the capacity of Abbott molecular, antigen, and serologic assays to detect circulating SARS-CoV-2 variants, including all current variants of concern (VOC): B.1.1.7 (alpha), B.1.351 (beta), P.1 (gamma) and B.1.617.2 (delta). Study design : Dilutions of variant virus cultures (B.1.1.7, B.1.351, B.1.429, B.1.526.1, B.1.526.2, B.1.617.1, B.1.617.2, P.1, R.1 and control isolate WA1) and a panel of N = 248 clinical samples from patients with sequence confirmed variant infections (B.1.1.7, B.1.351, B.1.427, B.1.429, B.1.526, B.1.526.1, B.1.526.2, P.1, P.2, R.1) were evaluated on at least one assay: Abbott ID NOW COVID-19, m2000 RealTime SARS-CoV-2, Alinity m SARS-CoV-2, and Alinity m Resp-4-Plex molecular assays; the BinaxNOW COVID-19 Ag Card and Panbio COVID-19 Ag Rapid Test Device; and the ARCHITECT/Alinity i SARS-CoV-2 IgG and AdviseDx IgM assays, Panbio COVID-19 IgG assay, and ARCHITECT/Alinity i AdviseDx SARS-CoV-2 IgG II assay. Results : Consistent with in silico predictions, each molecular and antigen assay detected VOC virus cultures with equivalent sensitivity to the WA1 control strain. Notably, 100% of all tested variant patient specimens were detected by molecular assays (N = 197 m2000, N = 88 Alinity m, N = 99 ID NOW), and lateral flow assays had a sensitivity of >94% for specimens with genome equivalents (GE) per device above 4 log (85/88, Panbio; 54/57 Binax). Furthermore, Abbott antibody assays detected IgG and IgM in 94–100% of sera from immune competent B.1.1.7 patients 15–26 days after symptom onset. Conclusions : These data confirm variant detection for 11 SARS-CoV-2 assays, which is consistent with each assay target region being highly conserved. Importantly, alpha, beta, gamma, and delta VOCs were detected by molecular and antigen assays, indicating that these tests may be suitable for widescale use where VOCs predominate.
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Affiliation(s)
| | - Ana Olivo
- Abbott Diagnostics, Abbott Park, IL, USA
| | | | - Chris Lark
- Abbott Diagnostics, Abbott Park, IL, USA
| | - Xinxin Luo
- Abbott Diagnostics, Abbott Park, IL, USA
| | | | | | | | | | | | | | | | | | | | | | | | - James Moy
- Rush University Medical Center, IL, USA
| | | | | | - Rahul Batra
- Guy's and St Thomas' NHS Foundation, London, UK
| | | | - Gaia Nebbia
- Guy's and St Thomas' NHS Foundation, London, UK
| | | | - Amilcar Tanuri
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Ambroise Ahouidi
- Institute for Health Research Epidemiological Surveillance and Training, Dakar, Senegal
| | - Souleymane Mboup
- Institute for Health Research Epidemiological Surveillance and Training, Dakar, Senegal
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17
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Scott L, Hsiao NY, Moyo S, Singh L, Tegally H, Dor G, Maes P, Pybus OG, Kraemer MUG, Semenova E, Bhatt S, Flaxman S, Faria NR, de Oliveira T. Track Omicron's spread with molecular data. Science 2021; 374:1454-1455. [PMID: 34882437 DOI: 10.1126/science.abn4543] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Lesley Scott
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Nei-Yuan Hsiao
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,National Health Laboratory Service, Cape Town, South Africa
| | - Sikhuline Moyo
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Lavanya Singh
- Centre for Epidemic Response and Innovation, Stellenbosch University, Stellenbosch, South Africa.,KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation, Stellenbosch University, Stellenbosch, South Africa.,KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
| | - Graeme Dor
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Piet Maes
- Laboratory of Clinical and Epidemiological Virology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.,Royal Veterinary College, London, UK
| | | | | | - Samir Bhatt
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.,MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.,The Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, UK.,MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.,The Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London, London, UK.,Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation, Stellenbosch University, Stellenbosch, South Africa.,KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban, South Africa
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18
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Cele S, Karim F, Lustig G, San JE, Hermanus T, Tegally H, Snyman J, Moyo-Gwete T, Wilkinson E, Bernstein M, Khan K, Hwa SH, Tilles SW, Singh L, Giandhari J, Mthabela N, Mazibuko M, Ganga Y, Gosnell BI, Karim SA, Hanekom W, Van Voorhis WC, Ndung’u T, Lessells RJ, Moore PL, Moosa MYS, de Oliveira T, Sigal A. SARS-CoV-2 evolved during advanced HIV disease immunosuppression has Beta-like escape of vaccine and Delta infection elicited immunity. medRxiv 2021:2021.09.14.21263564. [PMID: 34909798 PMCID: PMC8669865 DOI: 10.1101/2021.09.14.21263564] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Characterizing SARS-CoV-2 evolution in specific geographies may help predict the properties of variants coming from these regions. We mapped neutralization of a SARS-CoV-2 strain that evolved over 6 months from the ancestral virus in a person with advanced HIV disease. Infection was before the emergence of the Beta variant first identified in South Africa, and the Delta variant. We compared early and late evolved virus to the ancestral, Beta, Alpha, and Delta viruses and tested against convalescent plasma from ancestral, Beta, and Delta infections. Early virus was similar to ancestral, whereas late virus was similar to Beta, exhibiting vaccine escape and, despite pre-dating Delta, strong escape of Delta-elicited neutralization. This example is consistent with the notion that variants arising in immune-compromised hosts, including those with advanced HIV disease, may evolve immune escape of vaccines and enhanced escape of Delta immunity, with implications for vaccine breakthrough and reinfections. HIGHLIGHTS A prolonged ancestral SARS-CoV-2 infection pre-dating the emergence of Beta and Delta resulted in evolution of a Beta-like serological phenotypeSerological phenotype includes strong escape from Delta infection elicited immunity, intermediate escape from ancestral virus immunity, and weak escape from Beta immunityEvolved virus showed substantial but incomplete escape from antibodies elicited by BNT162b2 vaccination. GRAPHICAL ABSTRACT
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Affiliation(s)
- Sandile Cele
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Tandile Hermanus
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Jumari Snyman
- Africa Health Research Institute, Durban, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | | | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
| | | | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Shi-Hsia Hwa
- Africa Health Research Institute, Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Sasha W. Tilles
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, USA
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | | | | | - Yashica Ganga
- Africa Health Research Institute, Durban, South Africa
| | - Bernadett I. Gosnell
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Salim Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Willem Hanekom
- Africa Health Research Institute, Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Wesley C. Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, USA
| | - Thumbi Ndung’u
- Africa Health Research Institute, Durban, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | | | - Richard J. Lessells
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Penny L. Moore
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mahomed-Yunus S. Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- HIV Pathogenesis Programme, University of KwaZulu-Natal, Durban, South Africa
- Department of Global Health, University of Washington, Seattle, USA
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Max Planck Institute for Infection Biology, Berlin, Germany
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19
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Chimukangara B, Lessells RJ, Sartorius B, Gounder L, Manyana S, Pillay M, Singh L, Giandhari J, Govender K, Samuel R, Msomi N, Naidoo K, de Oliveira T, Moodley P, Parboosing R. HIV-1 drug resistance in adults and adolescents on protease inhibitor-based antiretroviral treatment in KwaZulu-Natal Province, South Africa. J Glob Antimicrob Resist 2021; 29:468-475. [PMID: 34785393 DOI: 10.1016/j.jgar.2021.10.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/19/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND In low- and middle-income countries, increasing levels of HIV drug resistance (HIVDR) on second-line protease inhibitor (PI)-based regimens are a cause for concern, given limited drug options for third-line antiretroviral therapy (ART). OBJECTIVES We conducted a retrospective analysis of routine HIV-1 genotyping laboratory data from KwaZulu-Natal, in South Africa, to describe the frequency and patterns of HIVDR mutations and their consequent impact on standardized third-line regimens. METHODS This was a cross-sectional analysis of all HIV-1 genotypic resistance tests conducted by the National Health Laboratory Service in KwaZulu-Natal, South Africa (Jan 2015 - Dec 2016), for adults and adolescents (age ≥10 years) on second-line PI-based ART with virological failure. We assigned a third-line regimen to each record, based on a national treatment algorithm and calculated the genotypic susceptibility score (GSS) for that regimen. RESULTS Of 348 samples analyzed, 287 (83%) had at least one drug resistance mutation (DRM) and 114 (33%) had at least one major PI DRM. Major PI resistance was associated with longer duration on second-line ART (aOR per 6-months, 1.11, 95% CI 1.04-1.19) and older age (aOR 1.03, 95% CI 1.01-1.05). Of 112 patients requiring third-line ART, 12 (11%) had a GSS of <2 for the algorithm-assigned third-line regimen. CONCLUSIONS One in three people failing second-line ART had significant PI DRMs. A subgroup of these individuals had extensive HIVDR, where the predicted activity of third-line ART was suboptimal, highlighting the need for continuous evaluation of outcomes on third-line regimens and close monitoring for emergent HIV-1 integrase-inhibitor resistance.
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Affiliation(s)
- Benjamin Chimukangara
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; Critical Care Medicine Department, NIH Clinical Center, Bethesda, MD, USA.
| | - Richard J Lessells
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Benn Sartorius
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Lilishia Gounder
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Sontaga Manyana
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Melendhran Pillay
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kerusha Govender
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Reshmi Samuel
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Nokukhanya Msomi
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Tulio de Oliveira
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Global Health, University of Washington, Seattle, United States
| | - Pravi Moodley
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
| | - Raveen Parboosing
- Department of Virology, University of KwaZulu-Natal/National Health Laboratory Service, Durban, South Africa
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20
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Fernandes GS, Spiers A, Vaidya N, Zhang Y, Sharma E, Holla B, Heron J, Hickman M, Murthy P, Chakrabarti A, Basu D, Subodh BN, Singh L, Singh R, Kalyanram K, Kartik K, Kumaran K, Krishnaveni G, Kuriyan R, Kurpad S, Barker GJ, Bharath RD, Desrivieres S, Purushottam M, Orfanos DP, Toledano MB, Schumann G, Benegal V. Adverse childhood experiences and substance misuse in young people in India: results from the multisite cVEDA cohort. BMC Public Health 2021; 21:1920. [PMID: 34686158 PMCID: PMC8539836 DOI: 10.1186/s12889-021-11892-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 09/07/2021] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Adverse childhood experiences (ACEs) increases vulnerability to externalising disorders such as substance misuse. The study aims to determine the prevalence of ACEs and its association with substance misuse. METHODS Data from the Consortium on Vulnerability to Externalising Disorders and Addictions (cVEDA) in India was used (n = 9010). ACEs were evaluated using the World Health Organisation (WHO) Adverse Childhood Experiences International Questionnaire whilst substance misuse was assessed using the WHO Alcohol, Smoking and Substance Involvement Screening Test. A random-effects, two-stage individual patient data meta-analysis explained the associations between ACEs and substance misuse with adjustments for confounders such as sex and family structure. RESULTS 1 in 2 participants reported child maltreatment ACEs and family level ACEs. Except for sexual abuse, males report more of every individual childhood adversity and are more likely to report misusing substances compared with females (87.3% vs. 12.7%). In adolescents, family level ACEs (adj OR 4.2, 95% CI 1.5-11.7) and collective level ACEs (adj OR 6.6, 95% CI 1.4-31.1) show associations with substance misuse whilst in young adults, child level ACEs such as maltreatment show similar strong associations (adj OR 2.0, 95% CI 1.1-3.5). CONCLUSION ACEs such as abuse and domestic violence are strongly associated with substance misuse, most commonly tobacco, in adolescent and young adult males in India. The results suggest enhancing current ACE resilience programmes and 'trauma-informed' approaches to tackling longer-term impact of ACEs in India. FUNDING Newton Bhabha Grant jointly funded by the Medical Research Council, UK (MR/N000390/1) and the Indian Council of Medical Research (ICMR/MRC-UK/3/M/2015-NCD-I).
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Affiliation(s)
- G S Fernandes
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK.
| | - A Spiers
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - N Vaidya
- Centre for Addiction Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India.,Centre for Population Neuroscience and Precision Medicine, Kings College London, London, UK
| | - Y Zhang
- Centre for Innovation in Mental Health, Department of Psychology, University of Southampton, Southampton, UK
| | - E Sharma
- Centre for Addiction Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - B Holla
- Centre for Addiction Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - J Heron
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - M Hickman
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - P Murthy
- Centre for Addiction Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - A Chakrabarti
- ICMR-Centre on Non-Communicable Diseases, Kolkata, India
| | - D Basu
- Department of Psychiatry, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - B N Subodh
- Department of Psychiatry, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - L Singh
- Department of Psychiatry, Regional Institute of Medical Sciences (RIMS), Imphal, Manipur, India
| | - R Singh
- Department of Psychiatry, Regional Institute of Medical Sciences (RIMS), Imphal, Manipur, India
| | - K Kalyanram
- Rishi Valley Rural Health Centre, Madanapalle, Chittoor, Andhra Pradesh, India
| | - K Kartik
- Rishi Valley Rural Health Centre, Madanapalle, Chittoor, Andhra Pradesh, India
| | - K Kumaran
- Epidemiology Research Unit, CSI Holdsworth Memorial Hospital, Mysore, India
| | - G Krishnaveni
- Epidemiology Research Unit, CSI Holdsworth Memorial Hospital, Mysore, India
| | - R Kuriyan
- Department of Psychiatry and Medical Ethics, St John's Medical College & Hospital, Bangalore, India
| | - S Kurpad
- Department of Psychiatry & Department of Medical Ethics, St. John's Medical College & Hospital, Bangalore, India
| | - G J Barker
- Centre for Population Neuroscience and Precision Medicine, Kings College London, London, UK.,Department of Neuroimaging, King's College London, London, UK
| | - R D Bharath
- Centre for Addiction Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - S Desrivieres
- Centre for Population Neuroscience and Precision Medicine, Kings College London, London, UK
| | - M Purushottam
- Centre for Addiction Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - D P Orfanos
- NeuroSpin, CEA, Université Paris-Saclay, Paris, France
| | - M B Toledano
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - G Schumann
- Centre for Population Neuroscience and Precision Medicine, Kings College London, London, UK
| | - V Benegal
- Centre for Addiction Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
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21
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Wilkinson E, Giovanetti M, Tegally H, San JE, Lessells R, Cuadros D, Martin DP, Rasmussen DA, Zekri ARN, Sangare AK, Ouedraogo AS, Sesay AK, Priscilla A, Kemi AS, Olubusuyi AM, Oluwapelumi AOO, Hammami A, Amuri AA, Sayed A, Ouma AEO, Elargoubi A, Ajayi NA, Victoria AF, Kazeem A, George A, Trotter AJ, Yahaya AA, Keita AK, Diallo A, Kone A, Souissi A, Chtourou A, Gutierrez AV, Page AJ, Vinze A, Iranzadeh A, Lambisia A, Ismail A, Rosemary A, Sylverken A, Femi A, Ibrahimi A, Marycelin B, Oderinde BS, Bolajoko B, Dhaala B, Herring BL, Njanpop-Lafourcade BM, Kleinhans B, McInnis B, Tegomoh B, Brook C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Peyrefitte C, Daubenberger C, Morang’a CM, Nokes DJ, Amoako DG, Bugembe DL, Park D, Baker D, Doolabh D, Ssemwanga D, Tshiabuila D, Bassirou D, Amuzu DSY, Goedhals D, Omuoyo DO, Maruapula D, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong’era EM, Ngabana EN, Shumba E, El Fahime E, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Leendertz F, Ajili F, Enoch FO, Wasfi F, Abdelmoula F, Mosha FS, Takawira FT, Derrar F, Bouzid F, Onikepe F, Adeola F, Muyembe FM, Tanser F, Dratibi FA, Mbunsu GK, Thilliez G, Kay GL, Githinji G, van Zyl G, Awandare GA, Schubert G, Maphalala GP, Ranaivoson HC, Lemriss H, Anise H, Abe H, Karray HH, Nansumba H, Elgahzaly HA, Gumbo H, Smeti I, Ayed IB, Odia I, Ben Boubaker IB, Gaaloul I, Gazy I, Mudau I, Ssewanyana I, Konstantinus I, Lekana-Douk JB, Makangara JCC, Tamfum JJM, Heraud JM, Shaffer JG, Giandhari J, Li J, Yasuda J, Mends JQ, Kiconco J, Morobe JM, Gyapong JO, Okolie JC, Kayiwa JT, Edwards JA, Gyamfi J, Farah J, Nakaseegu J, Ngoi JM, Namulondo J, Andeko JC, Lutwama JJ, O’Grady J, Siddle K, Adeyemi KT, Tumedi KA, Said KM, Hae-Young K, Duedu KO, Belyamani L, Fki-Berrajah L, Singh L, Martins LDO, Tyers L, Ramuth M, Mastouri M, Aouni M, el Hefnawi M, Matsheka MI, Kebabonye M, Diop M, Turki M, Paye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina M, Nwando M, Owusu M, Wiley MR, Youtchou MT, Ayekaba MO, Abouelhoda M, Seadawy MG, Khalifa MK, Sekhele M, Ouadghiri M, Diagne MM, Mwenda M, Allam M, Phan MVT, Abid N, Touil N, Rujeni N, Kharrat N, Ismael N, Dia N, Mabunda N, Hsiao NY, Silochi NB, Nsenga N, Gumede N, Mulder N, Ndodo N, Razanajatovo NH, Iguosadolo N, Judith O, Kingsley OC, Sylvanus O, Peter O, Femi O, Idowu O, Testimony O, Chukwuma OE, Ogah OE, Onwuamah CK, Cyril O, Faye O, Tomori O, Ondoa P, Combe P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Dussart P, Bester PA, Mbala PK, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Carr RAA, El Kabbaj S, Gargouri S, Masmoudi S, Sankhe S, Lawal SB, Kassim S, Trabelsi S, Metha S, Kammoun S, Lemriss S, Agwa SHA, Calvignac-Spencer S, Schaffner SF, Doumbia S, Mandanda SM, Aryeetey S, Ahmed SS, Elhamoumi S, Andriamandimby S, Tope S, Lekana-Douki S, Prosolek S, Ouangraoua S, Mundeke SA, Rudder S, Panji S, Pillay S, Engelbrecht S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Aanniz T, Mohale T, Le-Viet T, Schindler T, Anyaneji UJ, Chinedu U, Ramphal U, Jessica U, George U, Fonseca V, Enouf V, Gorova V, Roshdy WH, Ampofo WK, Preiser W, Choga WT, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Sall AA, Rebai A, von Gottberg A, Kouriba B, Williamson C, Bridges DJ, Chikwe I, Bhiman JN, Mine M, Cotten M, Moyo S, Gaseitsiwe S, Saasa N, Sabeti PC, Kaleebu P, Tebeje YK, Tessema SK, Happi C, Nkengasong J, de Oliveira T. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science 2021; 374:423-431. [PMID: 34672751 PMCID: PMC7613315 DOI: 10.1126/science.abj4336] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/03/2021] [Indexed: 01/05/2023]
Abstract
The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.
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Affiliation(s)
- Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James E. San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Diego Cuadros
- Department of Geography and GIS, University of Cincinnati, Cincinnati, OH, USA
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - David A. Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Abdel-Rahman N. Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Abdoul K. Sangare
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
| | - Abdoul-Salam Ouedraogo
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | | | - Abechi Priscilla
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Adedotun-Sulaiman Kemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Adeyemi O. O. Oluwapelumi
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Adnène Hammami
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Adrienne A. Amuri
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Ahmad Sayed
- Genomics Research Program, Children’s Cancer Hospital, Cairo, Egypt
| | - Ahmed E. O. Ouma
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Aida Elargoubi
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Nnennaya A. Ajayi
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Ajogbasile F. Victoria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Akano Kazeem
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Ali A. Yahaya
- World Health Organization, Africa Region, Brazzaville Congo
| | - Alpha K. Keita
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea
- TransVIHMI, Montpellier University/IRD/INSERM, Montpellier, France
| | - Amadou Diallo
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou Kone
- Mali-University Clinical Research Center (UCRC), Bamako, Mali
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Amel Chtourou
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | | | | | - Anika Vinze
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Arash Iranzadeh
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arnold Lambisia
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Arshad Ismail
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Audu Rosemary
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Ayoade Femi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Baba Marycelin
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bamidele S. Oderinde
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bankole Bolajoko
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | | | - Bronwyn Kleinhans
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Bronwyn McInnis
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Bryan Tegomoh
- The Biotechnology Center of the University of Yaoundé I, Cameroon and CDC Foundation, Yaounde, Cameroon
| | - Cara Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Chantal G. Akoua-Koffi
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | - Charles N. Agoti
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- School of Public Health, Pwani University, Kilifi, Kenya
| | | | | | - Collins M. Morang’a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - D. James Nokes
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Daniel G. Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Danny Park
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | | | - Deelan Doolabh
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Deogratius Ssemwanga
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Diarra Bassirou
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Dominic S. Y. Amuzu
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Dominique Goedhals
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | | | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | | | - Eddy K. Lusamaki
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Edgar Simulundu
- University of Zambia, School of Veterinary Medicine, Department of Disease Control, Lusaka, Zambia
| | | | - Edith N. Ngabana
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Edwin Shumba
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | - Elmostafa El Fahime
- Functional Genomic Platform/National Centre for Scientific and Technical Research (CNRST), Rabat, Morocco
| | - Emmanuel Lokilo
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
| | | | - Eromon Philomena
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Etilé A. Anoh
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | | | - Faida Ajili
- Research Unit of Autoimmune Diseases UR17DN02, Military Hospital of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Fakayode O. Enoch
- Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
| | - Fares Wasfi
- Laboratory of Clinical Virology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Fatma Abdelmoula
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | | | | | - Fawzi Derrar
- National Influenza Centre, Viral Respiratory Laboratory, Algiers, Algeria
| | - Feriel Bouzid
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Folarin Onikepe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Fowotade Adeola
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Francisca M. Muyembe
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Frank Tanser
- Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
| | | | - Gabriel K. Mbunsu
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | | | - George Githinji
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | | | - Gugu P. Maphalala
- Institution and Department, Ministry Of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
| | | | - Hajar Lemriss
- Laboratory of Health Sciences and Technologies, High Institute of Health Sciences, Hassan 1st University, Settat, Morocco
| | - Happi Anise
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Hela H. Karray
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | | | - Hesham A. Elgahzaly
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Hlanai Gumbo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Ibtihel Smeti
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ikhlas B. Ayed
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Ilhem Boutiba Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, 1006 Tunis, Tunisia
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Imed Gaaloul
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | - Inbal Gazy
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Innocent Mudau
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Jean B. Lekana-Douk
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | - Jean-Claude C. Makangara
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Jean-Jacques M. Tamfum
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Jean-Michel Heraud
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jingjing Li
- Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, PA, USA
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Joana Q. Mends
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | - John M. Morobe
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - John O. Gyapong
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Johnson C. Okolie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - John T. Kayiwa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Johnathan A. Edwards
- Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jones Gyamfi
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | | | - Joyce M. Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | | | - Julia C. Andeko
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | | | - Kayode T. Adeyemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Kefentse A. Tumedi
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
| | - Khadija M. Said
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Kim Hae-Young
- New York University Grossman School of Medicine, New York City, NY, USA
| | - Kwabena O. Duedu
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Lahcen Belyamani
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Lamia Fki-Berrajah
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Lynn Tyers
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Magalutcheemee Ramuth
- Virology/Molecular Biology Department, Central Health Laboratory, Ministry of Health and Wellness, Mauritius
| | - Maha Mastouri
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Mahjoub Aouni
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | - Mahmoud el Hefnawi
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo Egypt
| | | | | | - Mamadou Diop
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Manel Turki
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Marietou Paye
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | | | - Matoke-Muhia Damaris
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | - Maureen W. Mburu
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Maximillian Mpina
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- Ifakara Health Institute, Dar-es-Salaam, Tanzania
| | - Mba Nwando
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Michael Owusu
- Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Mirabeau T. Youtchou
- Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
| | | | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo 12613, Egypt
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Mohamed G. Seadawy
- Biological Prevention Department, Main Chemical Laboratories, Egypt Army, Cairo, Egypt
| | | | - Mooko Sekhele
- National Reference Laboratory Lesotho, Maseru, Lesotho
| | - Mouna Ouadghiri
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | | | | | - Mushal Allam
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - My V. T. Phan
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
- Department of Biotechnology, High Institute of Biotechnology of Sidi Thabet, University of Manouba, BP-66, 2020 Ariana-Tunis, Tunisia
| | - Nadia Touil
- Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Nadine Rujeni
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Najla Kharrat
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Nalia Ismael
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Nedio Mabunda
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Nei-yuan Hsiao
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | - Ngoy Nsenga
- World Health Organization, Africa Region, Brazzaville Congo
| | - Nicksy Gumede
- World Health Organization, Africa Region, Brazzaville Congo
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
| | | | | | - Nosamiefan Iguosadolo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Oguzie Judith
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Ojide C. Kingsley
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | | | | | - Oladiji Femi
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Olawoye Idowu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Olumade Testimony
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Omoruyi E. Chukwuma
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Onwe E. Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Chika K. Onwuamah
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Pascale Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | | | | | - Paul E. Oluniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Paulo Arnaldo
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Peter K. Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Phillip A. Bester
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | - Placide K. Mbala
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Reuben Ayivor-Djanie
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Richard Njouom
- Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
| | - Richard O. Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richmond Gorman
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Rosina A. A. Carr
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Saâd El Kabbaj
- Laboratoire de Recherche et d’Analyses Médicales de la Gendarmerie Royale, Rabat, Morocco
| | - Saba Gargouri
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Safietou Sankhe
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Salako B. Lawal
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Samar Kassim
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Sameh Trabelsi
- Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
| | - Samar Metha
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Sami Kammoun
- CHU Hedi Chaker Sfax, Service de Pneumologie, Tunis, Tunisia
| | - Sanaâ Lemriss
- Laboratoire de Recherche et d’Analyses Médicales de la Gendarmerie Royale, Rabat, Morocco
| | - Sara H. A. Agwa
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | | | | | - Seydou Doumbia
- Mali-University Clinical Research Center (UCRC), Bamako, Mali
| | - Sheila M. Mandanda
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | | | | | | | - Sobajo Tope
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Sonia Lekana-Douki
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Soumeya Ouangraoua
- Centre MURAZ, Ouagadougou, Burkina Faso
- National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
| | - Steve A. Mundeke
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | - Sumir Panji
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Susan Nabadda
- Central Public Health Laboratories (CPHL), Kampala, Uganda
| | - Sylvie Behillil
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | | | - Sylvie van der Werf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | | | - Tarik Aanniz
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Thabo Mohale
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ugwu Chinedu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
| | - Uwanibe Jessica
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Uwem George
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Coordenação Geral de Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Vincent Enouf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | - Vivianne Gorova
- World Health Organization, WHO Lesotho, Maseru, Lesotho
- Med24 Medical Centre, Ruwa, Zimbabwe
| | | | - William K. Ampofo
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Wonderful T. Choga
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Yvan Butera
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
| | | | - Amadou A. Sall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Bourema Kouriba
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | - Carolyn Williamson
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | | | - Jinal N. Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Matthew Cotten
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ngonda Saasa
- University of Zambia, School of Veterinary Medicine, Department of Disease Control, Lusaka, Zambia
| | | | | | - Yenew K. Tebeje
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Sofonias K. Tessema
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - John Nkengasong
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
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22
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Chimukangara B, Lessells RJ, Singh L, Grigalionyte I, Yende-Zuma N, Adams R, Dawood H, Dlamini L, Buthelezi S, Chetty S, Diallo K, Duffus WA, Mogashoa M, Hagen MB, Giandhari J, de Oliveira T, Moodley P, Padayatchi N, Naidoo K. Acquired HIV drug resistance and virologic monitoring in a HIV hyper-endemic setting in KwaZulu-Natal Province, South Africa. AIDS Res Ther 2021; 18:74. [PMID: 34656129 PMCID: PMC8520607 DOI: 10.1186/s12981-021-00393-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 09/22/2021] [Indexed: 11/17/2022] Open
Abstract
Background Introduction of tenofovir (TDF) plus lamivudine (3TC) and dolutegravir (DTG) in first- and second-line HIV treatment regimens in South Africa warrants characterization of acquired HIV-1 drug resistance (ADR) mutations that could impact DTG-based antiretroviral therapy (ART). In this study, we sought to determine prevalence of ADR mutations and their potential impact on susceptibility to drugs used in combination with DTG among HIV-positive adults (≥ 18 years) accessing routine care at a selected ART facility in KwaZulu-Natal, South Africa. Methods We enrolled adult participants in a cross-sectional study between May and September 2019. Eligible participants had a most recent documented viral load (VL) ≥ 1000 copies/mL after at least 6 months on ART. We genotyped HIV-1 reverse transcriptase and protease genes by Sanger sequencing and assessed ADR. We characterized the effect of ADR mutations on the predicted susceptibility to drugs used in combination with DTG. Results From 143 participants enrolled, we obtained sequence data for 115 (80%), and 92.2% (95% CI 85.7–96.4) had ADR. The proportion with ADR was similar for participants on first-line ART (65/70, 92.9%, 95% CI 84.1–97.6) and those on second-line ART (40/44, 90.9%, 95% CI 78.3–97.5), and was present for the single participant on third-line ART. Approximately 89% (62/70) of those on first-line ART had dual class NRTI and NNRTI resistance and only six (13.6%) of those on second-line ART had major PI mutations. Most participants (82%) with first-line viraemia maintained susceptibility to Zidovudine (AZT), and the majority of them had lost susceptibility to TDF (71%) and 3TC (84%). Approximately two in every five TDF-treated individuals had thymidine analogue mutations (TAMs). Conclusions Susceptibility to AZT among most participants with first-line viraemia suggests that a new second-line regimen of AZT + 3TC + DTG could be effective. However, atypical occurrence of TAMs in TDF-treated individuals suggests a less effective AZT + 3TC + DTG regimen in a subpopulation of patients. As most patients with first-line viraemia had at least low-level resistance to TDF and 3TC, identifying viraemia before switch to TDF + 3TC + DTG is important to avoid DTG functional monotherapy. These findings highlight a need for close monitoring of outcomes on new standardized treatment regimens. Supplementary Information The online version contains supplementary material available at 10.1186/s12981-021-00393-5.
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23
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Martin DP, Weaver S, Tegally H, San JE, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ, Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL. The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Cell 2021; 184:5189-5200.e7. [PMID: 34537136 PMCID: PMC8421097 DOI: 10.1016/j.cell.2021.09.003] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/05/2021] [Accepted: 09/01/2021] [Indexed: 12/18/2022]
Abstract
The independent emergence late in 2020 of the B.1.1.7, B.1.351, and P.1 lineages of SARS-CoV-2 prompted renewed concerns about the evolutionary capacity of this virus to overcome public health interventions and rising population immunity. Here, by examining patterns of synonymous and non-synonymous mutations that have accumulated in SARS-CoV-2 genomes since the pandemic began, we find that the emergence of these three "501Y lineages" coincided with a major global shift in the selective forces acting on various SARS-CoV-2 genes. Following their emergence, the adaptive evolution of 501Y lineage viruses has involved repeated selectively favored convergent mutations at 35 genome sites, mutations we refer to as the 501Y meta-signature. The ongoing convergence of viruses in many other lineages on this meta-signature suggests that it includes multiple mutation combinations capable of promoting the persistence of diverse SARS-CoV-2 lineages in the face of mounting host immune recognition.
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Affiliation(s)
- Darren P Martin
- Institute of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7701, South Africa.
| | - Steven Weaver
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa
| | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa
| | - Stephen D Shank
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa
| | - Alexander G Lucaci
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa
| | - Sureshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa
| | - Yeshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa
| | - Ravindra K Gupta
- Clinical Microbiology, University of Cambridge, Cambridge CB2 1TN, UK; Africa Health Research Institute, KwaZulu-Natal 4013, South Africa
| | - Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Anton Nekturenko
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA 16802, USA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 141 83, Sweden
| | - Gordon W Harkins
- South African Medical Research Council Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville 7635, South Africa
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven 3000, Belgium
| | - Oscar A MacLean
- MRC-University of Glasgow Centre for Virus Research, Glasgow 12 8QQ, Scotland, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow 12 8QQ, Scotland, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban 4001, South Africa; Department of Global Health, University of Washington, Seattle, WA 98195-4550, USA.
| | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA.
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24
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Singh L, Anyaneji UJ, Ndifon W, Turok N, Mattison SA, Lessells R, Sinayskiy I, San EJ, Tegally H, Barnett S, Lorimer T, Petruccione F, de Oliveira T. Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing. Sci Rep 2021; 11:17793. [PMID: 34493744 PMCID: PMC8423848 DOI: 10.1038/s41598-021-96934-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/18/2021] [Indexed: 12/21/2022] Open
Abstract
The rapid identification and isolation of infected individuals remains a key strategy for controlling the spread of SARS-CoV-2. Frequent testing of populations to detect infection early in asymptomatic or presymptomatic individuals can be a powerful tool for intercepting transmission, especially when the viral prevalence is low. However, RT-PCR testing-the gold standard of SARS-CoV-2 diagnosis-is expensive, making regular testing of every individual unfeasible. Sample pooling is one approach to lowering costs. By combining samples and testing them in groups the number of tests required is reduced, substantially lowering costs. Here we report on the implementation of pooling strategies using 3-d and 4-d hypercubes to test a professional sports team in South Africa. We have shown that infected samples can be reliably detected in groups of 27 and 81, with minimal loss of assay sensitivity for samples with individual Ct values of up to 32. We report on the automation of sample pooling, using a liquid-handling robot and an automated web interface to identify positive samples. We conclude that hypercube pooling allows for the reliable RT-PCR detection of SARS-CoV-2 infection, at significantly lower costs than lateral flow antigen (LFA) tests.
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Affiliation(s)
- Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Ugochukwu J Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Wilfred Ndifon
- African Institute for Mathematical Sciences, The Next Einstein Initiative, Kigali, Rwanda.
| | - Neil Turok
- Higgs Centre for Theoretical Physics, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Stacey A Mattison
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ilya Sinayskiy
- School of Chemistry and Physics, University of Kwa-Zulu Natal, Westville, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), KwaZulu-Natal, South Africa
| | - Emmanuel J San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Shaun Barnett
- Discipline of Electrical, Electronic and Computer Engineering, University of KwaZulu-Natal, Durban, South Africa
| | - Trevor Lorimer
- Discipline of Electrical, Electronic and Computer Engineering, University of KwaZulu-Natal, Durban, South Africa
| | - Francesco Petruccione
- School of Chemistry and Physics, University of Kwa-Zulu Natal, Westville, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), KwaZulu-Natal, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
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25
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Martin DP, Weaver S, Tegally H, San EJ, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ, Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL. The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. medRxiv 2021:2021.02.23.21252268. [PMID: 33688681 PMCID: PMC7941658 DOI: 10.1101/2021.02.23.21252268] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The emergence and rapid rise in prevalence of three independent SARS-CoV-2 "501Y lineages", B.1.1.7, B.1.351 and P.1, in the last three months of 2020 prompted renewed concerns about the evolutionary capacity of SARS-CoV-2 to adapt to both rising population immunity, and public health interventions such as vaccines and social distancing. Viruses giving rise to the different 501Y lineages have, presumably under intense natural selection following a shift in host environment, independently acquired multiple unique and convergent mutations. As a consequence, all have gained epidemiological and immunological properties that will likely complicate the control of COVID-19. Here, by examining patterns of mutations that arose in SARSCoV-2 genomes during the pandemic we find evidence of a major change in the selective forces acting on various SARS-CoV-2 genes and gene segments (such as S, nsp2 and nsp6), that likely coincided with the emergence of the 501Y lineages. In addition to involving continuing sequence diversification, we find evidence that a significant portion of the ongoing adaptive evolution of the 501Y lineages also involves further convergence between the lineages. Our findings highlight the importance of monitoring how members of these known 501Y lineages, and others still undiscovered, are convergently evolving similar strategies to ensure their persistence in the face of mounting infection and vaccine induced host immune recognition.
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Affiliation(s)
- Darren P Martin
- Institute of Infectious Diseases and Molecular Medicine, Division Of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Steven Weaver
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA
| | - Houryiah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Emmanuel James San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Stephen D Shank
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Alexander G Lucaci
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Sureshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Yeshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Ravindra K Gupta
- Clinical Microbiology, University of Cambridge, Cambridge, UK
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | - Joel O Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Anton Nekturenko
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Pennsylvania, USA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gordon W Harkins
- South African Medical Research Council Capacity Development Unit, South African National Bioinformatics Institute, University of the Western cape, Bellville, South Africa
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Oscar A MacLean
- MRC-University of Glasgow Centre for Virus Research, Scotland, UK
| | | | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
- Department of Global Health, University of Washington, Seattle, US
| | - Sergei L Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA
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26
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Navarosh J, Pushker N, Xess I, Singh L, Bajaj MS, Kashyap S, Thakar A. Correlation of serum galactomannan antigen with diagnosis and response to voriconazole in orbital/sino-orbital invasive aspergillosis. Int Ophthalmol 2021; 41:2635-2638. [PMID: 34110546 DOI: 10.1007/s10792-021-01848-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/08/2021] [Indexed: 11/25/2022]
Affiliation(s)
- J Navarosh
- Oculoplasty and Pediatric Ophthalmology Services, Dr. R. P. Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - N Pushker
- Oculoplasty and Pediatric Ophthalmology Services, Dr. R. P. Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, 110 029, India.
| | - I Xess
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - L Singh
- Ocular Pathology, Dr. R. P. Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, 110 029, India
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - M S Bajaj
- Oculoplasty and Pediatric Ophthalmology Services, Dr. R. P. Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - S Kashyap
- Ocular Pathology, Dr. R. P. Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, 110 029, India
| | - A Thakar
- Department of ENT, All India Institute of Medical Sciences, New Delhi, 110 029, India
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27
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Sharma V, Singh L, Wong H, Agartioglu M, Chen JW, Deniz M, Kerman S, Li H, Liu CP, Saraswat K, Singh M, Singh V. Studies of quantum-mechanical coherency effects in neutrino-nucleus elastic scattering. Int J Clin Exp Med 2021. [DOI: 10.1103/physrevd.103.092002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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28
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Vogels CBF, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, Kalinich CC, Earnest R, Rothman JE, Goes de Jesus J, Morales Claro I, Magalhães Ferreira G, Crispim MAE, Singh L, Tegally H, Anyaneji UJ, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, Grubaugh ND. Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2. PLoS Biol 2021; 19:e3001236. [PMID: 33961632 PMCID: PMC8133773 DOI: 10.1371/journal.pbio.3001236] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/19/2021] [Accepted: 04/16/2021] [Indexed: 12/25/2022] Open
Abstract
With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69-70, would cause a "spike gene target failure" (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Δ69-70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675-3677 as the primary target and spike Δ69-70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1.
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Affiliation(s)
- Chantal B. F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Anne E. Watkins
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Chaney C. Kalinich
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Jessica E. Rothman
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Jaqueline Goes de Jesus
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ingra Morales Claro
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Giulia Magalhães Ferreira
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Myuki A. E. Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | | | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Emma B. Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | - Gaurav Khullar
- Tempus Labs, Chicago, Illinois, United States of America
| | - Jessica Metti
- Tempus Labs, Chicago, Illinois, United States of America
| | - Joel T. Dudley
- Tempus Labs, Chicago, Illinois, United States of America
| | | | - Megan Nash
- Tempus Labs, Chicago, Illinois, United States of America
| | - Jianhui Wang
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Chen Liu
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Steven Murphy
- Murphy Medical Associates, Greenwich, Connecticut, United States of America
| | - Caleb Neal
- Murphy Medical Associates, Greenwich, Connecticut, United States of America
| | - Eva Laszlo
- Murphy Medical Associates, Greenwich, Connecticut, United States of America
| | - Marie L. Landry
- Departments of Laboratory Medicine and Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Anthony Muyombwe
- Connecticut State Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Randy Downing
- Connecticut State Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Jafar Razeq
- Connecticut State Department of Public Health, Rocky Hill, Connecticut, United States of America
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno R. Faria
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Ester C. Sabino
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Richard A. Neher
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
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29
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Jha J, Singh MK, Singh L, Pushker N, Lomi N, Meel R, Chosdol K, Sen S, Bakhshi S, Kashyap S. Association of TYRP1 with hypoxia and its correlation with patient outcome in uveal melanoma. Clin Transl Oncol 2021; 23:1874-1884. [PMID: 33811629 DOI: 10.1007/s12094-021-02597-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/12/2021] [Indexed: 11/30/2022]
Abstract
PURPOSE Molecular mechanisms of uveal melanoma development in association with high pigmentation are unclear. Tyrosinase Related Protein (TYRP1) is not only one of the important melanogenesis marker that contributes to melanin synthesis, but can also prevents the melanocyte death. The induction of melanogenesis leads to induction of HIF-1α which can affect the behavior of melanoma cells and its surrounding environment. The aim of our study was to determine the expression of TYRP1 and HIF-1α at the protein and RNA level and determine its prognostic significance. METHODS In the present study, the expression of TYRP1 and HIF-1α was investigated on 61 formalin-fixed paraffin-embedded choroidal melanoma samples by immunohistochemistry. Fresh 50 samples were validated by real-time PCR. Results were correlated with clinicopathological parameters and Kaplan-Meier was performed to determine the prognostic significance. RESULTS High immunoexpression of TYRP1 and HIF-1α was present in 61 and 54% of patients, respectively. Both TYRP1 and HIF-1α correlated well with high pigmentation and BAP1 (BRCA1 Associated Protein-1) loss (p < 0.05) at IHC level as well as transcriptional level. There was reduced metastatic free survival in patients with necrosis and this was statistically significant (p = 0.010). CONCLUSION Our findings indicate that TYRP1 can be used as a potential biomarker in the development of targeted therapy in UM. Further studies on melanogenesis markers associated with TYRP1 could provide us a better understanding in this field.
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Affiliation(s)
- J Jha
- Department of Ocular Pathology, Dr.R.P.Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - M K Singh
- Department of Dermatology, University of Wisconsin, Madison, USA
| | - L Singh
- Department of Paediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - N Pushker
- Department of Ophthalmology, Dr.R.P.Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - N Lomi
- Department of Ophthalmology, Dr.R.P.Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - R Meel
- Department of Ophthalmology, Dr.R.P.Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - K Chosdol
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - S Sen
- Department of Ocular Pathology, Dr.R.P.Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - S Bakhshi
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - S Kashyap
- Department of Ocular Pathology, Dr.R.P.Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India.
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30
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Vogels CB, Breban MI, Alpert T, Petrone ME, Watkins AE, Ott IM, de Jesus JG, Claro IM, Ferreira GM, Crispim MA, Singh L, Tegally H, Anyaneji UJ, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, Grubaugh ND. PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern. medRxiv 2021:2021.01.28.21250486. [PMID: 33758901 PMCID: PMC7987060 DOI: 10.1101/2021.01.28.21250486] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
With the emergence of SARS-CoV-2 variants that may increase transmissibility and/or cause escape from immune responses 1-3 , there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant first detected in the UK 4,5 could be serendipitously detected by the ThermoFisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69-70, would cause a "spike gene target failure" (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern that lack spike Δ69-70, such as B.1.351 (also 501Y.V2) detected in South Africa 6 and P.1 (also 501Y.V3) recently detected in Brazil 7 . We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all three variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675-3677 as the primary target and spike Δ69-70 to differentiate, we designed and validated an open source PCR assay to detect SARS-CoV-2 variants of concern 8 . Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence spread of B.1.1.7, B.1.351, and P.1.
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Affiliation(s)
- Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anne E. Watkins
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Isabel M. Ott
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Jaqueline Goes de Jesus
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
| | - Ingra Morales Claro
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
| | - Giulia Magalhães Ferreira
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
- Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, MG, Brazil
| | - Myuki A.E. Crispim
- Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil
| | | | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Emma B. Hodcroft
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | | | | | | | | | | | - Jianhui Wang
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Chen Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Pei Hui
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | | | - Caleb Neal
- Murphy Medical Associates, Greenwich, CT 06614, USA
| | - Eva Laszlo
- Murphy Medical Associates, Greenwich, CT 06614, USA
| | - Marie L. Landry
- Departments of Laboratory Medicine and Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Anthony Muyombwe
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Randy Downing
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Jafar Razeq
- Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno R. Faria
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
- Department of Zoology, University of Oxford, Oxford, UK
| | - Ester C. Sabino
- Departamento de Molestias Infecciosas e Parasitarias and Instituto de Medicina Tropical da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP 05403–000, Brazil
| | - Richard A. Neher
- Biozentrum, University of Basel, 4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA
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Giandhari J, Pillay S, Wilkinson E, Tegally H, Sinayskiy I, Schuld M, Lourenço J, Chimukangara B, Lessells R, Moosa Y, Gazy I, Fish M, Singh L, Sedwell Khanyile K, Fonseca V, Giovanetti M, Carlos Junior Alcantara L, Petruccione F, de Oliveira T. Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report. Int J Infect Dis 2021; 103:234-241. [PMID: 33189939 PMCID: PMC7658561 DOI: 10.1016/j.ijid.2020.11.128] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES The Network for Genomic Surveillance in South Africa (NGS-SA) was formed to investigate the introduction and understand the early transmission dynamics of the SARS-CoV-2 epidemic in South-Africa. DESIGN This paper presents the first results from this group, which is a molecular epidemiological study of the first 21 SARS-CoV-2 whole genomes sampled in the first port of entry - KwaZulu-Natal (KZN) - during the first month of the epidemic. By combining this with calculations of the effective reproduction number (R), it aimed to shed light on the patterns of infections in South Africa. RESULTS Two of the largest provinces - Gauteng and KZN - had a slow growth rate for the number of detected cases, while the epidemic spread faster in the Western Cape and Eastern Cape. The estimates of transmission potential suggested a decrease towards R = 1 since the first cases and deaths, but a subsequent estimated R average of 1.39 between 6-18 May 2020. It was also demonstrated that early transmission in KZN was associated with multiple international introductions and dominated by lineages B1 and B. Evidence for locally acquired infections in a hospital in Durban within the first month of the epidemic was also provided. CONCLUSION The COVID-19 pandemic in South Africa was very heterogeneous in its spatial dimension, with many distinct introductions of SARS-CoV2 in KZN and evidence of nosocomial transmission, which inflated early mortality in KZN. The epidemic at the local level was still developing and NGS-SA aimed to clarify the dynamics in South Africa and devise the most effective measures as the outbreak evolved.
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Affiliation(s)
- Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ilya Sinayskiy
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa; National Institute for Theoretical Physics (NITheP), KwaZulu-Natal, South Africa
| | - Maria Schuld
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, UK
| | - Benjamin Chimukangara
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Zoology, University of Oxford, Oxford, UK
| | - Yunus Moosa
- Department of Zoology, University of Oxford, Oxford, UK
| | - Inbal Gazy
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Maryam Fish
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Khulekani Sedwell Khanyile
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Laboratorio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil
| | - Luiz Carlos Junior Alcantara
- Laboratorio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil
| | - Francesco Petruccione
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa; National Institute for Theoretical Physics (NITheP), KwaZulu-Natal, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Centre for Aids Programme of Research in South Africa (CAPRISA), Durban, South Africa; Department of Global Health, University of Washington, Seattle, Washington, USA.
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32
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San JE, Ngcapu S, Kanzi AM, Tegally H, Fonseca V, Giandhari J, Wilkinson E, Nelson CW, Smidt W, Kiran AM, Chimukangara B, Pillay S, Singh L, Fish M, Gazy I, Martin DP, Khanyile K, Lessells R, de Oliveira T. Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa. Virus Evol 2021; 7:veab041. [PMID: 34035952 PMCID: PMC8135343 DOI: 10.1093/ve/veab041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes acute, highly transmissible respiratory infection in humans and a wide range of animal species. Its rapid global spread has resulted in a major public health emergency, necessitating commensurately rapid research to improve control strategies. In particular, the ability to effectively retrace transmission chains in outbreaks remains a major challenge, partly due to our limited understanding of the virus' underlying evolutionary dynamics within and between hosts. We used high-throughput sequencing whole-genome data coupled with bottleneck analysis to retrace the pathways of viral transmission in two nosocomial outbreaks that were previously characterised by epidemiological and phylogenetic methods. Additionally, we assessed the mutational landscape, selection pressures, and diversity at the within-host level for both outbreaks. Our findings show evidence of within-host selection and transmission of variants between samples. Both bottleneck and diversity analyses highlight within-host and consensus-level variants shared by putative source-recipient pairs in both outbreaks, suggesting that certain within-host variants in these outbreaks may have been transmitted upon infection rather than arising de novo independently within multiple hosts. Overall, our findings demonstrate the utility of combining within-host diversity and bottleneck estimations for elucidating transmission events in SARS-CoV-2 outbreaks, provide insight into the maintenance of viral genetic diversity, provide a list of candidate targets of positive selection for further investigation, and demonstrate that within-host variants can be transferred between patients. Together these results will help in developing strategies to understand the nature of transmission events and curtail the spread of SARS-CoV-2.
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Affiliation(s)
- James E San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Sinaye Ngcapu
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban, South Africa
| | - Aquillah M Kanzi
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Chase W Nelson
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Werner Smidt
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Anmol M Kiran
- Malawi-Liverpool-Wellcome Trust, Queen Elizabeth Central Hospital, College of Medicine, Blantyre, Malawi
- Centre for Inflammation Research, Queens Research Institute, University of Edinburgh, Edinburgh, UK
| | - Benjamin Chimukangara
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Maryam Fish
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Inbal Gazy
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Darren P Martin
- Institute of Infectious Diseases and Molecular Medicine, Division of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Khulekani Khanyile
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu- Natal, Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
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33
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Singh L, Singh M, Rizvi M, Kashyap S. 16P PD-1/PD-L1 expression in uveal melanoma: Prognostic significance with tumour-infiltrating lymphocytes and clinicopathological parameters. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.10.501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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34
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James SE, Ngcapu S, Kanzi AM, Tegally H, Fonseca V, Giandhari J, Wilkinson E, Chimukangara B, Pillay S, Singh L, Fish M, Gazy I, Khanyile K, Lessells R, de Oliveira T. High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital Outbreaks in South Africa Leveraging Intrahost Diversity. medRxiv 2020:2020.11.15.20231993. [PMID: 33236025 PMCID: PMC7685338 DOI: 10.1101/2020.11.15.20231993] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes acute, highly transmissible respiratory infection in both humans and wide range of animal species. Its rapid spread globally and devasting effects have resulted into a major public health emergency prompting the need for methodological interventions to understand and control its spread. In particular, The ability to effectively retrace its transmission pathways in outbreaks remains a major challenge. This is further exacerbated by our limited understanding of its underlying evolutionary mechanism. Using NGS whole-genome data, we determined whether inter- and intra-host diversity coupled with bottleneck analysis can retrace the pathway of viral transmission in two epidemiologically well characterised nosocomial outbreaks in healthcare settings supported by phylogenetic analysis. Additionally, we assessed the mutational landscape, selection pressure and diversity of the identified variants. Our findings showed evidence of intrahost variant transmission and evolution of SARS-CoV-2 after infection These observations were consistent with the results from the bottleneck analysis suggesting that certain intrahost variants in this study could have been transmitted to recipients. In both outbreaks, we observed iSNVs and SNVs shared by putative source-recipients pairs. Majority of the observed iSNVs were positioned in the S and ORF1ab region. AG, CT and TC nucleotide changes were enriched across SARS-COV-2 genome. Moreover, SARS-COV-2 genome had limited diversity in some loci while being highly conserved in others. Overall, Our findings show that the synergistic effect of combining withinhost diversity and bottleneck estimations greatly enhances resolution of transmission events in Sars-Cov-2 outbreaks. They also provide insight into the genome diversity suggesting purifying selection may be involved in the transmission. Together these results will help in developing strategies to elucidate transmission events and curtail the spread of Sars-Cov-2.
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Affiliation(s)
- San Emmanuel James
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sinaye Ngcapu
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Medical Microbiology, University of KwaZulu-Natal, Durban, South Africa
| | - Aquillah M Kanzi
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Benjamin Chimukangara
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Maryam Fish
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Inbal Gazy
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Khulekani Khanyile
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Department of Global Health, University of Washington, Seattle, USA
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
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35
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Pillay S, Giandhari J, Tegally H, Wilkinson E, Chimukangara B, Lessells R, Moosa Y, Mattison S, Gazy I, Fish M, Singh L, Khanyile KS, San JE, Fonseca V, Giovanetti M, Alcantara LC, de Oliveira T. Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic. Genes (Basel) 2020; 11:E949. [PMID: 32824573 PMCID: PMC7464704 DOI: 10.3390/genes11080949] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/16/2020] [Accepted: 07/24/2020] [Indexed: 12/22/2022] Open
Abstract
The COVID-19 pandemic has spread very fast around the world. A few days after the first detected case in South Africa, an infection started in a large hospital outbreak in Durban, KwaZulu-Natal (KZN). Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes can be used to trace the path of transmission within a hospital. It can also identify the source of the outbreak and provide lessons to improve infection prevention and control strategies. This manuscript outlines the obstacles encountered in order to genotype SARS-CoV-2 in near-real time during an urgent outbreak investigation. This included problems with the length of the original genotyping protocol, unavailability of reagents, and sample degradation and storage. Despite this, three different library preparation methods for Illumina sequencing were set up, and the hands-on library preparation time was decreased from twelve to three hours, which enabled the outbreak investigation to be completed in just a few weeks. Furthermore, the new protocols increased the success rate of sequencing whole viral genomes. A simple bioinformatics workflow for the assembly of high-quality genomes in near-real time was also fine-tuned. In order to allow other laboratories to learn from our experience, all of the library preparation and bioinformatics protocols are publicly available at protocols.io and distributed to other laboratories of the Network for Genomics Surveillance in South Africa (NGS-SA) consortium.
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Affiliation(s)
- Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Benjamin Chimukangara
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
- Centre for AIDS Programme of Research in South Africa (CAPRISA), Durban 4001, South Africa
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
- Infectious Diseases Department, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa;
| | - Yunus Moosa
- Infectious Diseases Department, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa;
| | - Stacey Mattison
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Inbal Gazy
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Maryam Fish
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Khulekani Sedwell Khanyile
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
- Laboratorio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro 21045-900, Brazil;
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro 21045-900, Brazil;
| | - Luiz Carlos Alcantara
- Laboratorio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro 21045-900, Brazil;
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; (S.P.); (J.G.); (H.T.); (E.W.); (B.C.); (R.L.); (S.M.); (I.G.); (M.F.); (L.S.); (K.S.K.); (J.E.S.); (V.F.)
- Centre for AIDS Programme of Research in South Africa (CAPRISA), Durban 4001, South Africa
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
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Singh MK, Singh L, Pushker N, Chosdol K, Bakhshi S, Meel R, Sen S, Kashyap S. Constitutive expression of c-REL in uveal melanoma patients: correlation with clinicopathological parameters and patient outcome. Clin Transl Oncol 2020; 22:1193-1204. [PMID: 31768922 DOI: 10.1007/s12094-019-02247-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/12/2019] [Indexed: 12/12/2022]
Abstract
PURPOSE Uveal melanoma (UM) is the most common intraocular cancer with a high mortality rate that requires new research in the field of prevention and treatment. c-REL is a member of the nuclear factor κB (NF-κB) transcription factor family and an emerging regulator of tumorigenesis. Therefore, the objective of the study is to evaluate the constitutive expression of c-REL in uveal melanoma patients and its prognostic significance. METHODS Detection of c-REL expression was carried out by immunohistochemistry in all 75 patients, and qRT-PCR performed on 58 fresh cases of uveal melanoma along with IL-6 status. Immunoblot was performed to validate immunohistochemistry results. Expression of c-REL protein correlated with clinicopathological parameters and overall survival of patients. RESULTS Immunohistochemistry results revealed nuclear expression of the c-REL protein (56%) in our cases. Out of 75 cases, 31 cases showed nuclear expression, and 11 cases had cytoplasmic expression. qRT-PCR showed upregulation of the REL gene in 56.89% cases at the transcriptional level. There was a statistically significant difference in the overall survival of patients with c-REL nuclear immunopositivity (p = 0.0048). On multivariate analysis, scleral invasion and c-REL nuclear expression found to be an independent prognostic factor (p < 0.05) CONCLUSIONS: To the best of our knowledge, this was the first study reporting the expression of the c-REL protein in uveal melanoma. Strong nuclear immunoexpression of c-Rel suggests NFκB pathway activation which might be involved in the progression of the disease. Differential expression of c-REL protein may be used as an attractive target for the development of anticancer strategies.
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Affiliation(s)
- M K Singh
- Department of Ocular Pathology, Dr. R. P. Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - L Singh
- Departrment of Biosciences, JMI, New Delhi, India
| | - N Pushker
- Department of Ophthalmology, Dr. R. P. Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - K Chosdol
- Department of Biochemistry, AIIMS, New Delhi, India
| | - S Bakhshi
- Department of Medical Oncology, IRCH, AIIMS, New Delhi, India
| | - R Meel
- Department of Ophthalmology, Dr. R. P. Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - S Sen
- Department of Ocular Pathology, Dr. R. P. Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India
| | - S Kashyap
- Department of Ocular Pathology, Dr. R. P. Centre for Ophthalmic Sciences, All India Institute of Medical Sciences, New Delhi, India.
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Giandhari J, Pillay S, Wilkinson E, Tegally H, Sinayskiy I, Schuld M, Lourenco J, Chimukangara B, Lessells R, Moosa Y, Gazy I, Fish M, Singh L, Khanyile KS, Fonseca V, Giovanetti M, Alcantara LC, Petruccione F, de Oliveira T. Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report. medRxiv 2020:2020.05.29.20116376. [PMID: 32511505 PMCID: PMC7273273 DOI: 10.1101/2020.05.29.20116376] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background The emergence of a novel coronavirus, SARS-CoV-2, in December 2019, progressed to become a world pandemic in a few months and reached South Africa at the beginning of March. To investigate introduction and understand the early transmission dynamics of the virus, we formed the South African Network for Genomics Surveillance of COVID (SANGS_COVID), a network of ten government and university laboratories. Here, we present the first results of this effort, which is a molecular epidemiological study of the first twenty-one SARS-CoV-2 whole genomes sampled in the first port of entry, KwaZulu-Natal (KZN), during the first month of the epidemic. By combining this with calculations of the effective reproduction number (R), we aim to shed light on the patterns of infections that define the epidemic in South Africa. Methods R was calculated using positive cases and deaths from reports provided by the four major provinces. Molecular epidemiology investigation involved sequencing viral genomes from patients in KZN using ARCTIC protocols and assembling whole genomes using meticulous alignment methods. Phylogenetic analysis was performed using maximum likelihood (ML) and Bayesian trees, lineage classification and molecular clock calculations. Findings The epidemic in South Africa has been very heterogeneous. Two of the largest provinces, Gauteng, home of the two large metropolis Johannesburg and Pretoria, and KwaZulu-Natal, home of the third largest city in the country Durban, had a slow growth rate on the number of detected cases. Whereas, Western Cape, home of Cape Town, and the Eastern Cape provinces the epidemic is spreading fast. Our estimates of transmission potential for South Africa suggest a decreasing transmission potential towards R=1 since the first cases and deaths have been reported. However, between 06 May and 18 May 2020, we estimate that R was on average 1.39 (1.04 - 2.15, 95% CI). We also demonstrate that early transmission in KZN, and most probably in all main regions of SA, was associated with multiple international introductions and dominated by lineages B1 and B. The study also provides evidence for locally acquired infections in a hospital in Durban within the first month of the epidemic, which inflated early mortality in KZN. Interpretation This first report of SANGS_COVID consortium focuses on understanding the epidemic heterogeneity and introduction of SARS-CoV-2 strains in the first month of the epidemic in South Africa. The early introduction of SARS-CoV-2 in KZN included caused a localized outbreak in a hospital, provides potential explanations for the initially high death rates in the province. The current high rate of transmission of COVID-19 in the Western Cape and Eastern Cape highlights the crucial need to strength local genomic surveillance in South Africa. Funding UKZN Flagship Program entitled: Afrocentric Precision Approach to Control Health Epidemic, by a research Flagship grant from the South African Medical Research Council (MRC-RFA-UFSP-01-2013/UKZN HIVEPI, by the the Technology Innovation Agency and the the Department of Science and Innovation and by National Human Genome Re- search Institute of the National Institutes of Health under Award Number U24HG006941. H3ABioNet is an initiative of the Human Health and Heredity in Africa Consortium (H3Africa).
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Affiliation(s)
- Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ilya Sinayskiy
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
- National Institute for Theoretical Physics (NITheP), KwaZulu-Natal, 4001, South Africa
| | - Maria Schuld
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
| | - Jose Lourenco
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Benjamin Chimukangara
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Infectious Diseases Department, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Yunus Moosa
- Infectious Diseases Department, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Inbal Gazy
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Maryam Fish
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Khulekani Sedwell Khanyile
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Laboratorio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil
| | - Luiz Carols Alcantara
- Laboratorio de Genetica Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Brazil
| | - Francesco Petruccione
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
- National Institute for Theoretical Physics (NITheP), KwaZulu-Natal, 4001, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Aids Programme of Research in South Africa (CAPRISA), Durban South Africa
- Department of Global Health, University of Washington, Seattle, Washington, USA
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She Z, Jia LP, Yue Q, Ma H, Kang KJ, Li YJ, Agartioglu M, An HP, Chang JP, Chen JH, Chen YH, Cheng JP, Dai WH, Deng Z, Geng XP, Gong H, Gu P, Guo QJ, Guo XY, He L, He SM, He HT, Hu JW, Huang TC, Huang HX, Li HB, Li H, Li JM, Li J, Li MX, Li X, Li XQ, Li YL, Liao B, Lin FK, Lin ST, Liu SK, Liu YD, Liu YY, Liu ZZ, Mao YC, Nie QY, Ning JH, Pan H, Qi NC, Qiao CK, Ren J, Ruan XC, Sevda B, Shang CS, Sharma V, Singh L, Singh MK, Sun TX, Tang CJ, Tang WY, Tian Y, Wang GF, Wang L, Wang Q, Wang Y, Wang YX, Wang Z, Wong HT, Wu SY, Xing HY, Xu Y, Xue T, Yan YL, Yang LT, Yi N, Yu CX, Yu HJ, Yue JF, Zeng M, Zeng Z, Zhang BT, Zhang L, Zhang FS, Zhang ZY, Zhao MG, Zhou JF, Zhou ZY, Zhu JJ. Direct Detection Constraints on Dark Photons with the CDEX-10 Experiment at the China Jinping Underground Laboratory. Phys Rev Lett 2020; 124:111301. [PMID: 32242731 DOI: 10.1103/physrevlett.124.111301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/26/2020] [Indexed: 06/11/2023]
Abstract
We report constraints on the dark photon effective kinetic mixing parameter (κ) with data taken from two p-type point-contact germanium detectors of the CDEX-10 experiment at the China Jinping Underground Laboratory. The 90% confidence level upper limits on κ of solar dark photon from 205.4 kg-day exposure are derived, probing new parameter space with masses (m_{V}) from 10 to 300 eV/c^{2} in direct detection experiments. Considering dark photon as the cosmological dark matter, limits at 90% confidence level with m_{V} from 0.1 to 4.0 keV/c^{2} are set from 449.6 kg-day data, with a minimum of κ=1.3×10^{-15} at m_{V}=200 eV/c^{2}.
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Affiliation(s)
- Z She
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - L P Jia
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Q Yue
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H Ma
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - K J Kang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Y J Li
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - M Agartioglu
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Dokuz Eylül University, İzmir 35160
| | - H P An
- Department of Physics, Tsinghua University, Beijing 100084
| | | | - J H Chen
- Institute of Physics, Academia Sinica, Taipei 11529
| | - Y H Chen
- YaLong River Hydropower Development Company, Chengdu 610051
| | - J P Cheng
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - W H Dai
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Z Deng
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - X P Geng
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H Gong
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - P Gu
- College of Physics, Sichuan University, Chengdu 610064
| | - Q J Guo
- School of Physics, Peking University, Beijing 100871
| | - X Y Guo
- YaLong River Hydropower Development Company, Chengdu 610051
| | - L He
- NUCTECH Company, Beijing 100084
| | - S M He
- YaLong River Hydropower Development Company, Chengdu 610051
| | - H T He
- College of Physics, Sichuan University, Chengdu 610064
| | - J W Hu
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - T C Huang
- Sino-French Institute of Nuclear and Technology, Sun Yat-sen University, Zhuhai, 519082
| | - H X Huang
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - H B Li
- Institute of Physics, Academia Sinica, Taipei 11529
| | - H Li
- NUCTECH Company, Beijing 100084
| | - J M Li
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - J Li
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - M X Li
- College of Physics, Sichuan University, Chengdu 610064
| | - X Li
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - X Q Li
- School of Physics, Nankai University, Tianjin 300071
| | - Y L Li
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - B Liao
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - F K Lin
- Institute of Physics, Academia Sinica, Taipei 11529
| | - S T Lin
- College of Physics, Sichuan University, Chengdu 610064
| | - S K Liu
- College of Physics, Sichuan University, Chengdu 610064
| | - Y D Liu
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - Y Y Liu
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - Z Z Liu
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Y C Mao
- School of Physics, Peking University, Beijing 100871
| | - Q Y Nie
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - J H Ning
- YaLong River Hydropower Development Company, Chengdu 610051
| | - H Pan
- NUCTECH Company, Beijing 100084
| | - N C Qi
- YaLong River Hydropower Development Company, Chengdu 610051
| | - C K Qiao
- College of Physics, Sichuan University, Chengdu 610064
| | - J Ren
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - X C Ruan
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - B Sevda
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Dokuz Eylül University, İzmir 35160
| | - C S Shang
- YaLong River Hydropower Development Company, Chengdu 610051
| | - V Sharma
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Banaras Hindu University, Varanasi 221005
| | - L Singh
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Banaras Hindu University, Varanasi 221005
| | - M K Singh
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Banaras Hindu University, Varanasi 221005
| | - T X Sun
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - C J Tang
- College of Physics, Sichuan University, Chengdu 610064
| | - W Y Tang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Y Tian
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - G F Wang
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - L Wang
- Department of Physics, Beijing Normal University, Beijing 100875
| | - Q Wang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- Department of Physics, Tsinghua University, Beijing 100084
| | - Y Wang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- Department of Physics, Tsinghua University, Beijing 100084
| | - Y X Wang
- School of Physics, Peking University, Beijing 100871
| | - Z Wang
- College of Physics, Sichuan University, Chengdu 610064
| | - H T Wong
- Institute of Physics, Academia Sinica, Taipei 11529
| | - S Y Wu
- YaLong River Hydropower Development Company, Chengdu 610051
| | - H Y Xing
- College of Physics, Sichuan University, Chengdu 610064
| | - Y Xu
- School of Physics, Nankai University, Tianjin 300071
| | - T Xue
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Y L Yan
- College of Physics, Sichuan University, Chengdu 610064
| | - L T Yang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - N Yi
- NUCTECH Company, Beijing 100084
| | - C X Yu
- School of Physics, Nankai University, Tianjin 300071
| | - H J Yu
- NUCTECH Company, Beijing 100084
| | - J F Yue
- YaLong River Hydropower Development Company, Chengdu 610051
| | - M Zeng
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Z Zeng
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - B T Zhang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - L Zhang
- College of Physics, Sichuan University, Chengdu 610064
| | - F S Zhang
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - Z Y Zhang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - M G Zhao
- School of Physics, Nankai University, Tianjin 300071
| | - J F Zhou
- YaLong River Hydropower Development Company, Chengdu 610051
| | - Z Y Zhou
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - J J Zhu
- College of Physics, Sichuan University, Chengdu 610064
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Singh M, Kashyap S, Singh L, Pushker N, Bakhshi S, Sen S. Loss of BAP-1 influences the activation of p52 and RelB proteins in the Inflammatory microenvironment of uveal melanoma. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz452.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Singh L, Singh M, Rizvi M, Pushker N, Sen S, Kashyap S. Differential expression patterns of immune checkpoint markers in tumour-stromal microenvironment of primary and chemoreduced retinoblastoma. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz447.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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41
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Yang LT, Li HB, Yue Q, Ma H, Kang KJ, Li YJ, Wong HT, Agartioglu M, An HP, Chang JP, Chen JH, Chen YH, Cheng JP, Deng Z, Du Q, Gong H, Guo QJ, He L, Hu JW, Hu QD, Huang HX, Jia LP, Jiang H, Li H, Li JM, Li J, Li X, Li XQ, Li YL, Liao B, Lin FK, Lin ST, Liu SK, Liu YD, Liu YY, Liu ZZ, Ma JL, Mao YC, Pan H, Ren J, Ruan XC, Sharma V, She Z, Shen MB, Singh L, Singh MK, Sun TX, Tang CJ, Tang WY, Tian Y, Wang GF, Wang JM, Wang L, Wang Q, Wang Y, Wang YX, Wu SY, Wu YC, Xing HY, Xu Y, Xue T, Yi N, Yu CX, Yu HJ, Yue JF, Zeng XH, Zeng M, Zeng Z, Zhang FS, Zhang YH, Zhao MG, Zhou JF, Zhou ZY, Zhu JJ, Zhu ZH. Search for Light Weakly-Interacting-Massive-Particle Dark Matter by Annual Modulation Analysis with a Point-Contact Germanium Detector at the China Jinping Underground Laboratory. Phys Rev Lett 2019; 123:221301. [PMID: 31868422 DOI: 10.1103/physrevlett.123.221301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Indexed: 06/10/2023]
Abstract
We present results on light weakly interacting massive particle (WIMP) searches with annual modulation (AM) analysis on data from a 1-kg mass p-type point-contact germanium detector of the CDEX-1B experiment at the China Jinping Underground Laboratory. Datasets with a total live time of 3.2 yr within a 4.2-yr span are analyzed with analysis threshold of 250 eVee. Limits on WIMP-nucleus (χ-N) spin-independent cross sections as function of WIMP mass (m_{χ}) at 90% confidence level (C.L.) are derived using the dark matter halo model. Within the context of the standard halo model, the 90% C.L. allowed regions implied by the DAMA/LIBRA and CoGeNT AM-based analysis are excluded at >99.99% and 98% C.L., respectively. These results correspond to the best sensitivity at m_{χ}<6 GeV/c^{2} among WIMP AM measurements to date.
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Affiliation(s)
- L T Yang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H B Li
- Institute of Physics, Academia Sinica, Taipei 11529
| | - Q Yue
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H Ma
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - K J Kang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Y J Li
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H T Wong
- Institute of Physics, Academia Sinica, Taipei 11529
| | - M Agartioglu
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Dokuz Eylül University, İzmir 35160
| | - H P An
- Department of Physics, Tsinghua University, Beijing 100084
| | | | - J H Chen
- Institute of Physics, Academia Sinica, Taipei 11529
| | - Y H Chen
- YaLong River Hydropower Development Company, Chengdu 610051
| | - J P Cheng
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - Z Deng
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Q Du
- College of Physical Science and Technology, Sichuan University, Chengdu 610064
| | - H Gong
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Q J Guo
- School of Physics, Peking University, Beijing 100871
| | - L He
- NUCTECH Company, Beijing 100084
| | - J W Hu
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Q D Hu
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H X Huang
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - L P Jia
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H Jiang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H Li
- NUCTECH Company, Beijing 100084
| | - J M Li
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - J Li
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - X Li
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - X Q Li
- School of Physics, Nankai University, Tianjin 300071
| | - Y L Li
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - B Liao
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - F K Lin
- Institute of Physics, Academia Sinica, Taipei 11529
| | - S T Lin
- College of Physical Science and Technology, Sichuan University, Chengdu 610064
| | - S K Liu
- College of Physical Science and Technology, Sichuan University, Chengdu 610064
| | - Y D Liu
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - Y Y Liu
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - Z Z Liu
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - J L Ma
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- Department of Physics, Tsinghua University, Beijing 100084
| | - Y C Mao
- School of Physics, Peking University, Beijing 100871
| | - H Pan
- NUCTECH Company, Beijing 100084
| | - J Ren
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - X C Ruan
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - V Sharma
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Banaras Hindu University, Varanasi 221005
| | - Z She
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - M B Shen
- YaLong River Hydropower Development Company, Chengdu 610051
| | - L Singh
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Banaras Hindu University, Varanasi 221005
| | - M K Singh
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Banaras Hindu University, Varanasi 221005
| | - T X Sun
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - C J Tang
- College of Physical Science and Technology, Sichuan University, Chengdu 610064
| | - W Y Tang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Y Tian
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - G F Wang
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - J M Wang
- YaLong River Hydropower Development Company, Chengdu 610051
| | - L Wang
- Department of Physics, Beijing Normal University, Beijing 100875
| | - Q Wang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- Department of Physics, Tsinghua University, Beijing 100084
| | - Y Wang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- Department of Physics, Tsinghua University, Beijing 100084
| | - Y X Wang
- School of Physics, Peking University, Beijing 100871
| | - S Y Wu
- YaLong River Hydropower Development Company, Chengdu 610051
| | - Y C Wu
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H Y Xing
- College of Physical Science and Technology, Sichuan University, Chengdu 610064
| | - Y Xu
- School of Physics, Nankai University, Tianjin 300071
| | - T Xue
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - N Yi
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - C X Yu
- School of Physics, Nankai University, Tianjin 300071
| | - H J Yu
- NUCTECH Company, Beijing 100084
| | - J F Yue
- YaLong River Hydropower Development Company, Chengdu 610051
| | - X H Zeng
- YaLong River Hydropower Development Company, Chengdu 610051
| | - M Zeng
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Z Zeng
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - F S Zhang
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - Y H Zhang
- YaLong River Hydropower Development Company, Chengdu 610051
| | - M G Zhao
- School of Physics, Nankai University, Tianjin 300071
| | - J F Zhou
- YaLong River Hydropower Development Company, Chengdu 610051
| | - Z Y Zhou
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - J J Zhu
- College of Physical Science and Technology, Sichuan University, Chengdu 610064
| | - Z H Zhu
- YaLong River Hydropower Development Company, Chengdu 610051
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42
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Jha J, Pushker N, Singh M, Singh L, Sen S, Kaur J, Kashyap S. Association of BAP1 with ATR protein and their clinical significance with patient outcome in uveal melanoma. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz429.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Liu ZZ, Yue Q, Yang LT, Kang KJ, Li YJ, Wong HT, Agartioglu M, An HP, Chang JP, Chen JH, Chen YH, Cheng JP, Deng Z, Du Q, Gong H, Guo XY, Guo QJ, He L, He SM, Hu JW, Hu QD, Huang HX, Jia LP, Jiang H, Li HB, Li H, Li JM, Li J, Li X, Li XQ, Li YL, Liao B, Lin FK, Lin ST, Liu SK, Liu YD, Liu YY, Ma H, Ma JL, Mao YC, Ning JH, Pan H, Qi NC, Ren J, Ruan XC, Sharma V, She Z, Singh L, Singh MK, Sun TX, Tang CJ, Tang WY, Tian Y, Wang GF, Wang L, Wang Q, Wang Y, Wang YX, Wu SY, Wu YC, Xing HY, Xu Y, Xue T, Yi N, Yu CX, Yu HJ, Yue JF, Zeng M, Zeng Z, Zhang FS, Zhao MG, Zhou JF, Zhou ZY, Zhu JJ. Constraints on Spin-Independent Nucleus Scattering with sub-GeV Weakly Interacting Massive Particle Dark Matter from the CDEX-1B Experiment at the China Jinping Underground Laboratory. Phys Rev Lett 2019; 123:161301. [PMID: 31702340 DOI: 10.1103/physrevlett.123.161301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 06/10/2023]
Abstract
We report results on the searches of weakly interacting massive particles (WIMPs) with sub-GeV masses (m_{χ}) via WIMP-nucleus spin-independent scattering with Migdal effect incorporated. Analysis on time-integrated (TI) and annual modulation (AM) effects on CDEX-1B data are performed, with 737.1 kg day exposure and 160 eVee threshold for TI analysis, and 1107.5 kg day exposure and 250 eVee threshold for AM analysis. The sensitive windows in m_{χ} are expanded by an order of magnitude to lower DM masses with Migdal effect incorporated. New limits on σ_{χN}^{SI} at 90% confidence level are derived as 2×10^{-32}∼7×10^{-35} cm^{2} for TI analysis at m_{χ}∼50-180 MeV/c^{2}, and 3×10^{-32}∼9×10^{-38} cm^{2} for AM analysis at m_{χ}∼75 MeV/c^{2}-3.0 GeV/c^{2}.
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Affiliation(s)
- Z Z Liu
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Q Yue
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - L T Yang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - K J Kang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Y J Li
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H T Wong
- Institute of Physics, Academia Sinica, Taipei 11529
| | - M Agartioglu
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Dokuz Eylül University, İzmir 35160
| | - H P An
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- Department of Physics, Tsinghua University, Beijing 100084
| | | | - J H Chen
- Institute of Physics, Academia Sinica, Taipei 11529
| | - Y H Chen
- YaLong River Hydropower Development Company, Chengdu 610051
| | - J P Cheng
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - Z Deng
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Q Du
- College of Physical Science and Technology, Sichuan University, Chengdu 610065
| | - H Gong
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - X Y Guo
- YaLong River Hydropower Development Company, Chengdu 610051
| | - Q J Guo
- School of Physics, Peking University, Beijing 100871
| | - L He
- NUCTECH Company, Beijing 100084
| | - S M He
- YaLong River Hydropower Development Company, Chengdu 610051
| | - J W Hu
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Q D Hu
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H X Huang
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - L P Jia
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H Jiang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H B Li
- Institute of Physics, Academia Sinica, Taipei 11529
| | - H Li
- NUCTECH Company, Beijing 100084
| | - J M Li
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - J Li
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - X Li
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - X Q Li
- School of Physics, Nankai University, Tianjin 300071
| | - Y L Li
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - B Liao
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - F K Lin
- Institute of Physics, Academia Sinica, Taipei 11529
| | - S T Lin
- College of Physical Science and Technology, Sichuan University, Chengdu 610065
| | - S K Liu
- College of Physical Science and Technology, Sichuan University, Chengdu 610065
| | - Y D Liu
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - Y Y Liu
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - H Ma
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - J L Ma
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- Department of Physics, Tsinghua University, Beijing 100084
| | - Y C Mao
- School of Physics, Peking University, Beijing 100871
| | - J H Ning
- YaLong River Hydropower Development Company, Chengdu 610051
| | - H Pan
- NUCTECH Company, Beijing 100084
| | - N C Qi
- YaLong River Hydropower Development Company, Chengdu 610051
| | - J Ren
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - X C Ruan
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - V Sharma
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Banaras Hindu University, Varanasi 221005
| | - Z She
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - L Singh
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Banaras Hindu University, Varanasi 221005
| | - M K Singh
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Banaras Hindu University, Varanasi 221005
| | - T X Sun
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - C J Tang
- College of Physical Science and Technology, Sichuan University, Chengdu 610065
| | - W Y Tang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Y Tian
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - G F Wang
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - L Wang
- Department of Physics, Beijing Normal University, Beijing 100875
| | - Q Wang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- Department of Physics, Tsinghua University, Beijing 100084
| | - Y Wang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- Department of Physics, Tsinghua University, Beijing 100084
| | - Y X Wang
- School of Physics, Peking University, Beijing 100871
| | - S Y Wu
- YaLong River Hydropower Development Company, Chengdu 610051
| | - Y C Wu
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H Y Xing
- College of Physical Science and Technology, Sichuan University, Chengdu 610065
| | - Y Xu
- School of Physics, Nankai University, Tianjin 300071
| | - T Xue
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - N Yi
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - C X Yu
- School of Physics, Nankai University, Tianjin 300071
| | - H J Yu
- NUCTECH Company, Beijing 100084
| | - J F Yue
- YaLong River Hydropower Development Company, Chengdu 610051
| | - M Zeng
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Z Zeng
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - F S Zhang
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - M G Zhao
- School of Physics, Nankai University, Tianjin 300071
| | - J F Zhou
- YaLong River Hydropower Development Company, Chengdu 610051
| | - Z Y Zhou
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - J J Zhu
- College of Physical Science and Technology, Sichuan University, Chengdu 610065
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Jha J, Singh M, Singh L, Pushker N, Sen S, Kashyap S. Synergistic role of BAP1 and DNA damage response pathway in uveal melanoma and its prognostic significance. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz269.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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45
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Nayak M, Khan A, Singh L. Polysomnographic parameters and their brain morphology correlates in depression: A comparative study. J Neurol Sci 2019. [DOI: 10.1016/j.jns.2019.10.1631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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46
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Kashyap S, Singh M, Singh L, Pushker N, Sen S, Meel R, Bakhshi S, Chawla B, Kaur J. Prognostic significance of c-Rel/p50 heterodimer in the tumor microenvironment of uveal melanoma. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz269.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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47
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Singh L, Dubey R, Singh S, Goel R, Nair S, Singh PK. Measuring quality of antenatal care: a secondary analysis of national survey data from India. BJOG 2019; 126 Suppl 4:7-13. [DOI: 10.1111/1471-0528.15825] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2019] [Indexed: 11/27/2022]
Affiliation(s)
- L Singh
- ICMR – National Institute of Medical StatisticsNew Delhi India
| | - R Dubey
- ICMR – National Institute of Medical StatisticsNew Delhi India
| | - S Singh
- Division of Reproductive Biology, Maternal and Child Health Indian Council of Medical Research (ICMR) New Delhi India
| | - R Goel
- Division of Reproductive Biology, Maternal and Child Health Indian Council of Medical Research (ICMR) New Delhi India
| | - S Nair
- ICMR – National Institute of Medical StatisticsNew Delhi India
| | - PK Singh
- Division of Preventive Oncology, ICMR – National Institute of Cancer Prevention and ResearchNoida India
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48
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Ang CS, Chan NN, Singh L. A comparison study of meat eaters and non-meat eaters on mind attribution and moral disengagement of animals. Appetite 2019; 136:80-85. [DOI: 10.1016/j.appet.2019.01.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 01/16/2019] [Accepted: 01/21/2019] [Indexed: 01/12/2023]
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49
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Singh L, Singh M, Pushker N, Bakhshi S, Rizvi M, Sen S, Kashyap S. Immune checkpoints and T-lymphocytes as immunotherapeutic target in the treatment of sebaceous gland carcinoma. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy288.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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50
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Jiang H, Jia LP, Yue Q, Kang KJ, Cheng JP, Li YJ, Wong HT, Agartioglu M, An HP, Chang JP, Chen JH, Chen YH, Deng Z, Du Q, Gong H, He L, Hu JW, Hu QD, Huang HX, Li HB, Li H, Li JM, Li J, Li X, Li XQ, Li YL, Liao B, Lin FK, Lin ST, Liu SK, Liu YD, Liu YY, Liu ZZ, Ma H, Ma JL, Pan H, Ren J, Ruan XC, Sevda B, Sharma V, Shen MB, Singh L, Singh MK, Sun TX, Tang CJ, Tang WY, Tian Y, Wang GF, Wang JM, Wang L, Wang Q, Wang Y, Wu SY, Wu YC, Xing HY, Xu Y, Xue T, Yang LT, Yang SW, Yi N, Yu CX, Yu HJ, Yue JF, Zeng XH, Zeng M, Zeng Z, Zhang FS, Zhang YH, Zhao MG, Zhou JF, Zhou ZY, Zhu JJ, Zhu ZH. Limits on Light Weakly Interacting Massive Particles from the First 102.8 kg×day Data of the CDEX-10 Experiment. Phys Rev Lett 2018; 120:241301. [PMID: 29956956 DOI: 10.1103/physrevlett.120.241301] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/07/2018] [Indexed: 06/08/2023]
Abstract
We report the first results of a light weakly interacting massive particles (WIMPs) search from the CDEX-10 experiment with a 10 kg germanium detector array immersed in liquid nitrogen at the China Jinping Underground Laboratory with a physics data size of 102.8 kg day. At an analysis threshold of 160 eVee, improved limits of 8×10^{-42} and 3×10^{-36} cm^{2} at a 90% confidence level on spin-independent and spin-dependent WIMP-nucleon cross sections, respectively, at a WIMP mass (m_{χ}) of 5 GeV/c^{2} are achieved. The lower reach of m_{χ} is extended to 2 GeV/c^{2}.
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Affiliation(s)
- H Jiang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - L P Jia
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Q Yue
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - K J Kang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - J P Cheng
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - Y J Li
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H T Wong
- Institute of Physics, Academia Sinica, Taipei 11529
| | - M Agartioglu
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Dokuz Eylül University, Ízmir 35160
| | - H P An
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- Department of Physics, Tsinghua University, Beijing 100084
| | | | - J H Chen
- Institute of Physics, Academia Sinica, Taipei 11529
| | - Y H Chen
- YaLong River Hydropower Development Company, Chengdu 610051
| | - Z Deng
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Q Du
- College of Physical Science and Technology, Sichuan University, Chengdu 610064
| | - H Gong
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - L He
- NUCTECH Company, Beijing 100084
| | - J W Hu
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Q D Hu
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H X Huang
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - H B Li
- Institute of Physics, Academia Sinica, Taipei 11529
| | - H Li
- NUCTECH Company, Beijing 100084
| | - J M Li
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - J Li
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - X Li
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - X Q Li
- School of Physics, Nankai University, Tianjin 300071
| | - Y L Li
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - B Liao
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - F K Lin
- Institute of Physics, Academia Sinica, Taipei 11529
| | - S T Lin
- College of Physical Science and Technology, Sichuan University, Chengdu 610064
| | - S K Liu
- College of Physical Science and Technology, Sichuan University, Chengdu 610064
| | - Y D Liu
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - Y Y Liu
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - Z Z Liu
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H Ma
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - J L Ma
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- Department of Physics, Tsinghua University, Beijing 100084
| | - H Pan
- NUCTECH Company, Beijing 100084
| | - J Ren
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - X C Ruan
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - B Sevda
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Dokuz Eylül University, Ízmir 35160
| | - V Sharma
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Banaras Hindu University, Varanasi 221005
| | - M B Shen
- YaLong River Hydropower Development Company, Chengdu 610051
| | - L Singh
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Banaras Hindu University, Varanasi 221005
| | - M K Singh
- Institute of Physics, Academia Sinica, Taipei 11529
- Department of Physics, Banaras Hindu University, Varanasi 221005
| | - T X Sun
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - C J Tang
- College of Physical Science and Technology, Sichuan University, Chengdu 610064
| | - W Y Tang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Y Tian
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - G F Wang
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - J M Wang
- YaLong River Hydropower Development Company, Chengdu 610051
| | - L Wang
- Department of Physics, Beijing Normal University, Beijing 100875
| | - Q Wang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- Department of Physics, Tsinghua University, Beijing 100084
| | - Y Wang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- Department of Physics, Tsinghua University, Beijing 100084
| | - S Y Wu
- YaLong River Hydropower Development Company, Chengdu 610051
| | - Y C Wu
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - H Y Xing
- College of Physical Science and Technology, Sichuan University, Chengdu 610064
| | - Y Xu
- School of Physics, Nankai University, Tianjin 300071
| | - T Xue
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - L T Yang
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
- Department of Physics, Tsinghua University, Beijing 100084
| | - S W Yang
- Institute of Physics, Academia Sinica, Taipei 11529
| | - N Yi
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - C X Yu
- School of Physics, Nankai University, Tianjin 300071
| | - H J Yu
- NUCTECH Company, Beijing 100084
| | - J F Yue
- YaLong River Hydropower Development Company, Chengdu 610051
| | - X H Zeng
- YaLong River Hydropower Development Company, Chengdu 610051
| | - M Zeng
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - Z Zeng
- Key Laboratory of Particle and Radiation Imaging (Ministry of Education) and Department of Engineering Physics, Tsinghua University, Beijing 100084
| | - F S Zhang
- College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875
| | - Y H Zhang
- YaLong River Hydropower Development Company, Chengdu 610051
| | - M G Zhao
- School of Physics, Nankai University, Tianjin 300071
| | - J F Zhou
- YaLong River Hydropower Development Company, Chengdu 610051
| | - Z Y Zhou
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413
| | - J J Zhu
- College of Physical Science and Technology, Sichuan University, Chengdu 610064
| | - Z H Zhu
- YaLong River Hydropower Development Company, Chengdu 610051
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