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Meng Z, Wang S, Yu L, Zhao K, Wu T, Zhu X, Yang N, Qiao Q, Ma J, Wu B, Ge Y, Cui L. A novel fast hybrid capture sequencing method for high-efficiency common human coronavirus whole-genome acquisition. mSystems 2024; 9:e0122223. [PMID: 38564711 PMCID: PMC11097644 DOI: 10.1128/msystems.01222-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
Rapid and accurate sequencing of the entire viral genome, coupled with continuous monitoring of genetic changes, is crucial for understanding the epidemiology of coronaviruses. We designed a novel method called micro target hybrid capture system (MT-Capture) to enable whole-genome sequencing in a timely manner. The novel design of probes used in target binding exhibits a unique and synergistic "hand-in-hand" conjugation effect. The entire hybrid capture process is within 2.5 hours, overcoming the time-consuming and complex operation characteristics of the traditional liquid-phase hybrid capture (T-Capture) system. By designing specific probes for these coronaviruses, MT-Capture effectively enriched isolated strains and 112 clinical samples of coronaviruses with cycle threshold values below 37. Compared to multiplex PCR sequencing, it does not require frequent primer updates and has higher compatibility. MT-Capture is highly sensitive and capable of tracking variants.IMPORTANCEMT-Capture is meticulously designed to enable the efficient acquisition of the target genome of the common human coronavirus. Coronavirus is a kind of virus that people are generally susceptible to and is epidemic and infectious, and it is the virus with the longest genome among known RNA viruses. Therefore, common human coronavirus samples are selected to evaluate the accuracy and sensitivity of MT-Capture. This method utilizes innovative probe designs optimized through probe conjugation techniques, greatly shortening the time and simplifying the handwork compared with traditional hybridization capture processes. Our results demonstrate that MT-Capture surpasses multiplex PCR in terms of sensitivity, exhibiting a thousandfold increase. Moreover, MT-Capture excels in the identification of mutation sites. This method not only is used to target the coronaviruses but also may be used to diagnose other diseases, including various infectious diseases, genetic diseases, or tumors.
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Affiliation(s)
- Zixinrong Meng
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuo Wang
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Liping Yu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Kangchen Zhao
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Tao Wu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Xiaojuan Zhu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Ning Yang
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qiao Qiao
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Junyan Ma
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Bin Wu
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yiyue Ge
- School of Public Health, Nanjing Medical University, Nanjing, China
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Lunbiao Cui
- School of Public Health, Nanjing Medical University, Nanjing, China
- NHC Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Province Engineering Research Center of Health Emergency, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
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Timsit S, Armand-Lefèvre L, Le Goff J, Salmona M. The clinical and epidemiological impacts of whole genomic sequencing on bacterial and virological agents. Infect Dis Now 2024; 54:104844. [PMID: 38101516 DOI: 10.1016/j.idnow.2023.104844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Whole Genome Sequencing (WGS) is a molecular biology tool consisting in the sequencing of the entire genome of a given organism. Due to its ability to provide the finest available resolution of bacterial and virological genetics, it is used at several levels in the field of infectiology. On an individual scale and through application of a single technique, it enables the typological identification and characterization of strains, the characterization of plasmids, and enhanced search for resistance genes and virulence factors. On a collective scale, it enables the characterization of strains and the determination of phylogenetic links between different microorganisms during community outbreaks and healthcare-associated epidemics. The information provided by WGS enables real-time monitoring of strain-level epidemiology on a worldwide scale, and facilitates surveillance of the resistance dissemination and the introduction or emergence of pathogenic variants in humans or their environment. There are several possible approaches to completion of an entire genome. The choice of one method rather than another is essentially dictated by the matrix, either a clinical sample or a culture isolate, and the clinical objective. WGS is an advanced technology that remains costly despite a gradual decrease in its expenses, potentially hindering its implementation in certain laboratories and thus its use in routine microbiology. Even though WGS is making steady inroads as a reference method, efforts remain needed in view of so harmonizing its interpretations and decreasing the time to generation of conclusive results.
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Affiliation(s)
- Sarah Timsit
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; Service de Bactériologie, Hôpital Bichat-Claude Bernard, APHP, Paris, France
| | - Laurence Armand-Lefèvre
- Service de Bactériologie, Hôpital Bichat-Claude Bernard, APHP, Paris, France; IAME UMR 1137, INSERM, Université Paris Cité, Paris, France
| | - Jérôme Le Goff
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; INSERM U976, Insight Team, Université Paris Cité, Paris, France
| | - Maud Salmona
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; INSERM U976, Insight Team, Université Paris Cité, Paris, France.
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3
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Olorunfemi AB, Suliman SA, Tran TT, Ayorinde B, Fowora MA, Iwalokun BA, Olowe OA, Opaleye OO, Osman M, Salako BL, Adegbola R, Thomas BN, Pallerla SR, Velavan TP, Ojurongbe O. Whole genome sequencing and phylogenetic analysis of SARS-CoV-2 strains isolated during the COVID-19 pandemic in Nigeria. IJID REGIONS 2024; 10:174-178. [PMID: 38322246 PMCID: PMC10845906 DOI: 10.1016/j.ijregi.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/08/2024]
Abstract
Objectives The emergence and spread of SARS-CoV-2 have stimulated ongoing research into the virus transmission dynamics, circulating variants, and potential mutations. This study was conducted to understand the genomic dynamics of the epidemic in Nigeria. Design Whole genome sequencing was conducted on SARS-CoV-2 samples collected during the first and second outbreaks using the Oxford Nanopore MinION sequencing platform. Phylogenetic analysis was conducted, and genomes were grouped into different pangolin lineages. Results The study revealed four circulating SARS-CoV-2 variants. The Alpha (B.1.1.7) variant was the most prevalent (32.7%), followed by Beta (B.1 B.1.1, L.3, and B.1.1.318) (30.8%), Eta (B.1.525) (28.9%), and Delta (B.1.617, AY.1, AY.109, and AY.36) (7.7%). Phylogenetic analysis revealed three clusters with four Nextstrain clades (20I, 20B, 21D, and 21J). The Alpha lineages (B.1.1.7) clustered with references from Italy. The Beta lineages (Clade 20B) (B.11, B.11318, and L3) and sub-lineage B.11 were distinct. Sub-lineage B.11318 is clustered with references from the USA, whereas sub-lineage L3 is clustered with references from Russia, the Philippines, Australia, and Japan. The 21D and 21J, belonging to two Pango lineages, Eta (B.1525) and Delta (B.1.617 and AY.109), showed high genetic similarity. Conclusion The phylogenetic relatedness of the lineages suggests multiple virus introduction, which could be a source of more virulent, locally adapted variants.
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Affiliation(s)
- Adedolapo B. Olorunfemi
- Center for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | | | - Tung T. Tran
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam
| | - Babatunde Ayorinde
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Muinah A. Fowora
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Bamidele A. Iwalokun
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Olugbenga A. Olowe
- Center for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Oluyinka O. Opaleye
- Center for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Mohamed Osman
- Institute of Endemic Diseases, University of Khartoum, Sudan
- York Biomedical Research Institute, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Babatunde L. Salako
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Richard Adegbola
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Bolaji N. Thomas
- Department of Biomedical Sciences, College of Health Sciences and Technology, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Srinivas Reddy Pallerla
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Universität Tübingen, Germany
| | - Thirumalaisamy P. Velavan
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Universität Tübingen, Germany
| | - Olusola Ojurongbe
- Center for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
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De Luca E, Álvarez-Narváez S, Baptista RP, Maboni G, Blas-Machado U, Sanchez S. Epidemiologic investigation and genetic characterization of canine respiratory coronavirus in the Southeastern United States. J Vet Diagn Invest 2024; 36:46-55. [PMID: 37968872 PMCID: PMC10734574 DOI: 10.1177/10406387231213662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023] Open
Abstract
Canine respiratory coronavirus (CRCoV) is one of the main causative agents of canine infectious respiratory disease (CIRD), an illness whose epidemiology is poorly understood. We assessed the prevalence, risk factors, and genetic characterization of CRCoV in privately owned dogs in the Southeastern United States. We PCR-screened 189 nasal swabs from dogs with and without CIRD clinical signs for 9 CIRD-related pathogens, including CRCoV; 14% of dogs, all diagnosed with CIRD, were positive for CRCoV, with a significantly higher rate of cases in younger dogs and during warmer weather. Notably, the presence of CRCoV, alone or in coinfection with other CIRD pathogens, was statistically associated with a worse prognosis. We estimated a CRCoV seroprevalence of 23.7% retrospectively from 540 serum samples, with no statistical association to dog age, sex, or season, but with a significantly higher presence in urban counties. Additionally, the genomes of 6 CRCoVs were obtained from positive samples using an in-house developed targeted amplicon-based approach specific to CRCoV. Subsequent phylogeny clustered their genomes in 2 distinct genomic groups, with most isolates sharing a higher similarity with CRCoVs from Sweden and only 1 more closely related to CRCoVs from Asia. We provide new insights into CIRD and CRCoV epidemiology in the Southeastern United States and further support the association of CRCoV with more severe cases of CIRD. Additionally, we developed and successfully tested a new amplicon-based approach for whole-genome sequencing of CRCoV that can be used to further investigate the genetic diversity within CRCoVs.
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Affiliation(s)
- Eliana De Luca
- Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Pathology, College of Veterinary Medicine, Midwestern University, Glendale, AZ, USA
| | - Sonsiray Álvarez-Narváez
- Southeast Poultry Research Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, USA
| | | | - Grazieli Maboni
- Departments of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Ontario, Canada
| | | | - Susan Sanchez
- Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
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5
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Chaves-Blanco L, de Salazar A, Fuentes A, Viñuela L, Perez-Florido J, Dopazo J, García F. Evaluation of a combined detection of SARS-CoV-2 and its variants using real-time allele-specific PCR strategy: an advantage for clinical practice. Epidemiol Infect 2023; 151:e201. [PMID: 37997654 PMCID: PMC10753446 DOI: 10.1017/s095026882300184x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/08/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023] Open
Abstract
This study aimed to assess the ability of a real-time reverse transcription polymerase chain reaction (RT-PCR) with multiple targets to detect SARS-CoV-2 and its variants in a single test. Nasopharyngeal specimens were collected from patients in Granada, Spain, between January 2021 and December 2022. Five allele-specific RT-PCR kits were used sequentially, with each kit designed to detect a predominant variant at the time. When the Alpha variant was dominant, the kit included the HV69/70 deletion, E and N genes. When Delta replaced Alpha, the kit incorporated the L452R mutation in addition to E and N genes. When Omicron became dominant, L452R was replaced with the N679K mutation. Before incorporating each variant kit, a comparative analysis was carried out with SARS-CoV-2 whole genome sequencing (WGS). The results demonstrated that RT-PCR with multiple targets can provide rapid and effective detection of SARS-CoV-2 and its variants in a single test. A very high degree of agreement (96.2%) was obtained between the comparison of RT-PCR and WGS. Allele-specific RT-PCR assays make it easier to implement epidemiological surveillance systems for effective public health decision making.
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Affiliation(s)
- Lucía Chaves-Blanco
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
| | - Adolfo de Salazar
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Ana Fuentes
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Laura Viñuela
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Javier Perez-Florido
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Sevilla, Sevilla, Spain
| | - Joaquín Dopazo
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, Sevilla, Spain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of Sevilla, Sevilla, Spain
- FPS/ELIXIR-ES, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, Sevilla, Spain
| | - Federico García
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
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Koen AL, Izu A, Baillie V, Kwatra G, Cutland CL, Fairlie L, Padayachee SD, Dheda K, Barnabas SL, Bhorat QE, Briner C, Ahmed K, Bhikha S, Bhiman JN, du Plessis J, Esmail A, Horne E, Hwa SH, Oommen-Jose A, Lambe T, Laubscher M, Malahleha M, Benade G, McKenzie S, Oelofse S, Patel F, Pillay S, Rhead S, Rodel H, Taoushanis C, Tegally H, Thombrayil A, Villafana TL, Gilbert S, Pollard AJ, Madhi SA. Efficacy of primary series AZD1222 (ChAdOx1 nCoV-19) vaccination against SARS-CoV-2 variants of concern: Final analysis of a randomized, placebo-controlled, phase 1b/2 study in South African adults (COV005). Vaccine 2023; 41:3486-3492. [PMID: 37149443 PMCID: PMC10133888 DOI: 10.1016/j.vaccine.2023.04.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 04/21/2023] [Accepted: 04/21/2023] [Indexed: 05/08/2023]
Abstract
COVID-19 vaccine efficacy (VE) has been observed to vary against antigenically distinct SARS-CoV-2 variants of concern (VoC). Here we report the final analysis of VE and safety from COV005: a phase 1b/2, multicenter, double-blind, randomized, placebo-controlled study of primary series AZD1222 (ChAdOx1 nCoV-19) vaccination in South African adults aged 18-65 years. South Africa's first, second, and third waves of SARS-CoV-2 infections were respectively driven by the ancestral SARS-CoV-2 virus (wild type, WT), and SARS-CoV-2 Beta and Delta VoCs. VE against asymptomatic and symptomatic infection was 90.6% for WT, 6.7% for Beta and 77.1% for Delta. No cases of severe COVID-19 were documented ahead of unblinding. Safety was consistent with the interim analysis, with no new safety concerns identified. Notably, South Africa's Delta wave occurred ≥ 9 months after primary series vaccination, suggesting that primary series AZD1222 vaccination offers a good durability of protection, potentially due to an anamnestic response. Clinical trial identifier: CT.gov NCT04444674.
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Affiliation(s)
- Anthonet L Koen
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit (Wits-VIDA), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Alane Izu
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit (Wits-VIDA), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Vicky Baillie
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit (Wits-VIDA), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gaurav Kwatra
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit (Wits-VIDA), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - Clare L Cutland
- African Leadership in Vaccinology Expertise (ALIVE), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lee Fairlie
- Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute, University of Cape Town, South Africa
| | - Shaun L Barnabas
- Family Centre for Research with Ubuntu, Department of Paediatrics, Stellenbosch University, Cape Town, South Africa
| | | | - Carmen Briner
- Perinatal HIV Research Unit, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Khatija Ahmed
- Setshaba Research Centre, Tshwane, South Africa; Faculty of Health Sciences, Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Sutika Bhikha
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit (Wits-VIDA), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jinal N Bhiman
- 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
| | - Jeanine du Plessis
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit (Wits-VIDA), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Aliasgar Esmail
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and University of Cape Town Lung Institute, Cape Town, South Africa
| | - Elizea Horne
- Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shi-Hsia Hwa
- Africa Health Research Institute, Durban, South Africa; Division of Infection and Immunity, University College London, London, UK
| | - Aylin Oommen-Jose
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit (Wits-VIDA), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Teresa Lambe
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK; Chinese Academy of Medical Science, Oxford Institute, University of Oxford, Oxford, UK
| | - Matt Laubscher
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit (Wits-VIDA), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mookho Malahleha
- Setshaba Research Centre, Tshwane, South Africa; Synergy Biomed Research Institute, East London, Eastern Cape, South Africa
| | - Gabriella Benade
- Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shakeel McKenzie
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit (Wits-VIDA), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Suzette Oelofse
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and University of Cape Town Lung Institute, Cape Town, South Africa
| | - Faeezah Patel
- Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 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; Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa
| | - Sarah Rhead
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK
| | - Hylton Rodel
- Africa Health Research Institute, Durban, South Africa; Division of Infection and Immunity, University College London, London, UK
| | - Carol Taoushanis
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit (Wits-VIDA), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 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; Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa
| | - Asha Thombrayil
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit (Wits-VIDA), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tonya L Villafana
- Clinical Development, Vaccines & Immune Therapies, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Sarah Gilbert
- Nuffield Department of Medicine, University of Oxford, ORCRB, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit (Wits-VIDA), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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7
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Pillay S, San JE, Tshiabuila D, Naidoo Y, Pillay Y, Maharaj A, Anyaneji UJ, Wilkinson E, Tegally H, Lessells RJ, Baxter C, de Oliveira T, Giandhari J. Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing. PLoS One 2023; 18:e0283219. [PMID: 37099540 PMCID: PMC10132692 DOI: 10.1371/journal.pone.0283219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/03/2023] [Indexed: 04/27/2023] Open
Abstract
The global pandemic caused by SARS-CoV-2 has increased the demand for scalable sequencing and diagnostic methods, especially for genomic surveillance. Although next-generation sequencing has enabled large-scale genomic surveillance, the ability to sequence SARS-CoV-2 in some settings has been limited by the cost of sequencing kits and the time-consuming preparations of sequencing libraries. We compared the sequencing outcomes, cost and turn-around times obtained using the standard Illumina DNA Prep kit protocol to three modified protocols with fewer clean-up steps and different reagent volumes (full volume, half volume, one-tenth volume). We processed a single run of 47 samples under each protocol and compared the yield and mean sequence coverage. The sequencing success rate and quality for the four different reactions were as follows: the full reaction was 98.2%, the one-tenth reaction was 98.0%, the full rapid reaction was 97.5% and the half-reaction, was 97.1%. As a result, uniformity of sequence quality indicated that libraries were not affected by the change in protocol. The cost of sequencing was reduced approximately seven-fold and the time taken to prepare the library was reduced from 6.5 hours to 3 hours. The sequencing results obtained using the miniaturised volumes showed comparability to the results obtained using full volumes as described by the manufacturer. The adaptation of the protocol represents a lower-cost, streamlined approach for SARS-CoV-2 sequencing, which can be used to produce genomic data quickly and more affordably, especially in resource-constrained settings.
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Affiliation(s)
- Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James Emmanuel San
- 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
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, 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
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Yusasha Pillay
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Akhil Maharaj
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ugochukwu J. Anyaneji
- 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
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, 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
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, 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
- Center for AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Center for AIDS Programme of Research in South Africa (CAPRISA), Durban, 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
- Center for AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, United States of America
| | - Jennifer Giandhari
- 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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8
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Ong'era EM, Mohammed KS, Makori TO, Bejon P, Ocholla-Oyier LI, Nokes DJ, Agoti CN, Githinji G. High-throughput sequencing approaches applied to SARS-CoV-2. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18701.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
High-throughput sequencing is crucial for surveillance and control of viral outbreaks. During the ongoing coronavirus disease 2019 (COVID-19) pandemic, advances in the high-throughput sequencing technology resources have enhanced diagnosis, surveillance, and vaccine discovery. From the onset of the pandemic in December 2019, several genome-sequencing approaches have been developed and supported across the major sequencing platforms such as Illumina, Oxford Nanopore, PacBio, MGI DNBSEQTM and Ion Torrent. Here, we share insights from the sequencing approaches developed for sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between December 2019 and October 2022.
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9
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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 GLOBAL 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] [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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Wagner J, Yuen L, Littlejohn M, Sozzi V, Jackson K, Martin R, Aeschbacher T, Suri V, Tan SK, Feierbach B, Gaggar A, Marcellin P, Buti Ferret M, Janssen HLA, Gane E, Meagher N, Price DJ, Wong D, Thompson AT, Revill PA. Hepatitis B virus haplotype number at baseline is a predictive marker of functional cure during antiviral therapy for patients with genotypes A and D HBeAg-positive chronic hepatitis B. Aliment Pharmacol Ther 2023; 57:509-523. [PMID: 36427857 DOI: 10.1111/apt.17299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/03/2022] [Accepted: 10/28/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUNDS AND AIMS We investigated associations between hepatitis B virus (HBV) genome-length haplotype number (HN) at baseline in subjects with HBeAg-positive chronic hepatitis B (CHB), and the likelihood of achieving functional cure during direct-acting antiviral therapy METHOD: We analysed 86 HBeAg-positive baseline samples from patients with HBV genotypes A and D who were enrolled in a Phase II trial of tenofovir disoproxil fumarate (TDF) to determine if HN was a biomarker of HBsAg loss during therapy. Findings were validated using baseline samples from 181 patients with HBV genotypes A and D from an independent clinical trial utilising TDF or tenofovir alafenamide therapy in HBeAg-positive CHB. RESULTS In the HBeAg-positive test cohort, patients with genotypes A or D and ≤2 haplotypes had a minimum of 21-fold higher likelihood of achieving HBsAg loss on TDF. Baseline HN (p < 0.0001) was a stronger predictor of HBsAg loss on therapy than HBsAg titre (p = 0.03), HBeAg titre (p = 0.0002), or the presence of HBV basal core promoter (A1762T, p = 0.0379 and G1764A, p = 0.0176) or G1896A precore mutations (p = 0.0218). This finding was validated in the independent validation cohort. HN was statistically higher in patients with HBV genotypes B or C infection compared to genotypes A and D. CONCLUSION Baseline HN ≤2 predicts which patients with HBV genotypes A or D will more likely progress to functional cure on current direct-acting antiviral therapy, with greater accuracy than current biomarkers including baseline HBsAg and HBeAg titre.
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Affiliation(s)
- Josef Wagner
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Lilly Yuen
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Vitina Sozzi
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kathy Jackson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ross Martin
- Gilead Sciences, Foster City, California, USA
| | | | | | | | | | - Anuj Gaggar
- Gilead Sciences, Foster City, California, USA
| | | | - Maria Buti Ferret
- Liver Unit, Valle d'Hebron (Ciberehd) University Hospital, Barcelona, Spain
| | - Harry L A Janssen
- Toronto Center for Liver Diseases, Toronto General Hospital, University: Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Ed Gane
- New Zealand Liver Transplant Unit, Auckland City Hospital, Auckland, New Zealand
| | - Niamh Meagher
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - David J Price
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Darren Wong
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Gastroenterology, St. Vincent's Hospital, Melbourne, Victoria, Australia
| | - Alexander T Thompson
- Department of Gastroenterology, St. Vincent's Hospital, Melbourne, Victoria, Australia
| | - Peter A Revill
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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11
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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] [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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12
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Transcriptomics and RNA-Based Therapeutics as Potential Approaches to Manage SARS-CoV-2 Infection. Int J Mol Sci 2022; 23:ijms231911058. [PMID: 36232363 PMCID: PMC9570475 DOI: 10.3390/ijms231911058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
SARS-CoV-2 is a coronavirus family member that appeared in China in December 2019 and caused the disease called COVID-19, which was declared a pandemic in 2020 by the World Health Organization. In recent months, great efforts have been made in the field of basic and clinical research to understand the biology and infection processes of SARS-CoV-2. In particular, transcriptome analysis has contributed to generating new knowledge of the viral sequences and intracellular signaling pathways that regulate the infection and pathogenesis of SARS-CoV-2, generating new information about its biology. Furthermore, transcriptomics approaches including spatial transcriptomics, single-cell transcriptomics and direct RNA sequencing have been used for clinical applications in monitoring, detection, diagnosis, and treatment to generate new clinical predictive models for SARS-CoV-2. Consequently, RNA-based therapeutics and their relationship with SARS-CoV-2 have emerged as promising strategies to battle the SARS-CoV-2 pandemic with the assistance of novel approaches such as CRISPR-CAS, ASOs, and siRNA systems. Lastly, we discuss the importance of precision public health in the management of patients infected with SARS-CoV-2 and establish that the fusion of transcriptomics, RNA-based therapeutics, and precision public health will allow a linkage for developing health systems that facilitate the acquisition of relevant clinical strategies for rapid decision making to assist in the management and treatment of the SARS-CoV-2-infected population to combat this global public health problem.
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13
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Simultaneous SARS-CoV-2 Genome Sequencing of 384 Samples on an Illumina MiSeq Instrument through Protocol Optimization. Genes (Basel) 2022; 13:genes13091648. [PMID: 36140815 PMCID: PMC9498777 DOI: 10.3390/genes13091648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022] Open
Abstract
In the present study, we propose a high-throughput sequencing protocol using aNextera XT Library DNA kit on an Illumina MiSeq instrument. We made major modifications to this library preparation in order to multiplex 384 samples in a single Illumina flow cell. To validate our protocol, we compared the sequences obtained with the modified Illumina protocol to those obtained with the GridION Nanopore protocol. For the modified Illumina protocol, our results showed that 94.9% (357/376) of the sequences were interpretable, with a viral genome coverage between 50.5% and 99.9% and an average depth of 421×. For the GridION Nanopore protocol, 94.6% (356/376) of the sequences were interpretable, with a viral genome coverage between 7.0% and 98.6% and an average depth of 2123×. The modified Illumina protocol allows for gaining EUR 4744 and returning results of 384 samples in 53.5 h versus four times 55.5 h with the standard Illumina protocol. Our modified MiSeq protocol yields similar genome sequence data as the GridION Nanopore protocol and has the advantage of being able to handle four times more samples simultaneously and hence is much less expensive.
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14
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Seadawy MG, Binsuwaidan R, Alotaibi B, El-Masry TA, El-Harty BE, Gad AF, Elkhatib WF, El-Bouseary MM. The Mutational Landscape of SARS-CoV-2 Variants of Concern Recovered From Egyptian Patients in 2021. Front Microbiol 2022; 13:923137. [PMID: 35875574 PMCID: PMC9300961 DOI: 10.3389/fmicb.2022.923137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/16/2022] [Indexed: 11/22/2022] Open
Abstract
In December 2019, a mysterious viral pneumonia first developed in Wuhan, China, resulting in a huge number of fatal cases. This pneumonia, which was named COVID-19, was attributed to a novel coronavirus, SARS-CoV-2. The emerging SARS-CoV-2 mutations pose the greatest risk to human health because they could result in an increase in the COVID-19 severity or the failure of current vaccines. One of these notable mutations is the SARS-CoV-2 Delta variant (B.1.617) that was first detected in India and has rapidly expanded to 115 countries worldwide. Consequently, in this study, we performed next-generation sequencing and phylogenetic analysis of SARS-CoV-2 during the third wave of the pandemic to determine the SARS-CoV-2 variants of concern (VOC) prevalence in Egypt. We observed several mutational patterns, revealing that SARS-CoV-2 evolution has expanded in Egypt with a considerable increase in the number of VOC. Therefore, the Egyptian authorities should take an appropriate approach to investigate the compatibility of already employed vaccines with this VOC and to examine the efficacy of the existing therapeutic regimen against new SARS-CoV-2 variants.
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Affiliation(s)
- Mohamed G. Seadawy
- Biological Prevention Department, Egypt Army, Cairo, Egypt
- Mohamed G. Seadawy, , orcid.org/0000-0001-6102-723X
| | - Reem Binsuwaidan
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Badriyah Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Thanaa A. El-Masry
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | | | - Ahmed F. Gad
- Biological Prevention Department, Egypt Army, Cairo, Egypt
| | - Walid F. Elkhatib
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Galala University, New Galala City, Egypt
| | - Maisra M. El-Bouseary
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
- *Correspondence: Maisra M. El-Bouseary, , orcid.org/0000-0001-6503-0719
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15
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Gupta AK, Kumar M. Benchmarking and Assessment of Eight De Novo Genome Assemblers on Viral Next-Generation Sequencing Data, Including the SARS-CoV-2. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:372-381. [PMID: 35759429 DOI: 10.1089/omi.2022.0042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Viral genomics has become crucial in clinical diagnostics and ecology, not to mention to stem the COVID-19 pandemic. Whole-genome sequencing (WGS) is pivotal in gaining an improved understanding of viral evolution, genomic epidemiology, infectious outbreaks, pathobiology, clinical management, and vaccine development. Genome assembly is one of the crucial steps in WGS data analyses. A series of different assemblers has been developed with the advent of high-throughput next-generation sequencing (NGS). Various studies have reported the evaluation of these assembly tools on distinct datasets; however, these lack data from viral origin. In this study, we performed a comparative evaluation and benchmarking of eight de novo assemblers: SOAPdenovo, Velvet, assembly by short sequences (ABySS), iterative De Bruijn graph assembler (IDBA), SPAdes, Edena, iterative virus assembler, and VICUNA on the viral NGS data from distinct Illumina (GAIIx, Hiseq, Miseq, and Nextseq) platforms. WGS data of diverse viruses, that is, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), dengue virus 3, human immunodeficiency virus 1, hepatitis B virus, human herpesvirus 8, human papillomavirus 16, rhinovirus A, and West Nile virus, were utilized to assess these assemblers. Performance metrics such as genome fraction recovery, assembly lengths, NG50, N50, contig length, contig numbers, mismatches, and misassemblies were analyzed. Overall, three assemblers, that is, SPAdes, IDBA, and ABySS, performed consistently well, including for genome assembly of SARS-CoV-2. These assembly methods should be considered and recommended for future studies of viruses. The study also suggests that implementing two or more assembly approaches should be considered in viral NGS studies, especially in clinical settings. Taken together, the benchmarking of eight de novo genome assemblers reported in this study can inform future public health and ecology research concerning the viruses, the COVID-19 pandemic, and viral outbreaks.
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Affiliation(s)
- Amit Kumar Gupta
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Manoj Kumar
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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16
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Umunnakwe CN, Makatini ZN, Maphanga M, Mdunyelwa A, Mlambo KM, Manyaka P, Nijhuis M, Wensing A, Tempelman HA. Evaluation of a commercial SARS-CoV-2 multiplex PCR genotyping assay for variant identification in resource-scarce settings. PLoS One 2022; 17:e0269071. [PMID: 35749403 PMCID: PMC9231807 DOI: 10.1371/journal.pone.0269071] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 05/13/2022] [Indexed: 11/24/2022] Open
Abstract
The rapid emergence and spread of numerous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants across the globe underscores the crucial need for continuous SARS-CoV-2 surveillance to ensure that potentially more pathogenic variants are detected early and contained. Whole genome sequencing (WGS) is currently the gold standard for COVID-19 surveillance; however, it remains cost-prohibitive and requires specialized technical skills. To increase surveillance capacity, especially in resource-scarce settings, supplementary methods that are cost- and time-effective are needed. Real-time multiplex PCR genotyping assays offer an economical and fast solution for screening circulating and emerging variants while simultaneously complementing existing WGS approaches. In this study we evaluated the AllplexTM SARS-CoV-2 Variants II multiplex real-time PCR genotyping assay, Seegene (South Korea), and implemented it in retrospectively characterizing circulating SARS-CoV-2 variants in a rural South African setting between April and October 2021, prior to the emergence of the Omicron variant in South Africa. The AllplexTM SARS-CoV-2 Variants II real-time PCR assay demonstrated perfect concordance with whole-genome sequencing in detecting Beta and Delta variants and exhibited high specificity, sensitivity and reproducibility. Implementation of the assay in characterization of SARS-CoV-2 variants between April and October 2021 in a rural South African setting revealed a rapid shift from the Beta to the Delta variant between April and June. All specimens successfully genotyped in April were Beta variants and the Delta variant was not detected until May. By June, 78% of samples genotyped were Delta variants and in July >95% of all genotyped samples were Delta variants. The Delta variant continued to predominate through to the end of our analysis in October 2021. Taken together, a commercial SARS-CoV-2 variant genotyping assay detected the rapid rate at which the Delta variant displaced the Beta variant in Limpopo, an under-monitored province in South Africa. Such assays provide a quick and cost-effective method of monitoring circulating variants and should be used to complement genomic sequencing for COVID-19 surveillance especially in resource-scarce settings.
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Affiliation(s)
- Chijioke N. Umunnakwe
- Ndlovu Research Centre and Laboratories, Dennilton, Limpopo Province, South Africa
- Ndlovu Research Consortium, Dennilton, Limpopo Province, South Africa
- * E-mail:
| | - Zinhle N. Makatini
- Ndlovu Research Consortium, Dennilton, Limpopo Province, South Africa
- Department of Virology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mathapelo Maphanga
- Ndlovu Research Centre and Laboratories, Dennilton, Limpopo Province, South Africa
| | - Anele Mdunyelwa
- Ndlovu Research Centre and Laboratories, Dennilton, Limpopo Province, South Africa
| | - Khamusi M. Mlambo
- Ndlovu Research Centre and Laboratories, Dennilton, Limpopo Province, South Africa
| | - Puseletso Manyaka
- Ndlovu Research Centre and Laboratories, Dennilton, Limpopo Province, South Africa
| | - Monique Nijhuis
- Ndlovu Research Consortium, Dennilton, Limpopo Province, South Africa
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- HIV Pathogenesis Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Annemarie Wensing
- Ndlovu Research Consortium, Dennilton, Limpopo Province, South Africa
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- Wits Reproductive Health and HIV Institute (Wits RHI), University of the Witwatersrand, Johannesburg, South Africa
| | - Hugo A. Tempelman
- Ndlovu Research Centre and Laboratories, Dennilton, Limpopo Province, South Africa
- Ndlovu Research Consortium, Dennilton, Limpopo Province, South Africa
- Wits Reproductive Health and HIV Institute (Wits RHI), University of the Witwatersrand, Johannesburg, South Africa
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17
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Receptor-Binding-Motif-Targeted Sanger Sequencing: a Quick and Cost-Effective Strategy for Molecular Surveillance of SARS-CoV-2 Variants. Microbiol Spectr 2022; 10:e0066522. [PMID: 35638906 PMCID: PMC9241651 DOI: 10.1128/spectrum.00665-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Whole-genome sequencing (WGS) is the gold standard for characterizing the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and identification of new variants. However, the cost involved and time needed for WGS prevent routine, rapid clinical use. This study aimed to develop a quick and cost-effective surveillance strategy for SARS-CoV-2 variants in saliva and nasal swab samples by spike protein receptor-binding-motif (RBM)-targeted Sanger sequencing. Saliva and nasal swabs prescreened for the presence of the nucleocapsid (N) gene of SARS-CoV-2 were subjected to RBM-specific single-amplicon generation and Sanger sequencing. Sequences were aligned by CLC Sequence Viewer 8, and variants were identified based upon specific mutation signature. Based on this strategy, the present study identified Alpha, Beta/Gamma, Delta, and Omicron variants in a quick and cost-effective manner. IMPORTANCE The coronavirus disease 2019 (COVID-19) pandemic resulted in 427 million infections and 5.9 million deaths globally as of 21 February 2022. SARS-CoV-2, the causative agent of the COVID-19 pandemic, frequently mutates and has developed into variants of major public health concerns. Following the Alpha variant (B.1.1.7) infection wave, the Delta variant (B.1.617.2) became prevalent, and now the recently identified Omicron (B.1.1.529) variant is spreading rapidly and forming BA.1, BA.1.1, BA.2, BA.3, BA.4, and BA.5 lineages of concern. Prompt identification of mutational changes in SARS-CoV-2 variants is challenging but critical to managing the disease spread and vaccine/therapeutic modifications. Considering the cost involved and resource limitation of WGS globally, an RBM-targeted Sanger sequencing strategy is adopted in this study for quick molecular surveillance of SARS-CoV-2 variants.
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Chrzastek K, Tennakoon C, Bialy D, Freimanis G, Flannery J, Shelton H. A random priming amplification method for whole genome sequencing of SARS-CoV-2 virus. BMC Genomics 2022; 23:406. [PMID: 35644636 PMCID: PMC9148844 DOI: 10.1186/s12864-022-08563-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 03/24/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Non-targeted whole genome sequencing is a powerful tool to comprehensively identify constituents of microbial communities in a sample. There is no need to direct the analysis to any identification before sequencing which can decrease the introduction of bias and false negatives results. It also allows the assessment of genetic aberrations in the genome (e.g., single nucleotide variants, deletions, insertions and copy number variants) including in noncoding protein regions. METHODS The performance of four different random priming amplification methods to recover RNA viral genetic material of SARS-CoV-2 were compared in this study. In method 1 (H-P) the reverse transcriptase (RT) step was performed with random hexamers whereas in methods 2-4 RT incorporating an octamer primer with a known tag. In methods 1 and 2 (K-P) sequencing was applied on material derived from the RT-PCR step, whereas in methods 3 (SISPA) and 4 (S-P) an additional amplification was incorporated before sequencing. RESULTS The SISPA method was the most effective and efficient method for non-targeted/random priming whole genome sequencing of SARS-CoV-2 that we tested. The SISPA method described in this study allowed for whole genome assembly of SARS-CoV-2 and influenza A(H1N1)pdm09 in mixed samples. We determined the limit of detection and characterization of SARS-CoV-2 virus which was 103 pfu/ml (Ct, 22.4) for whole genome assembly and 101 pfu/ml (Ct, 30) for metagenomics detection. CONCLUSIONS The SISPA method is predominantly useful for obtaining genome sequences from RNA viruses or investigating complex clinical samples as no prior sequence information is needed. It might be applied to monitor genomic virus changes, virus evolution and can be used for fast metagenomics detection or to assess the general picture of different pathogens within the sample.
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Affiliation(s)
| | | | - Dagmara Bialy
- The Pirbright Institute, Pirbright, Woking, Surrey, UK
| | | | - John Flannery
- The Pirbright Institute, Pirbright, Woking, Surrey, UK
| | - Holly Shelton
- The Pirbright Institute, Pirbright, Woking, Surrey, UK.
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19
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Goswami C, Sheldon M, Bixby C, Keddache M, Bogdanowicz A, Wang Y, Schultz J, McDevitt J, LaPorta J, Kwon E, Buyske S, Garbolino D, Biloholowski G, Pastuszak A, Storella M, Bhalla A, Charlier-Rodriguez F, Hager R, Grimwood R, Nahas SA. Identification of SARS-CoV-2 variants using viral sequencing for the Centers for Disease Control and Prevention genomic surveillance program. BMC Infect Dis 2022; 22:404. [PMID: 35468749 PMCID: PMC9035976 DOI: 10.1186/s12879-022-07374-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Centers for Disease Control and Prevention contracted with laboratories to sequence the SARS-CoV-2 genome from positive samples across the United States to enable public health officials to investigate the impact of variants on disease severity as well as the effectiveness of vaccines and treatment. Herein we present the initial results correlating RT-PCR quality control metrics with sample collection and sequencing methods from full SARS-CoV-2 viral genomic sequencing of 24,441 positive patient samples between April and June 2021. METHODS RT-PCR confirmed (N Gene Ct value < 30) positive patient samples, with nucleic acid extracted from saliva, nasopharyngeal and oropharyngeal swabs were selected for viral whole genome SARS-CoV-2 sequencing. Sequencing was performed using Illumina COVIDSeq™ protocol on either the NextSeq550 or NovaSeq6000 systems. Informatic variant calling, and lineage analysis were performed using DRAGEN COVID Lineage applications on Illumina's Basespace cloud analytical system. All sequence data and variant calls were uploaded to NCBI and GISAID. RESULTS An association was observed between higher sequencing coverage, quality, and samples with a lower Ct value, with < 27 being optimal, across both sequencing platforms and sample collection methods. Both nasopharyngeal swabs and saliva samples were found to be optimal samples of choice for SARS-CoV-2 surveillance sequencing studies, both in terms of strain identification and sequencing depth of coverage, with NovaSeq 6000 providing higher coverage than the NextSeq 550. The most frequent variants identified were the B.1.617.2 Delta (India) and P.1 Gamma (Brazil) variants in the samples sequenced between April 2021 and June 2021. At the time of submission, the most common variant > 99% of positives sequenced was Omicron. CONCLUSION These initial analyses highlight the importance of sequencing platform, sample collection methods, and RT-PCR Ct values in guiding surveillance efforts. These surveillance studies evaluating genetic changes of SARS-CoV-2 have been identified as critical by the CDC that can affect many aspects of public health including transmission, disease severity, diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Chirayu Goswami
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Michael Sheldon
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Christian Bixby
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | | | | | - Yihe Wang
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Jonathan Schultz
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Jessica McDevitt
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - James LaPorta
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Elaine Kwon
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Steven Buyske
- Rutgers University, 559 Hill Center, 110 Frelinghuysen Rd, Piscataway, NJ, 08854, USA
| | - Dana Garbolino
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | | | - Alex Pastuszak
- Vault Health, 115 Broadway Suite 1800, 18th Floor, Dobbs Ferry, NY, 10522, USA
| | - Mary Storella
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Amit Bhalla
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | | | - Russ Hager
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Robin Grimwood
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA
| | - Shareef A Nahas
- Infinity-Biologix LLC, 30 Knightsbridge Road, Piscataway, NJ, 08854, USA.
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20
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Tshiabuila D, Giandhari J, Pillay S, Ramphal U, Ramphal Y, Maharaj A, Anyaneji UJ, Naidoo Y, Tegally H, San EJ, Wilkinson E, Lessells RJ, de Oliveira T. Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq. BMC Genomics 2022; 23:319. [PMID: 35459088 PMCID: PMC9026045 DOI: 10.1186/s12864-022-08541-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/08/2022] [Indexed: 11/24/2022] Open
Abstract
Background Over 4 million SARS-CoV-2 genomes have been sequenced globally in the past 2 years. This has been crucial in elucidating transmission chains within communities, the development of new diagnostic methods, vaccines, and antivirals. Although several sequencing technologies have been employed, Illumina and Oxford Nanopore remain the two most commonly used platforms. The sequence quality between these two platforms warrants a comparison of the genomes produced by the two technologies. Here, we compared the SARS-CoV-2 consensus genomes obtained from the Oxford Nanopore Technology GridION and the Illumina MiSeq for 28 sequencing runs. Results Our results show that the MiSeq had a significantly higher number of consensus genomes classified by Nextclade as good and mediocre compared to the GridION. The MiSeq also had a significantly higher genome coverage and mutation counts than the GridION. Conclusion Due to the low genome coverage, high number of indels, and sensitivity to SARS-CoV-2 viral load noted with the GridION when compared to MiSeq, we can conclude that the MiSeq is more favourable for SARS-CoV-2 genomic surveillance, as successful genomic surveillance is dependent on high quality, near-whole consensus genomes.
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Affiliation(s)
- Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal Durban 4001, KwaZulu-Natal, South Africa. .,Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa.
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal Durban 4001, KwaZulu-Natal, South Africa.,Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal Durban 4001, KwaZulu-Natal, South Africa.,Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal Durban 4001, KwaZulu-Natal, South Africa.,Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Yajna Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal Durban 4001, KwaZulu-Natal, South Africa.,Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa
| | - Arisha Maharaj
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal Durban 4001, KwaZulu-Natal, South Africa.,Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa
| | - Ugochukwu Jacob Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal Durban 4001, KwaZulu-Natal, South Africa.,Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal Durban 4001, KwaZulu-Natal, South Africa.,Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal Durban 4001, KwaZulu-Natal, South Africa.,Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa
| | - Emmanuel James San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal Durban 4001, KwaZulu-Natal, South Africa.,Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal Durban 4001, KwaZulu-Natal, South Africa.,Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal Durban 4001, KwaZulu-Natal, South Africa.,Centre for Epidemic Response and Innovation (CERI), Stellenbosch University, Stellenbosch, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal Durban 4001, KwaZulu-Natal, South Africa.,Centre for Epidemic Response and Innovation (CERI), 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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21
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de Oliveira PSS, de Oliveira Silva B, e Silva RP, Galdino LV, de Carvalho VMF, de Almeida AR, da Rosa MM, de Melo Rêgo MJB, da Rocha Pitta MG, Pereira MC. Evaluation of long-term stability of SARS-CoV-2 nucleic acid extracted from human nasopharyngeal samples. J Virol Methods 2022; 305:114529. [PMID: 35398116 PMCID: PMC8985402 DOI: 10.1016/j.jviromet.2022.114529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/29/2022] [Accepted: 04/02/2022] [Indexed: 11/30/2022]
Abstract
The maintenance of SARS-Cov-2 RNA samples poses a new challenge for laboratories and researchers. In addition, it is a requirement in order to identify what strain of the new coronavirus is predominant in a region, for instance. Therefore, it is a must to keep the quality and viability of stored RNA to respond to this and other valid questions. In other to test the quality of our samples and storing protocols, we randomly checked RNA samples four different times over one year using a second RT-PCR assay after the first test. The virus genes, N1 and N2, showed no significant increase in the media of the CT value between the first assay and subsequent times with p > 0.05. However, the human RP gene showed differences in the first three times analyzed, but within the acceptable sample cut-off, according to the test manufacturer. After one year, the RNA extracted from human nasopharyngeal specimens are viable to detect the virus SARS-CoV-2 genes with minor changes.
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22
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Habibi N, Uddin S, Behbehani M, Abdul Razzack N, Zakir F, Shajan A. SARS-CoV-2 in hospital air as revealed by comprehensive respiratory viral panel sequencing. Infect Prev Pract 2022; 4:100199. [PMID: 34977533 PMCID: PMC8711137 DOI: 10.1016/j.infpip.2021.100199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Nosocomially acquired severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection has become the most significant pandemic of our lifetime. Though its transmission was essentially attributed to droplets from an infected person, with recent advancements in knowledge, aerosol transmission seems to be a viable pathway, as well. Because of the lower biological load in ambient aerosol, detection of SARS-CoV-2 is challenging. A few recent attempts of sampling large aerosol volumes and using next-generation sequencing (NGS) to detect the presence of SARS-CoV-2 in the air at very low levels gave positive results. These results suggest the potential of using this technique to detect the presence of SARS-CoV-2 and use it as an early warning signal for possible outbreak or recurrence of coronavirus disease 2019 (COVID-19). AIM To assess efficacy of comprehensive respiratory viral panel (CRVP) sequencing and RT-PCR for low-level identification of SARS-CoV-2 and other respiratory viruses in indoor air. METHODS A large volume of indoor aerosol samples from three major hospitals involved in COVID-19 care in Kuwait was collected. Viral RNA was isolated and subjected to comprehensive respiratory viral panel sequencing (CRVP) as per the standard protocol to detect the SARS-CoV-2 and other respiratory viruses in the hospital aerosol and monitor variations within the sequences. RT-PCR was also employed to estimate the viral load of SARS-CoV-2. FINDINGS 13 of 15 (86.7%) samples exhibited SARS-CoV-2 with a relative abundance of 0.2-33.3%. The co-occurrence of human adenoviruses (type C1, C2, C5, C4), respiratory syncytial virus (RSV), influenza B, and non-SARS-CoV-229E were also recorded. Alignment of SARS-CoV-2 sequences against the reference strain of Wuhan China revealed variations in the form of single nucleotide polymorphisms (SNPs-17), insertions and deletions (indels-1). These variations were predicted to create missense (16), synonymous (15), frameshift (1) and stop-gained (1) mutations with a high (2), low (15), and moderate (16) impact. CONCLUSIONS Our results suggest that using CRVP on a large volume aerosol sample was a valuable tool for detecting SARS-CoV-2 in indoor aerosols of health care settings. Owing to its higher sensitivity, it can be employed as a surveillance strategy in the post COVID times to act as an early warning system to possibly control future outbreaks.
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Affiliation(s)
- Nazima Habibi
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Saif Uddin
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Montaha Behbehani
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Nasreem Abdul Razzack
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Farhana Zakir
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Anisha Shajan
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
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23
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Castañeda-Mogollón D, Kamaliddin C, Fine L, Oberding LK, Pillai DR. SARS-CoV-2 variant detection with ADSSpike. Diagn Microbiol Infect Dis 2022; 102:115606. [PMID: 34963097 PMCID: PMC8608664 DOI: 10.1016/j.diagmicrobio.2021.115606] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/06/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022]
Abstract
The SARS-CoV-2 coronavirus pandemic has been an unprecedented challenge to global pandemic response and preparedness. With the continuous appearance of new SARS-CoV-2 variants, it is imperative to implement tools for genomic surveillance and diagnosis in order to decrease viral transmission and prevalence. The ADSSpike workflow was developed with the goal of identifying signature SNPs from the S gene associated with SARS-CoV-2 variants through amplicon deep sequencing. Seventy-two samples were sequenced, and 30 mutations were identified. Among those, signature SNPs were linked to 2 Zeta-VOI (P.2) samples and one to the Alpha-VOC (B.1.17). An average depth of 700 reads was found to properlycorrectly identify all SNPs and deletions pertinent to SARS-CoV-2 mutants. ADSSpike is the first workflow to provide a practical, cost-effective, and scalable solution to diagnose SARS-CoV-2 VOC/VOI in the clinical laboratory, adding a valuable tool to public health measures to fight the COVID-19 pandemic for approximately $41.85 USD/reaction.
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24
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Alotaibi B, El-Masry TA, Seadawy MG, Farghali MH, El-Harty BE, Saleh A, Mahran YF, Fahim JS, Desoky MS, Abd El-Monsef MM, El-Bouseary MM. SARS-CoV-2 in Egypt: epidemiology, clinical characterization and bioinformatics analysis. Heliyon 2022; 8:e08864. [PMID: 35128118 PMCID: PMC8801622 DOI: 10.1016/j.heliyon.2022.e08864] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/29/2021] [Accepted: 01/27/2022] [Indexed: 12/28/2022] Open
Abstract
COVID-19 is an infectious disease caused by SARS-CoV-2 and has spread globally, resulting in the ongoing coronavirus pandemic. The current study aimed to analyze the clinical and epidemiological features of COVID-19 in Egypt. Oropharyngeal swabs were collected from 197 suspected patients who were admitted to the Army Hospital and confirmation of the positivity was performed by rRT-PCR assay. Whole genomic sequencing was conducted using Illumina iSeq 100® System. The average age of the participants was 48 years, of which 132 (67%) were male. The main clinical symptoms were pneumonia (98%), fever (92%), and dry cough (66%). The results of the laboratory showed that lymphocytopenia (79.2%), decreased levels of haemoglobin (77.7%), increased levels of interleukin 6, C-reactive protein, serum ferritin, and D-dimer (77.2%, 55.3%, 55.3%, and 25.9%, respectively), and leukocytopenia (25.9%) were more common. The CT findings showed that scattered opacities (55.8%) and ground-glass appearance (27.9%) were frequently reported. The recovered validated sequences (n = 144) were submitted to NCBI Virus GenBank. All sequenced viruses have at least 99% identity to Wuhan-Hu-1. All variants were GH clade, B.1 PANGO lineage, and L.GP.YP.HT haplotype. The most predominant subclade was D614G/Q57H/V5F/G823S. Our findings have aided in a deep understanding of COVID-19 evolution and identifying strains with unique mutational patterns in Egypt. Isolation and clinical characterization of SARS-CoV-2 from Egyptian patients. Whole Genome Sequencing of recovered isolates revealed unique sequences. Egyptian SARS-CoV-2 variants in 2020 with at least 99% identity to Wuhan-Hu-1. Egyptian SARS-CoV-2 variants were GH clade and L.GP.YP.HT haplotype. A unique mutation (D614G/Q57H/V5F/G823S) pattern was predominant among SARS-CoV-2.
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Affiliation(s)
- Badriyah Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Thanaa A. El-Masry
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | | | - Mahmoud H. Farghali
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | | | - Asmaa Saleh
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
- Department of Biochemistry, Faculty of Pharmacy, Al Azhar University, Cairo, Egypt
| | - Yasmen F. Mahran
- Department of Pharmacology & Toxicology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | | | | | | | - Maisra M. El-Bouseary
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta, Egypt
- Corresponding author.
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25
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Kuang X, Liu Z. Mining the Biomarkers and Associated-Drugs for Esophageal Squamous Cell Carcinoma by Bioinformatic Methods. TOHOKU J EXP MED 2022; 256:27-36. [PMID: 35067492 DOI: 10.1620/tjem.256.27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) showed limited treatment outcome and poor prognosis. This study aimed to screen potential biomarkers and drugs in ESCC. Firstly, GSE26886, GSE111044 and GSE77861 were downloaded from the Gene Expression Omnibus (GEO) database. Next, the differentially expressed genes (DEGs) between cancer and noncancerous tissues were analyzed by the GEO2R. The Gene Ontology (GO) annotation, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation, the protein-protein interaction (PPI) analysis and hub genes screened were conducted by some bioinformatic methods, respectively. Lastly, the hub genes and potential drugs were verified by the GEPIA2 and the QuartataWeb database. The results showed that 13 up-regulated genes and 81 down-regulated genes were identified. In GO terms, DEGs were mainly associated with cell proliferation, cell migration and cell differentiation. DEGs did not cluster into the KEGG pathway. After hub genes validated, nine genes (FLG, COL1A1, COL1A2, PSCA, SCEL, PPL, ACPP, CNFN, and A2ML1) expression trends showed no change. Moreover, higher COL1A1 or COL1A2 expression for ESCC patients showed poor prognosis. Finally, five drugs used for promoting blood coagulation were identified. Probably, these drugs could show anticancer effects by promoting blood coagulation or inhibiting vascular formation in cancers, which offers a novel idea for the treatment of ESCC.
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Affiliation(s)
- Xiuying Kuang
- The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine
| | - Zhihui Liu
- The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine
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26
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ViralFlow: A Versatile Automated Workflow for SARS-CoV-2 Genome Assembly, Lineage Assignment, Mutations and Intrahost Variant Detection. Viruses 2022; 14:v14020217. [PMID: 35215811 PMCID: PMC8877152 DOI: 10.3390/v14020217] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/30/2021] [Accepted: 01/17/2022] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic is driven by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) that emerged in 2019 and quickly spread worldwide. Genomic surveillance has become the gold standard methodology used to monitor and study this fast-spreading virus and its constantly emerging lineages. The current deluge of SARS-CoV-2 genomic data generated worldwide has put additional pressure on the urgent need for streamlined bioinformatics workflows. Here, we describe a workflow developed by our group to process and analyze large-scale SARS-CoV-2 Illumina amplicon sequencing data. This workflow automates all steps of SARS-CoV-2 reference-based genomic analysis: data processing, genome assembly, PANGO lineage assignment, mutation analysis and the screening of intrahost variants. The pipeline is capable of processing a batch of around 100 samples in less than half an hour on a personal laptop or in less than five minutes on a server with 50 threads. The workflow presented here is available through Docker or Singularity images, allowing for implementation on laptops for small-scale analyses or on high processing capacity servers or clusters. Moreover, the low requirements for memory and CPU cores and the standardized results provided by ViralFlow highlight it as a versatile tool for SARS-CoV-2 genomic analysis.
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Wegner F, Roloff T, Huber M, Cordey S, Ramette A, Gerth Y, Bertelli C, Stange M, Seth-Smith HMB, Mari A, Leuzinger K, Cerutti L, Harshman K, Xenarios I, Le Mercier P, Bittel P, Neuenschwander S, Opota O, Fuchs J, Panning M, Michel C, Hallin M, Demuyser T, De Mendonca R, Savelkoul P, Dingemans J, van der Veer B, Boers SA, Claas ECJ, Coolen JPM, Melchers WJG, Gunell M, Kallonen T, Vuorinen T, Hakanen AJ, Bernhoff E, Hetland MAK, Golan Berman H, Adar S, Moran-Gilad J, Wolf DG, Leib SL, Nolte O, Kaiser L, Schmutz S, Kufner V, Zaheri M, Trkola A, Aamot HV, Hirsch HH, Greub G, Egli A. External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories. J Clin Microbiol 2022; 60:e0169821. [PMID: 34757834 PMCID: PMC8769736 DOI: 10.1128/jcm.01698-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/05/2021] [Indexed: 12/01/2022] Open
Abstract
This first pilot trial on external quality assessment (EQA) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequencing, initiated by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic and Molecular Diagnostics (ESGMD) and the Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing. Ten samples with various viral loads were sent out to 15 clinical laboratories that had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centers were compared were the identification of (i) single nucleotide polymorphisms (SNPs) and indels, (ii) Pango lineages, and (iii) clusters between samples. The participating laboratories used a wide array of methods and analysis pipelines. Most were able to generate whole genomes for all samples. Genomes were sequenced to various depths (up to a 100-fold difference across centers). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignments. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data. The pilot EQA was overall a success. It was able to show the high quality of participating laboratories and provide valuable feedback in cases where problems occurred, thereby improving the sequencing setup of laboratories. A larger follow-up EQA should, however, improve on defining the variables and format of the report. Additionally, contamination and/or minority variants should be a further aspect of assessment.
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Affiliation(s)
- Fanny Wegner
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Tim Roloff
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, University Hospital Geneva, Geneva, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Yannick Gerth
- Center for Laboratory Medicine, Saint Gall, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Madlen Stange
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Helena M. B. Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Alfredo Mari
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Karoline Leuzinger
- Clinical Virology, University Hospital Basel, Basel, Switzerland
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | | | | | | | - Pascal Bittel
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - Onya Opota
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Jonas Fuchs
- Institute of Virology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marcus Panning
- Institute of Virology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Charlotte Michel
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles, Brussels, Belgium
| | - Marie Hallin
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles, Brussels, Belgium
| | - Thomas Demuyser
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Paul Savelkoul
- Department of Medical Microbiology, Maastricht University, Maastricht, Netherlands
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Jozef Dingemans
- Department of Medical Microbiology, Maastricht University, Maastricht, Netherlands
| | - Brian van der Veer
- Department of Medical Microbiology, Maastricht University, Maastricht, Netherlands
| | - Stefan A. Boers
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Eric C. J. Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Marianne Gunell
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Teemu Kallonen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Tytti Vuorinen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Antti J. Hakanen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Eva Bernhoff
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | | | - Hadar Golan Berman
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah University Hospital, Jerusalem, Israel
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Jacob Moran-Gilad
- School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Dana G. Wolf
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah University Hospital, Jerusalem, Israel
- Lautenberg Center for General and Tumor Immunology, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Stephen L. Leib
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Oliver Nolte
- Center for Laboratory Medicine, Saint Gall, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, University Hospital Geneva, Geneva, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Hege Vangstein Aamot
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- Department of Clinical Molecular Biology (EPIGEN), Akershus University Hospital and University of Oslo, Lørenskog, Norway
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Hans H. Hirsch
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- Infectious Diseases and Hospital Epidemiology, University of Basel, Basel, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
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Carpenter RE, Tamrakar VK, Almas S, Brown E, Sharma R. COVIDSeq as Laboratory Developed Test (LDT) for Diagnosis of SARS-CoV-2 Variants of Concern (VOC). ARCHIVES OF CLINICAL AND BIOMEDICAL RESEARCH 2022; 6:954-970. [PMID: 36588916 PMCID: PMC9802674 DOI: 10.26502/acbr.50170309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Rapid classification and detection of SARS-CoV-2 variants have been critical in comprehending the virus's transmission dynamics. Clinical manifestation of the infection is influenced by comorbidities such as age, immune status, diabetes, and the infecting variant. Thus, clinical management may differ for new variants. For example, some monoclonal antibody treatments are variant-specific. Yet, a U.S. Food and Drug Administration (FDA)-approved test for detecting the SARS-CoV-2 variant is unavailable. A laboratory-developed test (LDT) remains a viable option for reporting the infecting variant for clinical intervention or epidemiological purposes. Accordingly, we have validated the Illumina COVIDSeq assay as an LDT according to the guidelines prescribed by the College of American Pathologists (CAP) and Clinical Laboratory Improvement Amendments (CLIA). The limit of detection (LOD) of this test is Ct<30 (~15 viral copies) and >200X genomic coverage, and the test is 100% specific in the detection of existing variants. The test demonstrated 100% precision in inter-day, intra-day, and intra-laboratory reproducibility studies. It is also 100% accurate, defined by reference strain testing and split sample testing with other CLIA laboratories. Advanta Genetics LDT COVIDSeq has been reviewed by CAP inspectors and is under review by FDA for Emergency Use Authorization.
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Affiliation(s)
- Rob E Carpenter
- Advanta Genetics, 10935 CR 159, Tyler, Texas 75703, USA
- University of Texas at Tyler, 3900 University Boulevard, Tyler, Texas 75799, USA
- Scienetix, 10935 CR 159, Tyler, Texas 75703, USA
| | - Vaibhav K Tamrakar
- ICMR-National Institute of Research in Tribal Health, Jabalpur, MP 482003, INDIA
- RetroBioTech LLC, 838 Dalmalley Ln, Coppell, TX 75019, USA
| | - Sadia Almas
- Advanta Genetics, 10935 CR 159, Tyler, Texas 75703, USA
| | - Emily Brown
- Advanta Genetics, 10935 CR 159, Tyler, Texas 75703, USA
| | - Rahul Sharma
- Advanta Genetics, 10935 CR 159, Tyler, Texas 75703, USA
- RetroBioTech LLC, 838 Dalmalley Ln, Coppell, TX 75019, USA
- Scienetix, 10935 CR 159, Tyler, Texas 75703, USA
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29
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Lund AJ, Wade KJ, Nikolakis ZL, Ivey KN, Perry BW, Pike HNC, Paull SH, Liu Y, Castoe TA, Pollock DD, Carlton EJ. Integrating genomic and epidemiologic data to accelerate progress toward schistosomiasis elimination. eLife 2022; 11:79320. [PMID: 36040013 PMCID: PMC9427098 DOI: 10.7554/elife.79320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
The global community has adopted ambitious goals to eliminate schistosomiasis as a public health problem, and new tools are needed to achieve them. Mass drug administration programs, for example, have reduced the burden of schistosomiasis, but the identification of hotspots of persistent and reemergent transmission threaten progress toward elimination and underscore the need to couple treatment with interventions that reduce transmission. Recent advances in DNA sequencing technologies make whole-genome sequencing a valuable and increasingly feasible option for population-based studies of complex parasites such as schistosomes. Here, we focus on leveraging genomic data to tailor interventions to distinct social and ecological circumstances. We consider two priority questions that can be addressed by integrating epidemiological, ecological, and genomic information: (1) how often do non-human host species contribute to human schistosome infection? and (2) what is the importance of locally acquired versus imported infections in driving transmission at different stages of elimination? These questions address processes that can undermine control programs, especially those that rely heavily on treatment with praziquantel. Until recently, these questions were difficult to answer with sufficient precision to inform public health decision-making. We review the literature related to these questions and discuss how whole-genome approaches can identify the geographic and taxonomic sources of infection, and how such information can inform context-specific efforts that advance schistosomiasis control efforts and minimize the risk of reemergence.
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Affiliation(s)
- Andrea J Lund
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado AnschutzAuroraUnited States
| | - Kristen J Wade
- Department of Biochemistry & Molecular Genetics, University of Colorado School of MedicineAuroraUnited States
| | - Zachary L Nikolakis
- Department of Biology, University of Texas at ArlingtonArlingtonUnited States
| | - Kathleen N Ivey
- Department of Biology, University of Texas at ArlingtonArlingtonUnited States
| | - Blair W Perry
- Department of Biology, University of Texas at ArlingtonArlingtonUnited States
| | - Hamish NC Pike
- Department of Biochemistry & Molecular Genetics, University of Colorado School of MedicineAuroraUnited States
| | - Sara H Paull
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado AnschutzAuroraUnited States
| | - Yang Liu
- Sichuan Centers for Disease Control and PreventionChengduChina
| | - Todd A Castoe
- Department of Biology, University of Texas at ArlingtonArlingtonUnited States
| | - David D Pollock
- Department of Biochemistry & Molecular Genetics, University of Colorado School of MedicineAuroraUnited States
| | - Elizabeth J Carlton
- Department of Environmental and Occupational Health, Colorado School of Public Health, University of Colorado AnschutzAuroraUnited States
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30
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Greninger AL, Zerr DM. NGSocomial Infections: High-Resolution Views of Hospital-Acquired Infections Through Genomic Epidemiology. J Pediatric Infect Dis Soc 2021; 10:S88-S95. [PMID: 34951469 PMCID: PMC8755322 DOI: 10.1093/jpids/piab074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Hospital outbreak investigations are high-stakes epidemiology. Contacts between staff and patients are numerous; environmental and community exposures are plentiful; and patients are highly vulnerable. Having the best data is paramount to understanding an outbreak in order to stop ongoing transmission and prevent future outbreaks. In the past 5 years, the high-resolution view of transmission offered by analyzing pathogen whole-genome sequencing (WGS) is increasingly part of hospital outbreak investigations. Concerns over speed and actionability, assay validation, liability, cost, and payment models lead to further opportunities for work in this area. Now accelerated by funding for COVID-19, the use of genomics in hospital outbreak investigations has firmly moved from the academic literature to more quotidian operations, with associated concerns involving regulatory affairs, data integration, and clinical interpretation. This review details past uses of WGS data in hospital-acquired infection outbreaks as well as future opportunities to increase its utility and growth in hospital infection prevention.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, USA,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA,Corresponding Author: Alexander L. Greninger MD, PhD, MS, MPhil, 1616 Eastlake Ave East Suite 320, Seattle, WA 98102, USA. E-mail:
| | - Danielle M Zerr
- Department of Pediatrics, University of Washington Medical Center, Seattle, Washington, USA,Division of Infectious Diseases, Seattle Children’s Hospital, Seattle, Washington, USA
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31
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Development of an efficient Sanger sequencing-based assay for detecting SARS-CoV-2 spike mutations. PLoS One 2021; 16:e0260850. [PMID: 34905589 PMCID: PMC8670694 DOI: 10.1371/journal.pone.0260850] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/17/2021] [Indexed: 12/23/2022] Open
Abstract
Novel strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) harboring nucleotide changes (mutations) in the spike gene have emerged and are spreading rapidly. These mutations are associated with SARS-CoV-2 transmissibility, virulence, or resistance to some neutralizing antibodies. Thus, the accurate detection of spike mutants is crucial for controlling SARS-CoV-2 transmission and identifying neutralizing antibody-resistance caused by amino acid changes in the receptor-binding domain. Here, we developed five SARS-CoV-2 spike gene primer pairs (5-SSG primer assay; 69S, 144S, 417S, 484S, and 570S) and verified their ability to detect nine key spike mutations (ΔH69/V70, T95I, G142D, ΔY144, K417T/N, L452R, E484K/Q, N501Y, and H655Y) using a Sanger sequencing-based assay. The 5-SSG primer assay showed 100% specificity and a conservative limit of detection with a median tissue culture infective dose (TCID50) values of 1.4 × 102 TCID50/mL. The accuracy of the 5-SSG primer assay was confirmed by next generation sequencing. The results of these two approaches showed 100% consistency. Taken together, the ability of the 5-SSG primer assay to accurately detect key SARS-CoV-2 spike mutants is reliable. Thus, it is a useful tool for detecting SARS-CoV-2 spike gene mutants in a clinical setting, thereby helping to improve the management of patients with COVID-19.
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32
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Coolen JPM, Wolters F, Tostmann A, van Groningen LFJ, Bleeker-Rovers CP, Tan ECTH, van der Geest-Blankert N, Hautvast JLA, Hopman J, Wertheim HFL, Rahamat-Langendoen JC, Storch M, Melchers WJG. SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis. J Clin Virol 2021; 144:104993. [PMID: 34619382 PMCID: PMC8487099 DOI: 10.1016/j.jcv.2021.104993] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/21/2021] [Accepted: 09/29/2021] [Indexed: 12/28/2022]
Abstract
During the course of the SARS-CoV-2 pandemic reports of mutations with effects on spreading and vaccine effectiveness emerged. Large scale mutation analysis using rapid SARS-CoV-2 Whole Genome Sequencing (WGS) is often unavailable but could support public health organizations and hospitals in monitoring transmission and rising levels of mutant strains. Here we report a novel WGS technique for SARS-CoV-2, the EasySeq™ RC-PCR SARS-CoV-2 WGS kit. By applying a reverse complement polymerase chain reaction (RC-PCR), an Illumina library preparation is obtained in a single PCR, thereby saving time, resources and facilitating high-throughput screening. Using this WGS technique, we evaluated SARS-CoV-2 diversity and possible transmission within a group of 173 patients and healthcare workers (HCW) of the Radboud university medical center during 2020. Due to the emergence of variants of concern, we screened SARS-CoV-2 positive samples in 2021 for identification of mutations and lineages. With use of EasySeq™ RC-PCR SARS-CoV-2 WGS kit we were able to obtain reliable results to confirm outbreak clusters and additionally identify new previously unassociated links in a considerably easier workaround compared to current methods. Furthermore, various SARS-CoV-2 variants of interest were detected among samples and validated against an Oxford Nanopore sequencing amplicon strategy which illustrates this technique is suitable for surveillance and monitoring current circulating variants.
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Affiliation(s)
- Jordy P M Coolen
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands.
| | - Femke Wolters
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Alma Tostmann
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | | | - Chantal P Bleeker-Rovers
- Department of Internal Medicine, division of Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Edward C T H Tan
- Department of Emergency Medicine, Radboud university medical center, Nijmegen, The Netherlands; Department of Surgery, Radboud university medical center, Nijmegen, The Netherlands
| | | | | | - Joost Hopman
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Heiman F L Wertheim
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Janette C Rahamat-Langendoen
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Marko Storch
- London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 84 Wood Lane, London, W12 0BZ, United Kingdom of Great Britain and Northern Ireland, United Kingdom
| | - Willem J G Melchers
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands
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Jacot D, Pillonel T, Greub G, Bertelli C. Assessment of SARS-CoV-2 Genome Sequencing: Quality Criteria and Low-Frequency Variants. J Clin Microbiol 2021; 59:e0094421. [PMID: 34319802 PMCID: PMC8451431 DOI: 10.1128/jcm.00944-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/19/2021] [Indexed: 11/24/2022] Open
Abstract
Although many laboratories worldwide have developed their sequencing capacities in response to the need for SARS-CoV-2 genome-based surveillance of variants, only a few reported some quality criteria to ensure sequence quality before lineage assignment and submission to public databases. Hence, we aimed here to provide simple quality control criteria for SARS-CoV-2 sequencing to prevent erroneous interpretation of low-quality or contaminated data. We retrospectively investigated 647 SARS-CoV-2 genomes obtained over 10 tiled amplicons sequencing runs. We extracted 26 potentially relevant metrics covering the entire workflow from sample selection to bioinformatics analysis. Based on data distribution, critical values were established for 11 selected metrics to prompt further quality investigations for problematic samples, in particular those with a low viral RNA quantity. Low-frequency variants (<70% of supporting reads) can result from PCR amplification errors, sample cross contaminations, or presence of distinct SARS-CoV2 genomes in the sample sequenced. The number and the prevalence of low-frequency variants can be used as a robust quality criterion to identify possible sequencing errors or contaminations. Overall, we propose 11 metrics with fixed cutoff values as a simple tool to evaluate the quality of SARS-CoV-2 genomes, among which are cycle thresholds, mean depth, proportion of genome covered at least 10×, and the number of low-frequency variants combined with mutation prevalence data.
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Affiliation(s)
- Damien Jacot
- Institute of Microbiology, Laboratory of Genomics and Metagenomics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, Laboratory of Genomics and Metagenomics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Laboratory of Genomics and Metagenomics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Laboratory of Genomics and Metagenomics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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34
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The first SARS-CoV-2 genetic variants of concern (VOC) in Poland: The concept of a comprehensive approach to monitoring and surveillance of emerging variants. Adv Med Sci 2021; 66:237-245. [PMID: 33827042 DOI: 10.1016/j.advms.2021.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 01/17/2023]
Abstract
PURPOSE We analyzed the SARS-CoV-2 genome using our integrated genome analysis system and present the concept of a comprehensive approach to monitoring and surveillance of emerging variants. MATERIAL/METHODS A total of 69 SARS-CoV-2 positive samples (with Ct value ≤ 28) were tested. Samples included in this study were selected from 7 areas of eastern Poland. All samples were sequenced on an Illumina MiSeq platform using a 300-cycle MiSeq Reagent Kit v2. BWA was used for reads mapping on the reference SARS-CoV-2 sequence. SAMTools were used for post-processing of reads to genome assembly. Pango lineage and Nexstrain were used to identify variants and amino acid mutations. Statistical analysis was performed with R 4.0.2. RESULTS This study shows the first confirmed case of SARS-CoV-2 in Poland with the lineage B.1.351 (known as 501Y.V2 South African variant), as well as another 18 cases with epidemiologically relevant lineage B.1.1.7, known as British variant. Supplementary analysis of SARS-CoV-2 sequences deposited in GISAID shows that the share of a new variant can change rapidly within one month. In addition, we show a complete, integrated concept of a networked system for analyzing the variability of the SARS-CoV-2 genome, which, used in the present study, generated data and a variant report within 6 days. CONCLUSION The analyzed viral genomes showed considerable variability with simultaneous clear distinction of local clusters of genomes showing high similarity. Implementing real-time monitoring of new SARS-CoV-2 variants in Poland is urgently needed, and our developed system is available to be implemented on a large scale.
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35
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Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. PLoS One 2021; 16:e0244468. [PMID: 34432798 PMCID: PMC8386831 DOI: 10.1371/journal.pone.0244468] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 08/09/2021] [Indexed: 02/06/2023] Open
Abstract
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity among samples. Mixed allelic frequencies along the 20kb ORF1ab gene in one sample, suggested the presence of a defective viral RNA species subpopulation maintained in mixture with functional RNA in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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Affiliation(s)
- Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Sucgang
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vipin Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Erin Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Felipe-Andres Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
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Sars-CoV-2 Genome Sequencing Methods Differ In Their Ability To Detect Variants From Low Viral Load Samples. J Clin Microbiol 2021; 59:e0104621. [PMID: 34379527 PMCID: PMC8525559 DOI: 10.1128/jcm.01046-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SARS-CoV-2 genomic surveillance has been vital in understanding the spread of COVID-19, the emergence of viral escape mutants and variants of concern. However, low viral loads in clinical specimens affect variant calling for phylogenetic analyses and detection of low frequency variants, important in uncovering infection transmission chains. We systematically evaluated three widely adopted SARS-CoV-2 whole genome sequencing methods for their sensitivity, specificity, and ability to reliably detect low frequency variants. Our analyses highlight that the ARTIC v3 protocol consistently displays high sensitivity for generating complete genomes at low viral loads compared with the probe-based Illumina respiratory viral oligo panel, and a pooled long-amplicon method. We show substantial variability in the number and location of low-frequency variants detected using the three methods, highlighting the importance of selecting appropriate methods to obtain high quality sequence data from low viral load samples for public health and genomic surveillance purposes.
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Mboowa G, Mwesigwa S, Kateete D, Wayengera M, Nasinghe E, Katagirya E, Katabazi AF, Kigozi E, Kirimunda S, Kamulegeya R, Kabahita JM, Luutu MN, Nabisubi P, Kanyerezi S, Bagaya BS, Joloba ML. Whole-genome sequencing of SARS-CoV-2 in Uganda: implementation of the low-cost ARTIC protocol in resource-limited settings. F1000Res 2021; 10:598. [PMID: 34457243 PMCID: PMC8378408 DOI: 10.12688/f1000research.53567.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/18/2021] [Indexed: 12/29/2022] Open
Abstract
Background: In January 2020, a previously unknown coronavirus strain was identified as the cause of a severe acute respiratory syndrome (SARS-CoV-2). The first viral whole-genome was sequenced using high-throughput sequencing from a sample collected in Wuhan, China. Whole-genome sequencing (WGS) is imperative in investigating disease outbreak transmission dynamics and guiding decision-making in public health. Methods: We retrieved archived SARS-CoV-2 samples at the Integrated Biorepository of H3Africa Uganda, Makerere University (IBRH3AU). These samples were collected previously from individuals diagnosed with coronavirus disease 2019 (COVID-19) using real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR). 30 samples with cycle thresholds (Cts) values <25 were selected for WGS using SARS-CoV-2 ARTIC protocol at Makerere University Molecular Diagnostics Laboratory. Results: 28 out of 30 (93.3%) samples generated analyzable genomic sequence reads. We detected SARS-CoV-2 and lineages A (22/28) and B (6/28) from the samples. We further show phylogenetic relatedness of these isolates alongside other 328 Uganda (lineage A = 222, lineage B = 106) SARS-CoV-2 genomes available in GISAID by April 22, 2021 and submitted by the Uganda Virus Research Institute. Conclusions: Our study demonstrated adoption and optimization of the low-cost ARTIC SARS-CoV-2 WGS protocol in a resource limited laboratory setting. This work has set a foundation to enable rapid expansion of SARS-CoV-2 WGS in Uganda as part of the Presidential Scientific Initiative on Epidemics (PRESIDE) CoV-bank project and IBRH3AU.
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Affiliation(s)
- Gerald Mboowa
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
| | - Savannah Mwesigwa
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | - David Kateete
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | - Misaki Wayengera
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | - Emmanuel Nasinghe
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | - Eric Katagirya
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | | | - Edgar Kigozi
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | - Samuel Kirimunda
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | - Rogers Kamulegeya
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | - Jupiter Marina Kabahita
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
- The Supranational Tuberculosis Reference Laboratory, Uganda National Health Laboratories - UNHLS, Luzira, Uganda
| | | | - Patricia Nabisubi
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
| | - Stephen Kanyerezi
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
| | | | - Moses L Joloba
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
- The Supranational Tuberculosis Reference Laboratory, Uganda National Health Laboratories - UNHLS, Luzira, Uganda
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Hemida MG. The next-generation coronavirus diagnostic techniques with particular emphasis on the SARS-CoV-2. J Med Virol 2021; 93:4219-4241. [PMID: 33751621 PMCID: PMC8207115 DOI: 10.1002/jmv.26926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 12/15/2022]
Abstract
The potential zoonotic coronaviruses (SARS-CoV, MERS-CoV, and SARS-CoV-2) are of global health concerns. Early diagnosis is the milestone in their mitigation, control, and eradication. Many diagnostic techniques are showing great success and have many advantages, such as the rapid turnover of the results, high accuracy, and high specificity and sensitivity. However, some of these techniques have several pitfalls if samples were not collected, processed, and transported in the standard ways and if these techniques were not practiced with extreme caution and precision. This may lead to false-negative/positive results. This may affect the downstream management of the affected cases. These techniques require regular fine-tuning, upgrading, and optimization. The continuous evolution of new strains and viruses belong to the coronaviruses is hampering the success of many classical techniques. There are urgent needs for next generations of coronaviruses diagnostic assays that overcome these pitfalls. This new generation of diagnostic tests should be able to do simultaneous, multiplex, and high-throughput detection of various coronavirus in one reaction. Furthermore, the development of novel assays and techniques that enable the in situ detection of the virus on the environmental samples, especially air, water, and surfaces, should be given considerable attention in the future. These approaches will have a substantial positive impact on the mitigation and eradication of coronaviruses, including the current SARS-CoV-2 pandemic.
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Affiliation(s)
- Maged G. Hemida
- Department of Microbiology, College of Veterinary MedicineKing Faisal UniversityAl AhsaSaudi Arabia
- Department of Virology, Faculty of Veterinary MedicineKafrelsheikh UniversityKafr ElsheikhEgypt
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Marcolungo L, Beltrami C, Degli Esposti C, Lopatriello G, Piubelli C, Mori A, Pomari E, Deiana M, Scarso S, Bisoffi Z, Grosso V, Cosentino E, Maestri S, Lavezzari D, Iadarola B, Paterno M, Segala E, Giovannone B, Gallinaro M, Rossato M, Delledonne M. ACoRE: Accurate SARS-CoV-2 genome reconstruction for the characterization of intra-host and inter-host viral diversity in clinical samples and for the evaluation of re-infections. Genomics 2021; 113:1628-1638. [PMID: 33839270 PMCID: PMC8028595 DOI: 10.1016/j.ygeno.2021.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/26/2021] [Accepted: 04/06/2021] [Indexed: 01/04/2023]
Abstract
Sequencing the SARS-CoV-2 genome from clinical samples can be challenging, especially in specimens with low viral titer. Here we report Accurate SARS-CoV-2 genome Reconstruction (ACoRE), an amplicon-based viral genome sequencing workflow for the complete and accurate reconstruction of SARS-CoV-2 sequences from clinical samples, including suboptimal ones that would usually be excluded even if unique and irreplaceable. The protocol was optimized to improve flexibility and the combination of technical replicates was established as the central strategy to achieve accurate analysis of low-titer/suboptimal samples. We demonstrated the utility of the approach by achieving complete genome reconstruction and the identification of false-positive variants in >170 clinical samples, thus avoiding the generation of inaccurate and/or incomplete sequences. Most importantly, ACoRE was crucial to identify the correct viral strain responsible of a relapse case, that would be otherwise mis-classified as a re-infection due to missing or incorrect variant identification by a standard workflow.
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Affiliation(s)
- Luca Marcolungo
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Cristina Beltrami
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Chiara Degli Esposti
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Giulia Lopatriello
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Chiara Piubelli
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Antonio Mori
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Elena Pomari
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Michela Deiana
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Salvatore Scarso
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy
| | - Zeno Bisoffi
- Department of Infectious and Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy,Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
| | - Valentina Grosso
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Emanuela Cosentino
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Simone Maestri
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Denise Lavezzari
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Barbara Iadarola
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Marta Paterno
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Elena Segala
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Barbara Giovannone
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Martina Gallinaro
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy,Genartis srl, via IV Novembre 24, 37126 Verona, Italy
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy,Genartis srl, via IV Novembre 24, 37126 Verona, Italy,Corresponding author at: Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
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Simonetti M, Zhang N, Harbers L, Milia MG, Brossa S, Huong Nguyen TT, Cerutti F, Berrino E, Sapino A, Bienko M, Sottile A, Ghisetti V, Crosetto N. COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance. Nat Commun 2021; 12:3903. [PMID: 34162869 PMCID: PMC8222401 DOI: 10.1038/s41467-021-24078-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/01/2021] [Indexed: 11/21/2022] Open
Abstract
While mass-scale vaccination campaigns are ongoing worldwide, genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the emergence and global spread of viral variants of concern (VOC). Here, we present a streamlined workflow-COVseq-which can be used to generate highly multiplexed sequencing libraries compatible with Illumina platforms from hundreds of SARS-CoV-2 samples in parallel, in a rapid and cost-effective manner. We benchmark COVseq against a standard library preparation method (NEBNext) on 29 SARS-CoV-2 positive samples, reaching 95.4% of concordance between single-nucleotide variants detected by both methods. Application of COVseq to 245 additional SARS-CoV-2 positive samples demonstrates the ability of the method to reliably detect emergent VOC as well as its compatibility with downstream phylogenetic analyses. A cost analysis shows that COVseq could be used to sequence thousands of samples at less than 15 USD per sample, including library preparation and sequencing costs. We conclude that COVseq is a versatile and scalable method that is immediately applicable for SARS-CoV-2 genomic surveillance and easily adaptable to other pathogens such as influenza viruses.
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Affiliation(s)
- Michele Simonetti
- Bienko-Crosetto Lab for Quantitative Genome Biology, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Ning Zhang
- Bienko-Crosetto Lab for Quantitative Genome Biology, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
- Department of Breast Surgery, Qilu hospital of Shandong University, Ji'nan, China
| | - Luuk Harbers
- Bienko-Crosetto Lab for Quantitative Genome Biology, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Maria Grazia Milia
- Laboratory of Microbiology and Virology, Ospedale 'Amedeo di Savoia', Turin, Italy
| | - Silvia Brossa
- Instituto di Candiolo FPO-IRCCS, Candiolo, Turin, Italy
| | - Thi Thu Huong Nguyen
- Bienko-Crosetto Lab for Quantitative Genome Biology, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Francesco Cerutti
- Laboratory of Microbiology and Virology, Ospedale 'Amedeo di Savoia', Turin, Italy
| | - Enrico Berrino
- Instituto di Candiolo FPO-IRCCS, Candiolo, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Anna Sapino
- Instituto di Candiolo FPO-IRCCS, Candiolo, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Magda Bienko
- Bienko-Crosetto Lab for Quantitative Genome Biology, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | | | - Valeria Ghisetti
- Laboratory of Microbiology and Virology, Ospedale 'Amedeo di Savoia', Turin, Italy.
| | - Nicola Crosetto
- Bienko-Crosetto Lab for Quantitative Genome Biology, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Science for Life Laboratory, Solna, Sweden.
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Safiabadi Tali SH, LeBlanc JJ, Sadiq Z, Oyewunmi OD, Camargo C, Nikpour B, Armanfard N, Sagan SM, Jahanshahi-Anbuhi S. Tools and Techniques for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)/COVID-19 Detection. Clin Microbiol Rev 2021; 34:e00228-20. [PMID: 33980687 PMCID: PMC8142517 DOI: 10.1128/cmr.00228-20] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory disease coronavirus 2 (SARS-CoV-2), has led to millions of confirmed cases and deaths worldwide. Efficient diagnostic tools are in high demand, as rapid and large-scale testing plays a pivotal role in patient management and decelerating disease spread. This paper reviews current technologies used to detect SARS-CoV-2 in clinical laboratories as well as advances made for molecular, antigen-based, and immunological point-of-care testing, including recent developments in sensor and biosensor devices. The importance of the timing and type of specimen collection is discussed, along with factors such as disease prevalence, setting, and methods. Details of the mechanisms of action of the various methodologies are presented, along with their application span and known performance characteristics. Diagnostic imaging techniques and biomarkers are also covered, with an emphasis on their use for assessing COVID-19 or monitoring disease severity or complications. While the SARS-CoV-2 literature is rapidly evolving, this review highlights topics of interest that have occurred during the pandemic and the lessons learned throughout. Exploring a broad armamentarium of techniques for detecting SARS-CoV-2 will ensure continued diagnostic support for clinicians, public health, and infection prevention and control for this pandemic and provide advice for future pandemic preparedness.
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Affiliation(s)
- Seyed Hamid Safiabadi Tali
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
- Department of Mechanical, Industrial, and Aerospace Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
| | - Jason J LeBlanc
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Medicine (Infectious Diseases), Dalhousie University, Halifax, Nova Scotia, Canada
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada
| | - Zubi Sadiq
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
| | - Oyejide Damilola Oyewunmi
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
| | - Carolina Camargo
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Bahareh Nikpour
- Department of Electrical and Computer Engineering, McGill University, Montréal, Québec, Canada
| | - Narges Armanfard
- Department of Electrical and Computer Engineering, McGill University, Montréal, Québec, Canada
- Mila-Quebec AI Institute, Montréal, Québec, Canada
| | - Selena M Sagan
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Sana Jahanshahi-Anbuhi
- Department of Chemical and Materials Engineering, Gina Cody School of Engineering, Concordia University, Montréal, Québec, Canada
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42
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Zella D, Giovanetti M, Cella E, Borsetti A, Ciotti M, Ceccarelli G, D’Ettorre G, Pezzuto A, Tambone V, Campanozzi L, Magheri M, Unali F, Bianchi M, Benedetti F, Pascarella S, Angeletti S, Ciccozzi M. The importance of genomic analysis in cracking the coronavirus pandemic. Expert Rev Mol Diagn 2021; 21:547-562. [PMID: 33849359 PMCID: PMC8095159 DOI: 10.1080/14737159.2021.1917998] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/13/2021] [Indexed: 12/11/2022]
Abstract
Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has pushed the scientific community to undertake intense research efforts. Understanding SARS-CoV-2 biology is necessary to discover therapeutic or preventive strategies capable of containing the pandemic. Knowledge of the structural characteristics of the virus genome and proteins is essential to find targets for therapies and immunological interventions.Areas covered: This review covers different areas of expertise, genomic analysis of circulating strains, structural biology, viral mutations, molecular diagnostics, disease, and vaccines. In particular, the review is focused on the molecular approaches and modern clinical strategies used in these fields.Expert opinion: Molecular approaches to SARS-CoV-2 pandemic have been critical to shorten time for new diagnostic, therapeutic and prevention strategies. In this perspective, the entire scientific community is moving in the same direction. Vaccines, together with the development of new drugs to treat the disease, represent the most important strategy to protect human from viral disease and prevent further spread. In this regard, new molecular technologies have been successfully implemented. The use of a novel strategy of communication is suggested for a better diffusion to the broader public of new data and results.
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Affiliation(s)
- Davide Zella
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, USA
- , Member of the Global Virus Network, Baltimore, USA
| | - Marta Giovanetti
- Flavivirus Laboratory, Oswaldo Cruz Institute Oswaldo Cruz Foundation, Rio De Janeiro, Brazil
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA
| | - Alessandra Borsetti
- Department of infectious diseases, National HIV/AIDS Research Center Istituto Superiore Di Sanità, Rome, Italy
| | - Marco Ciotti
- Virology Unit, Laboratory of Clinical Microbiology and Virology, Polyclinic Tor Vergata Foundation, Rome, Italy
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Gabriella D’Ettorre
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Aldo Pezzuto
- Cardiovascular-Respiratory Science Department, Sant’ Andrea Hospital-Sapienza University, Rome, Italy
| | - Vittoradolfo Tambone
- Institute of Philosophy of Scientific and Technological Practice, Campus Bio-Medico University, Rome, Italy
| | - Laura Campanozzi
- Institute of Philosophy of Scientific and Technological Practice, Campus Bio-Medico University, Rome, Italy
| | - Marco Magheri
- Communication Division, University Campus Bio-Medico of Rome, Rome, Italy
| | - Francesco Unali
- Communication Division, University Campus Bio-Medico of Rome, Rome, Italy
| | - Martina Bianchi
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome “La Sapienza”, Rome, Italy
| | - Francesca Benedetti
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, USA
| | - Stefano Pascarella
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome “La Sapienza”, Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
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Li P, Wang L, Yang J, Di LJ, Li J. Applications of the CRISPR-Cas system for infectious disease diagnostics. Expert Rev Mol Diagn 2021; 21:723-732. [PMID: 33899643 DOI: 10.1080/14737159.2021.1922080] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Rapid and accurate diagnostic approaches are essential for impeding the spread of infectious diseases. This review aims to summarize current progress of clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) systems in the applications for diagnostics of infectious diseases including the ongoing COVID-19 epidemic. AREAS COVERED In this review, we discuss class 2 CRISPR-Cas biosensing systems-based diagnostics in various emerging and reemerging infectious diseases, CRISPR-Cas systems have created a new era for early diagnostics of infectious diseases, especially with the discovery of the collateral cleavage activity of Cas12 and Cas13. We mainly focus on different CRISPR-Cas effectors for the detection of pathogenic microorganisms as well as provide a detailed explanation of the pros and cons of CRISPR-Cas biosensing systems. In addition, we also introduce future research perspectives. EXPERT COMMENTARY However, further improvement of newly discovered systems and engineering existing ones should be developed to increase the specificity, sensitivity or stability of the diagnostic tools. It may be a long journey to finish the clinical transition from research use. CRISPR-Cas approaches will emerge as more promising and robust tools for infectious disease diagnosis in the future.
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Affiliation(s)
- Peipei Li
- Kobilka Institute of Innovative Drug Discovery, Faculty of Life and Health Sciences, the Chinese University of Hong Kong, Shenzhen, Guangdong, China.,Cancer Center, Faculty of Health Sciences, University of Macau, China
| | - Li Wang
- Metabolomics Core, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Junning Yang
- Frontage Laboratories Inc, Exton, Pennsylvania, USA
| | - Li-Jun Di
- Cancer Center, Faculty of Health Sciences, University of Macau, China
| | - Jingjing Li
- Jinming Yu Academician Workstation of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China.,Cancer Center, Faculty of Health Sciences, University of Macau, China
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Cavanaugh AM, Fortier S, Lewis P, Arora V, Johnson M, George K, Tobias J, Lunn S, Miller T, Thoroughman D, Spicer KB. COVID-19 Outbreak Associated with a SARS-CoV-2 R.1 Lineage Variant in a Skilled Nursing Facility After Vaccination Program - Kentucky, March 2021. MMWR. MORBIDITY AND MORTALITY WEEKLY REPORT 2021; 70:639-643. [PMID: 33914720 PMCID: PMC8084128 DOI: 10.15585/mmwr.mm7017e2] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Although COVID-19 mRNA vaccines demonstrated high efficacy in clinical trials (1), they were not 100% efficacious. Thus, some infections postvaccination are expected. Limited data are available on effectiveness in skilled nursing facilities (SNFs) and against emerging variants. The Kentucky Department for Public Health (KDPH) and a local health department investigated a COVID-19 outbreak in a SNF that occurred after all residents and health care personnel (HCP) had been offered vaccination. Among 83 residents and 116 HCP, 75 (90.4%) and 61 (52.6%), respectively, received 2 vaccine doses. Twenty-six residents and 20 HCP received positive test results for SARS-CoV-2, the virus that causes COVID-19, including 18 residents and four HCP who had received their second vaccine dose >14 days before the outbreak began. An R.1 lineage variant was detected with whole genome sequencing (WGS). Although the R.1 variant has multiple spike protein mutations, vaccinated residents and HCP were 87% less likely to have symptomatic COVID-19 compared with those who were unvaccinated. Vaccination of SNF populations, including HCP, is critical to reduce the risk for SARS-CoV-2 introduction, transmission, and severe outcomes in SNFs. An ongoing focus on infection prevention and control practices is also essential.
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Engelbrecht S, Delaney K, Kleinhans B, Wilkinson E, Tegally H, Stander T, van Zyl G, Preiser W, de Oliveira T. Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa. Viruses 2021; 13:v13030526. [PMID: 33810168 PMCID: PMC8005015 DOI: 10.3390/v13030526] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/10/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Cape Town was the first city in South Africa to experience the full impact of the coronavirus disease 2019 (COVID-19) pandemic. We acquired samples from all suspected cases and their contacts during the first month of the pandemic from Tygerberg Hospital. Nanopore sequencing generated SARS-CoV-2 whole genomes. Phylogenetic inference with maximum likelihood and Bayesian methods were used to determine lineages that seeded the local epidemic. Three patients were known to have travelled internationally and an outbreak was detected in a nearby supermarket. Sequencing of 50 samples produced 46 high-quality genomes. The sequences were classified as lineages: B, B.1, B.1.1.1, B.1.1.161, B.1.1.29, B.1.8, B.39, and B.40. All the sequences from persons under investigation (PUIs) in the supermarket outbreak (lineage B.1.8) fall within a clade from the Netherlands with good support (p > 0.9). In addition, a new mutation, 5209A>G, emerged within the Cape Town cluster. The molecular clock analysis suggests that this occurred around 13 March 2020 (95% confidence interval: 9-17 March). The phylogenetic reconstruction suggests at least nine early introductions of SARS-CoV-2 into Cape Town and an early localized transmission in a shopping environment. Genomic surveillance was successfully used to investigate and track the spread of early introductions of SARS-CoV-2 in Cape Town.
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Affiliation(s)
- Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa; (K.D.); (B.K.); (G.v.Z.); (W.P.)
- Tygerberg Business Unit, National Health Laboratory Service (NHLS), Cape Town 8000, South Africa;
- Correspondence: (S.E.); (T.d.O.); Tel.: +27-21-9389357 (S.E.)
| | - Kayla Delaney
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa; (K.D.); (B.K.); (G.v.Z.); (W.P.)
| | - Bronwyn Kleinhans
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa; (K.D.); (B.K.); (G.v.Z.); (W.P.)
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (E.W.); (H.T.)
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (E.W.); (H.T.)
| | - Tania Stander
- Tygerberg Business Unit, National Health Laboratory Service (NHLS), Cape Town 8000, South Africa;
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa; (K.D.); (B.K.); (G.v.Z.); (W.P.)
- Tygerberg Business Unit, National Health Laboratory Service (NHLS), Cape Town 8000, South Africa;
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa; (K.D.); (B.K.); (G.v.Z.); (W.P.)
- Tygerberg Business Unit, National Health Laboratory Service (NHLS), Cape Town 8000, South Africa;
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (E.W.); (H.T.)
- Centre for Aids Programme of Research in South Africa (CAPRISA), Durban 4000, South Africa
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Correspondence: (S.E.); (T.d.O.); Tel.: +27-21-9389357 (S.E.)
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Chiara M, D’Erchia AM, Gissi C, Manzari C, Parisi A, Resta N, Zambelli F, Picardi E, Pavesi G, Horner DS, Pesole G. Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. Brief Bioinform 2021; 22:616-630. [PMID: 33279989 PMCID: PMC7799330 DOI: 10.1093/bib/bbaa297] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/27/2020] [Accepted: 10/07/2020] [Indexed: 12/31/2022] Open
Abstract
Various next generation sequencing (NGS) based strategies have been successfully used in the recent past for tracing origins and understanding the evolution of infectious agents, investigating the spread and transmission chains of outbreaks, as well as facilitating the development of effective and rapid molecular diagnostic tests and contributing to the hunt for treatments and vaccines. The ongoing COVID-19 pandemic poses one of the greatest global threats in modern history and has already caused severe social and economic costs. The development of efficient and rapid sequencing methods to reconstruct the genomic sequence of SARS-CoV-2, the etiological agent of COVID-19, has been fundamental for the design of diagnostic molecular tests and to devise effective measures and strategies to mitigate the diffusion of the pandemic. Diverse approaches and sequencing methods can, as testified by the number of available sequences, be applied to SARS-CoV-2 genomes. However, each technology and sequencing approach has its own advantages and limitations. In the current review, we will provide a brief, but hopefully comprehensive, account of currently available platforms and methodological approaches for the sequencing of SARS-CoV-2 genomes. We also present an outline of current repositories and databases that provide access to SARS-CoV-2 genomic data and associated metadata. Finally, we offer general advice and guidelines for the appropriate sharing and deposition of SARS-CoV-2 data and metadata, and suggest that more efficient and standardized integration of current and future SARS-CoV-2-related data would greatly facilitate the struggle against this new pathogen. We hope that our 'vademecum' for the production and handling of SARS-CoV-2-related sequencing data, will contribute to this objective.
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Affiliation(s)
- Matteo Chiara
- molecular biology and bioinformatics at the University of Milan
| | - Anna Maria D’Erchia
- molecular biology at the University of Bari and research associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
| | - Carmela Gissi
- molecular biology at the University of Bari and research associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
| | - Caterina Manzari
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
| | - Antonio Parisi
- Genetic and Molecular Epidemiology Laboratory at the Experimental Zooprophylactic Institute of Apulia and Basilicata
| | - Nicoletta Resta
- Medical Genetics at the University of Bari. She heads the Laboratory Unit of Medical Genetics and the School of Specialization in Medical Genetics
| | | | - Ernesto Picardi
- molecular biology and bioinformatics at the University of Bari and research associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
| | - Giulio Pavesi
- Associate Professor of bioinformatics at the University of Milan (Italy)
| | - David S Horner
- molecular biology and bioinformatics at the University of Milan
| | - Graziano Pesole
- molecular biology at the University of Bari and Research Associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
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Moyo-Gwete T, Madzivhandila M, Makhado Z, Ayres F, Mhlanga D, Oosthuysen B, Lambson BE, Kgagudi P, Tegally H, Iranzadeh A, Doolabh D, Tyers L, Chinhoyi LR, Mennen M, Skelem S, Marais G, Wibmer CK, Bhiman JN, Ueckermann V, Rossouw T, Boswell M, de Oliveira T, Williamson C, Burgers WA, Ntusi N, Morris L, Moore PL. SARS-CoV-2 501Y.V2 (B.1.351) elicits cross-reactive neutralizing antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.06.434193. [PMID: 33688657 PMCID: PMC7941631 DOI: 10.1101/2021.03.06.434193] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Neutralization escape by SARS-CoV-2 variants, as has been observed in the 501Y.V2 (B.1.351) variant, has impacted the efficacy of first generation COVID-19 vaccines. Here, the antibody response to the 501Y.V2 variant was examined in a cohort of patients hospitalized with COVID-19 in early 2021 - when over 90% of infections in South Africa were attributed to 501Y.V2. Robust binding and neutralizing antibody titers to the 501Y.V2 variant were detected and these binding antibodies showed high levels of cross-reactivity for the original variant, from the first wave. In contrast to an earlier study where sera from individuals infected with the original variant showed dramatically reduced potency against 501Y.V2, sera from 501Y.V2-infected patients maintained good cross-reactivity against viruses from the first wave. Furthermore, sera from 501Y.V2-infected patients also neutralized the 501Y.V3 (P.1) variant first described in Brazil, and now circulating globally. Collectively these data suggest that the antibody response in patients infected with 501Y.V2 has a broad specificity and that vaccines designed with the 501Y.V2 sequence may elicit more cross-reactive responses.
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Affiliation(s)
- Thandeka Moyo-Gwete
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mashudu Madzivhandila
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Zanele Makhado
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Frances Ayres
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Donald Mhlanga
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Brent Oosthuysen
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Bronwen E. Lambson
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Prudence Kgagudi
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Arash Iranzadeh
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Deelan Doolabh
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Lynn Tyers
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Lionel R. Chinhoyi
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
- Division of Cardiology, Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Hatter Institute for Cardiovascular Research in Africa, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mathilda Mennen
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
- Division of Cardiology, Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Hatter Institute for Cardiovascular Research in Africa, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Sango Skelem
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
- Division of Cardiology, Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Hatter Institute for Cardiovascular Research in Africa, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gert Marais
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Services, Groote Schuur Hospital, Cape Town, South Africa
| | - Constantinos Kurt Wibmer
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jinal N Bhiman
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Virology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Veronica Ueckermann
- Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa
| | - Theresa Rossouw
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Michael Boswell
- Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, 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, USA
| | - Carolyn Williamson
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Services, Groote Schuur Hospital, Cape Town, South Africa
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
| | - Ntobeko Ntusi
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
- Division of Cardiology, Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Hatter Institute for Cardiovascular Research in Africa, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lynn Morris
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Penny L Moore
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
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48
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Detection of a SARS-CoV-2 variant of concern in South Africa. Nature 2021; 592:438-443. [PMID: 33690265 DOI: 10.1038/s41586-021-03402-9] [Citation(s) in RCA: 1068] [Impact Index Per Article: 356.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/26/2021] [Indexed: 12/15/2022]
Abstract
Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus1,2. Here we describe a newly arisen lineage of SARS-CoV-2 (designated 501Y.V2; also known as B.1.351 or 20H) that is defined by eight mutations in the spike protein, including three substitutions (K417N, E484K and N501Y) at residues in its receptor-binding domain that may have functional importance3-5. This lineage was identified in South Africa after the first wave of the epidemic in a severely affected metropolitan area (Nelson Mandela Bay) that is located on the coast of the Eastern Cape province. This lineage spread rapidly, and became dominant in Eastern Cape, Western Cape and KwaZulu-Natal provinces within weeks. Although the full import of the mutations is yet to be determined, the genomic data-which show rapid expansion and displacement of other lineages in several regions-suggest that this lineage is associated with a selection advantage that most plausibly results from increased transmissibility or immune escape6-8.
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Izzedine H, Jhaveri KD, Perazella MA. Genes, COVID-19 and phenotype. Clin Kidney J 2021; 14:1485-1487. [PMID: 34221375 PMCID: PMC7928999 DOI: 10.1093/ckj/sfab044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 02/11/2021] [Indexed: 12/02/2022] Open
Affiliation(s)
- Hassan Izzedine
- Department of Nephrology, Peupliers Private Hospital, Ramsay Générale de Santé, Paris, France
| | - Kenar D Jhaveri
- Department of Medicine, Donald and Barbara School of Medicine at Hofstra/Northwell, Northwell Health, Great Neck, NY, USA
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50
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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] [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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