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Sow MS, Togo J, Simons LM, Diallo ST, Magassouba ML, Keita MB, Somboro AM, Coulibaly Y, Ozer EA, Hultquist JF, Murphy RL, Maiga AI, Maiga M, Lorenzo-Redondo R. Genomic characterization of SARS-CoV-2 in Guinea, West Africa. PLoS One 2024; 19:e0299082. [PMID: 38446806 PMCID: PMC10917296 DOI: 10.1371/journal.pone.0299082] [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: 08/28/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024] Open
Abstract
SARS-CoV-2 has claimed several million lives since its emergence in late 2019. The ongoing evolution of the virus has resulted in the periodic emergence of new viral variants with distinct fitness advantages, including enhanced transmission and immune escape. While several SARS-CoV-2 variants of concern trace their origins back to the African continent-including Beta, Eta, and Omicron-most countries in Africa remain under-sampled in global genomic surveillance efforts. In an effort to begin filling these knowledge gaps, we conducted retrospective viral genomic surveillance in Guinea from October 2020 to August 2021. We found that SARS-CoV-2 clades 20A, 20B, and 20C dominated throughout 2020 until the coincident emergence of the Alpha and Eta variants of concern in January 2021. The Alpha variant remained dominant throughout early 2021 until the arrival of the Delta variant in July. Surprisingly, despite the small sample size of our study, we also found the persistence of the early SARS-CoV-2 clade 19B as late as April 2021. Together, these data help fill in our understanding of the SARS-CoV-2 population dynamics in West Africa early in the COVID-19 pandemic.
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Affiliation(s)
- Mamadou Saliou Sow
- Service de Maladie Infectieuse du Centre Hospitalier de Donka, Conakry, Guinée
| | - Josue Togo
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
- Département de Biologie médicale, Centre Hospitalier Universitaire Gabriel Toure, Bamako, Mali
| | - Lacy M. Simons
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, United States of America
| | | | | | - Mamadou Bhoye Keita
- Département de laboratoire, Institut National de la Santé Publique, Conakry, Guinée
- Département de biologie, Université Gamal Abdel Nasser de Conakry, Conakry, Guinée
| | - Anou Moise Somboro
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Youssouf Coulibaly
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Egon A. Ozer
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, United States of America
| | - Judd F. Hultquist
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, United States of America
| | - Robert Leo Murphy
- Institute for Global Health, Northwestern University, Chicago, IL, United States of America
| | - Almoustapha Issiaka Maiga
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
- Département de Biologie médicale, Centre Hospitalier Universitaire Gabriel Toure, Bamako, Mali
| | - Mamoudou Maiga
- Institute for Global Health, Northwestern University, Chicago, IL, United States of America
| | - Ramon Lorenzo-Redondo
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States of America
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL, United States of America
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Fokam J, Essomba RG, Njouom R, Okomo MCA, Eyangoh S, Godwe C, Tegomoh B, Otshudiema JO, Nwobegahay J, Ndip L, Akenji B, Takou D, Moctar MMM, Mbah CK, Ndze VN, Maidadi-Foudi M, Kouanfack C, Tonmeu S, Ngono D, Nkengasong J, Ndembi N, Bissek ACZK, Mouangue C, Ndongo CB, Epée E, Mandeng N, Kamso Belinga S, Ayouba A, Fernandez N, Tongo M, Colizzi V, Halle-Ekane GE, Perno CF, Ndjolo A, Ndongmo CB, Shang J, Esso L, de-Tulio O, Diagne MM, Boum Y, Mballa GAE, Njock LR. Genomic surveillance of SARS-CoV-2 reveals highest severity and mortality of delta over other variants: evidence from Cameroon. Sci Rep 2023; 13:21654. [PMID: 38066020 PMCID: PMC10709425 DOI: 10.1038/s41598-023-48773-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
While the SARS-CoV-2 dynamic has been described globally, there is a lack of data from Sub-Saharan Africa. We herein report the dynamics of SARS-CoV-2 lineages from March 2020 to March 2022 in Cameroon. Of the 760 whole-genome sequences successfully generated by the national genomic surveillance network, 74% were viral sub-lineages of origin and non-variants of concern, 15% Delta, 6% Omicron, 3% Alpha and 2% Beta variants. The pandemic was driven by SARS-CoV-2 lineages of origin in wave 1 (16 weeks, 2.3% CFR), the Alpha and Beta variants in wave 2 (21 weeks, 1.6% CFR), Delta variants in wave 3 (11 weeks, 2.0% CFR), and omicron variants in wave 4 (8 weeks, 0.73% CFR), with a declining trend over time (p = 0.01208). Even though SARS-CoV-2 heterogeneity did not seemingly contribute to the breadth of transmission, the viral lineages of origin and especially the Delta variants appeared as drivers of COVID-19 severity in Cameroon.
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Affiliation(s)
- Joseph Fokam
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health, Yaoundé, Cameroon.
- COVID-19 Genomic Surveillance Platform (PSG), Ministry of Public Health, Yaoundé, Cameroon.
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon.
- Faculty of Health Sciences (FHS), University of Buea, Buea, Cameroon.
| | - Rene Ghislain Essomba
- COVID-19 Genomic Surveillance Platform (PSG), Ministry of Public Health, Yaoundé, Cameroon
- National Public Health Laboratory (NPHL), Ministry of Public Health, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences (FMBS), University of Yaounde I, Yaounde, Cameroon
| | - Richard Njouom
- COVID-19 Genomic Surveillance Platform (PSG), Ministry of Public Health, Yaoundé, Cameroon
- Centre Pasteur du Cameroun (CPC), Yaoundé, Cameroon
| | - Marie-Claire A Okomo
- COVID-19 Genomic Surveillance Platform (PSG), Ministry of Public Health, Yaoundé, Cameroon
- National Public Health Laboratory (NPHL), Ministry of Public Health, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences (FMBS), University of Yaounde I, Yaounde, Cameroon
| | - Sara Eyangoh
- COVID-19 Genomic Surveillance Platform (PSG), Ministry of Public Health, Yaoundé, Cameroon
- Centre Pasteur du Cameroun (CPC), Yaoundé, Cameroon
| | - Celestin Godwe
- Centre de Recherche en Maladies Emergentes et Re-emergentes (CREMER), Yaounde, Cameroon
| | - Bryan Tegomoh
- School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - John O Otshudiema
- World Health Organization (WHO), Cameroon Country Office, Yaounde, Cameroon
| | - Julius Nwobegahay
- COVID-19 Genomic Surveillance Platform (PSG), Ministry of Public Health, Yaoundé, Cameroon
- Centre de Recherche Pour la Santé des Armées (CRESAR), Ministry of Defence, Yaoundé, Cameroon
| | - Lucy Ndip
- Faculty of Health Sciences (FHS), University of Buea, Buea, Cameroon
| | - Blaise Akenji
- National Public Health Laboratory (NPHL), Ministry of Public Health, Yaoundé, Cameroon
| | - Desire Takou
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Mohamed M M Moctar
- USAID's Infectious Diseases Detection and Surveillance, Yaounde, Cameroon
| | | | - Valantine Ngum Ndze
- Faculty of Health Sciences (FHS), University of Buea, Buea, Cameroon
- African Society for Laboratory Medicine (ASLM), Yaounde, Cameroon
| | - Martin Maidadi-Foudi
- Centre de Recherche en Maladies Emergentes et Re-emergentes (CREMER), Yaounde, Cameroon
| | - Charles Kouanfack
- Centre de Recherche en Maladies Emergentes et Re-emergentes (CREMER), Yaounde, Cameroon
| | - Sandrine Tonmeu
- National Public Health Laboratory (NPHL), Ministry of Public Health, Yaoundé, Cameroon
| | - Dorine Ngono
- School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - John Nkengasong
- Africa Centres for Disease Control and Prevention (Africa CDC), Addis-Ababa, Ethiopia
| | - Nicaise Ndembi
- Africa Centres for Disease Control and Prevention (Africa CDC), Addis-Ababa, Ethiopia
| | - Anne-Cecile Z K Bissek
- Faculty of Health Sciences (FHS), University of Buea, Buea, Cameroon
- Division for Operational Health Research (DROS), Ministry of Public Health, Yaoundé, Cameroon
| | - Christian Mouangue
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health, Yaoundé, Cameroon
- Department of Disease, Epidemic and Pandemic Control (DLMEP), Ministry of Public Health, Yaounde, Cameroon
| | - Chanceline B Ndongo
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health, Yaoundé, Cameroon
- Department of Disease, Epidemic and Pandemic Control (DLMEP), Ministry of Public Health, Yaounde, Cameroon
- Faculty of Medicine and Pharmaceutical Sciences (FMPS), University of Douala, Douala, Cameroon
| | - Emilienne Epée
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences (FMBS), University of Yaounde I, Yaounde, Cameroon
- Department of Disease, Epidemic and Pandemic Control (DLMEP), Ministry of Public Health, Yaounde, Cameroon
| | - Nadia Mandeng
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health, Yaoundé, Cameroon
- Department of Disease, Epidemic and Pandemic Control (DLMEP), Ministry of Public Health, Yaounde, Cameroon
- Faculty of Health Sciences (FHS), University of Bamenda, Bamenda, Cameroon
| | - Sandrine Kamso Belinga
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health, Yaoundé, Cameroon
- Department of Disease, Epidemic and Pandemic Control (DLMEP), Ministry of Public Health, Yaounde, Cameroon
| | - Ahidjo Ayouba
- Institut de Recherche Pour le Developpement (IRD), Montpellier, France
| | - Nicolas Fernandez
- Institut de Recherche Pour le Developpement (IRD), Montpellier, France
| | - Marcel Tongo
- Centre de Recherche en Maladies Emergentes et Re-emergentes (CREMER), Yaounde, Cameroon
| | - Vittorio Colizzi
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
- Chair of UNESCO Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | | | - Carlo-Federico Perno
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
- Bambino Gesu Pediatric Hospital, Rome, Italy
| | - Alexis Ndjolo
- Chantal BIYA International Reference Centre for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences (FMBS), University of Yaounde I, Yaounde, Cameroon
| | - Clement B Ndongmo
- US Centres for Disease Control and Prevention (CDC), Cameroon Country Office, Yaounde, Cameroon
| | - Judith Shang
- US Centres for Disease Control and Prevention (CDC), Cameroon Country Office, Yaounde, Cameroon.
| | - Linda Esso
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health, Yaoundé, Cameroon
- Department of Disease, Epidemic and Pandemic Control (DLMEP), Ministry of Public Health, Yaounde, Cameroon
| | - Oliviera de-Tulio
- University of KwaZulu-Natal and Stellenbosch University, Stellenbosch, South Africa
| | | | - Yap Boum
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences (FMBS), University of Yaounde I, Yaounde, Cameroon
- Epicentre, Medecins Sans Frontières (MSF), Yaounde, Cameroon
| | - Georges A E Mballa
- National Public Health Emergencies Operations Coordination Centre (NPHEOCC), Ministry of Public Health, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences (FMBS), University of Yaounde I, Yaounde, Cameroon
- Department of Disease, Epidemic and Pandemic Control (DLMEP), Ministry of Public Health, Yaounde, Cameroon
| | - Louis R Njock
- COVID-19 Genomic Surveillance Platform (PSG), Ministry of Public Health, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences (FMBS), University of Yaounde I, Yaounde, Cameroon
- Faculty of Medicine and Pharmaceutical Sciences (FMPS), University of Douala, Douala, Cameroon
- General Secretariat, Ministry of Public Health, Yaounde, Cameroon
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3
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Gonzalez-Reiche AS. SARS-CoV-2 in low-income countries: the need for sustained genomic surveillance. Lancet Glob Health 2023; 11:e815-e816. [PMID: 37202013 DOI: 10.1016/s2214-109x(23)00197-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 04/13/2023] [Indexed: 05/20/2023]
Affiliation(s)
- Ana S Gonzalez-Reiche
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Martínez-Martínez FJ, Massinga AJ, De Jesus Á, Ernesto RM, Cano-Jiménez P, Chiner-Oms Á, Gómez-Navarro I, Guillot-Fernández M, Guinovart C, Sitoe A, Vubil D, Bila R, Gujamo R, Enosse S, Jiménez-Serrano S, Torres-Puente M, Comas I, Mandomando I, López MG, Mayor A. Tracking SARS-CoV-2 introductions in Mozambique using pandemic-scale phylogenies: a retrospective observational study. Lancet Glob Health 2023; 11:e933-e941. [PMID: 37202028 DOI: 10.1016/s2214-109x(23)00169-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/09/2023] [Accepted: 03/23/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND From the start of the SARS-CoV-2 outbreak, global sequencing efforts have generated an unprecedented amount of genomic data. Nonetheless, unequal sampling between high-income and low-income countries hinders the implementation of genomic surveillance systems at the global and local level. Filling the knowledge gaps of genomic information and understanding pandemic dynamics in low-income countries is essential for public health decision making and to prepare for future pandemics. In this context, we aimed to discover the timing and origin of SARS-CoV-2 variant introductions in Mozambique, taking advantage of pandemic-scale phylogenies. METHODS We did a retrospective, observational study in southern Mozambique. Patients from Manhiça presenting with respiratory symptoms were recruited, and those enrolled in clinical trials were excluded. Data were included from three sources: (1) a prospective hospital-based surveillance study (MozCOVID), recruiting patients living in Manhiça, attending the Manhiça district hospital, and fulfilling the criteria of suspected COVID-19 case according to WHO; (2) symptomatic and asymptomatic individuals with SARS-CoV-2 infection recruited by the National Surveillance system; and (3) sequences from SARS-CoV-2-infected Mozambican cases deposited on the Global Initiative on Sharing Avian Influenza Data database. Positive samples amenable for sequencing were analysed. We used Ultrafast Sample placement on Existing tRees to understand the dynamics of beta and delta waves, using available genomic data. This tool can reconstruct a phylogeny with millions of sequences by efficient sample placement in a tree. We reconstructed a phylogeny (~7·6 million sequences) adding new and publicly available beta and delta sequences. FINDINGS A total of 5793 patients were recruited between Nov 1, 2020, and Aug 31, 2021. During this time, 133 328 COVID-19 cases were reported in Mozambique. 280 good quality new SARS-CoV-2 sequences were obtained after the inclusion criteria were applied and an additional 652 beta (B.1.351) and delta (B.1.617.2) public sequences were included from Mozambique. We evaluated 373 beta and 559 delta sequences. We identified 187 beta introductions (including 295 sequences), divided in 42 transmission groups and 145 unique introductions, mostly from South Africa, between August, 2020 and July, 2021. For delta, we identified 220 introductions (including 494 sequences), with 49 transmission groups and 171 unique introductions, mostly from the UK, India, and South Africa, between April and November, 2021. INTERPRETATION The timing and origin of introductions suggests that movement restrictions effectively avoided introductions from non-African countries, but not from surrounding countries. Our results raise questions about the imbalance between the consequences of restrictions and health benefits. This new understanding of pandemic dynamics in Mozambique can be used to inform public health interventions to control the spread of new variants. FUNDING European and Developing Countries Clinical Trials, European Research Council, Bill & Melinda Gates Foundation, and Agència de Gestió d'Ajuts Universitaris i de Recerca.
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Affiliation(s)
- Francisco José Martínez-Martínez
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | | | - Áuria De Jesus
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
| | - Rita M Ernesto
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
| | - Pablo Cano-Jiménez
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Álvaro Chiner-Oms
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Inmaculada Gómez-Navarro
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Marina Guillot-Fernández
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | | | - António Sitoe
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
| | - Delfino Vubil
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
| | - Rubão Bila
- Hospital Distrital da Manhiça, Marracuene, Mozambique
| | | | - Sónia Enosse
- Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Santiago Jiménez-Serrano
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Manuela Torres-Puente
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Iñaki Comas
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Inácio Mandomando
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique; Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Mariana G López
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain.
| | - Alfredo Mayor
- Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique; ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Department of Physiologic Sciences, Faculty of Medicine, Universidade Eduardo Mondlane, Maputo, Mozambique
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Christoffels A, Mboowa G, van Heusden P, Makhubela S, Githinji G, Mwangi S, Onywera H, Nnaemeka N, Amoako DG, Olawoye I, Diallo A, Mbala-Kingebeni P, Oyola SO, Adu B, Mvelase C, Ondoa P, Dratibi FA, Sow A, Gumede N, Tessema SK, Ouma AO, Tebeje YK. A pan-African pathogen genomics data sharing platform to support disease outbreaks. Nat Med 2023; 29:1052-1055. [PMID: 37161068 DOI: 10.1038/s41591-023-02266-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Alan Christoffels
- Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia.
- South African National Bioinformatics Institute, SAMRC Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa.
| | - Gerald Mboowa
- Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia
| | - Peter van Heusden
- South African National Bioinformatics Institute, SAMRC Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa
| | | | - George Githinji
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Sarah Mwangi
- Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia
| | - Harris Onywera
- Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia
| | | | - Daniel Gyamfi Amoako
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- College of Health Sciences, University of KwaZulu Natal, Durban, South Africa
| | - Idowu Olawoye
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | | | - Placide Mbala-Kingebeni
- Institut National de Recherche Biomédicale, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Samuel O Oyola
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Bright Adu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | | | - Pascale Ondoa
- African Society for Laboratory Medicine (ASLM), Addis Ababa, Ethiopia
| | | | | | - Nicksy Gumede
- WHO Regional Office for Africa, Brazzaville, Republic of Congo
| | - Sofonias K Tessema
- Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia.
| | - Ahmed Ogwell Ouma
- Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia
| | - Yenew Kebede Tebeje
- Africa Centres for Disease Control and Prevention (Africa CDC), African Union Commission, Addis Ababa, Ethiopia
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Grant DS, Samuels RJ, Garry RF, Schieffelin JS. Lassa Fever Natural History and Clinical Management. Curr Top Microbiol Immunol 2023. [PMID: 37106159 DOI: 10.1007/82_2023_263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Lassa fever is caused by Lassa virus (LASV), an Old World Mammarenavirus that is carried by Mastomys natalensis and other rodents. It is endemic in Sierra Leone, Nigeria, and other countries in West Africa. The clinical presentation of LASV infection is heterogenous varying from an inapparent or mild illness to a fatal hemorrhagic fever. Exposure to LASV is usually through contact with rodent excreta. After an incubation period of 1-3 weeks, initial symptoms such as fever, headache, and fatigue develop that may progress to sore throat, retrosternal chest pain, conjunctival injection, vomiting, diarrhea, and abdominal pain. Severe illness, including hypotension, shock, and multiorgan failure, develops in a minority of patients. Patient demographics and case fatality rates are distinctly different in Sierra Leone and Nigeria. Laboratory diagnosis relies on the detection of LASV antigens or genomic RNA. LASV-specific immunoglobulin G and M assays can also contribute to clinical management. The mainstay of treatment for Lassa fever is supportive care. The nucleoside analog ribavirin is commonly used to treat acute Lassa fever but is considered useful only if treatment is begun early in the disease course. Drugs in development, including a monoclonal antibody cocktail, have the potential to impact the management of Lassa fever.
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Affiliation(s)
- Donald S Grant
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health, Kenema, Sierra Leone
- College of Medicine and Allied Health Sciences (COMAHS), University of Sierra Leone, Freetown, Sierra Leone
| | - Robert J Samuels
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health, Kenema, Sierra Leone
| | - Robert F Garry
- School of Medicine, Department of Microbiology and Immunology, Tulane University, New Orleans, LA, 70112, USA
- Zalgen Labs, Frederick, MD, 21703, USA
- Global Virus Network (GVN), Baltimore, MD, 21201, USA
| | - John S Schieffelin
- School of Medicine, Department of Pediatrics, Tulane University, New Orleans, LA, 70112, USA.
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Paz M, Moreno P, Moratorio G. Perspective Chapter: Real-Time Genomic Surveillance for SARS-CoV-2 on Center Stage. Infect Dis (Lond) 2023. [DOI: 10.5772/intechopen.107842] [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] [Indexed: 03/30/2023] Open
Abstract
The course of the COVID-19 pandemic depends not only on how the SARS-CoV-2 virus mutates but on the actions taken to respond to it. Important public health decisions can only be taken if we know viral dynamics, viral variants distribution, and whether new variants are emerging that may be more transmissible or/and more virulent, displaying evasion to vaccines or antiviral treatments. This situation has put the use of different approaches, such as molecular techniques and real-time genomic sequencing, to support public health decision-making on center stage. To achieve this, robust programs based on: (i) diagnostic capacity; (ii) high-throughput sequencing technologies; and (iii) high-performance bioinformatic resources, need to be established. This chapter focuses on how SARS-CoV-2 evolved since its discovery and it summarizes the scientific efforts to obtain genomic data as the virus spread throughout the globe.
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Chikomba C, Dlamini S, George JA, Pillay T. COVID Diagnostics: From Molecules to Omics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1412:141-158. [PMID: 37378765 DOI: 10.1007/978-3-031-28012-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
The identification and genetic sequencing of a novel coronavirus was key to the diagnosis and management of the global pandemic. An understanding of the SARS-CoV-2 structure and mechanism of injury is vital to explaining the disease course and the pathophysiology of the signs and symptoms observed. This particularly as the presentation, disease course, and severity are noted to be highly variable. The role of the spike protein and angiotensin-converting enzyme 2 (ACE-2) receptor in immune response and viral entry provides great insight into current and future diagnostics and therapeutics. This article reviews the traditional diagnostic methods, which include molecular testing methods, antigen testing, and antibody testing. The gold standard for diagnosis of COVID-19 is reverse transcriptase polymerase chain reaction (RT-PCR). There have been multiple improvements to these principles to help optimize the sensitivity, specificity, and user friendliness of the method. In addition, advancements in gene sequencing and identification have been integral to identifying variants and managing outbreaks. Serological and immunological testing have made significant contributions to the management of the COVID-19 pandemic, each with its unique benefits and limitations. A growing role of the laboratory is in triaging patients to determine which patients will most benefit from hospitalization and specialized care. This is imperative for rationalizing resources during outbreaks. As we learn to live with the pandemic, novel testing methods include the use of multiomic technologies and the greater utility of point of care.
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Affiliation(s)
- Chemedzai Chikomba
- Department of Chemical Pathology. National Health Laboratory Services and University of Witwatersrand, Johannesburg, South Africa
| | - Siphelele Dlamini
- Department of Chemical Pathology. National Health Laboratory Services and University of Witwatersrand, Johannesburg, South Africa
| | - Jaya A George
- Wits Diagnostic and Innovation Hub, University of Witwatersrand, Johannesburg, South Africa.
| | - Taryn Pillay
- Department of Chemical Pathology. National Health Laboratory Services and University of Witwatersrand, Johannesburg, South Africa
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9
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Wahengbam R, Bharali P, Manna P, Phukan T, Singh MG, Gogoi G, Tapadar YB, Singh AK, Konwar R, Chikkaputtaiah C, Velmurugan N, Nagamani S, Mahanta HJ, Sarma H, Sahu RK, Dutta P, Wann SB, Kalita J, Sastry GN. Seroepidemiological and genomic investigation of SARS-CoV-2 spread in North East region of India. Indian J Med Microbiol 2022; 43:58-65. [PMID: 36371334 PMCID: PMC9644374 DOI: 10.1016/j.ijmmb.2022.10.011] [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: 06/04/2022] [Revised: 10/08/2022] [Accepted: 10/21/2022] [Indexed: 11/11/2022]
Abstract
Purpose Seroepidemiology and genomic surveillance are valuable tools to investigate infection transmission during a pandemic. North East (NE) India is a strategically important region being the gateway connecting the country with Southeast Asia. Here, we examined the spread of SARS-CoV-2 in NE India during the first and second waves of COVID-19 using serological and whole genome sequencing approaches. Methods qRT-PCR analysis was performed on a selected population (n = 16,295) from June 2020 to July 2021, and metadata was collected. Immunoassays were studied (n = 2026) at three-time points (August 2020, February 2021, and June 2021) and in a cohort (n = 35) for a year. SARS-CoV-2 whole genomes (n = 914) were sequenced and analyzed with those obtained from the databases. Results Test positivity rates (TPR) in the first and second waves were 6.34% and 6.64% in Assam, respectively, and a similar pattern was observed in other NE states. Seropositivity in the three time points was 10.63%, 40.3%, and 46.33%, respectively, and neutralizing antibody prevalence was 90.91%, 52.14%, and 69.30%, respectively. Persistence of pan-IgG-N SARS-CoV-2 antibody for over a year was observed among three subjects in the cohort group. Normal variants dominated the first wave, while B.1.617.2 and AY-sublineages dominated the second wave in the region. The prevalence of the variants co-related well with high TPR and seropositivity rate in the region and identified mostly among vaccinated individuals. Conclusion The COVID-19 first wave in the region witnessed low transmission with the evolution of diverse variants. Seropositivity increased during the study period with over half of the individuals carrying neutralizing antibodies against SARS-CoV-2. High infection and seroprevalence in NE India during the second wave were associated with the dominant emergence of variants of concern.
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Affiliation(s)
- Romi Wahengbam
- Centre for Infectious Diseases, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India,Corresponding author. Centre for Infectious Diseases, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India
| | - Pankaj Bharali
- Centre for Infectious Diseases, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Prasenjit Manna
- Centre for Infectious Diseases, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Tridip Phukan
- Centre for Infectious Diseases, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Moirangthem Goutam Singh
- Centre for Infectious Diseases, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Gayatri Gogoi
- Centre for Infectious Diseases, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India
| | - Yasmin Begam Tapadar
- Centre for Infectious Diseases, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India
| | - Anil Kumar Singh
- Biological Sciences and Technology Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Rituraj Konwar
- Biological Sciences and Technology Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Natarajan Velmurugan
- Branch Laboratory, CSIR–North East Institute of Science and Technology, Naharlagun, Papumpare, Arunachal Pradesh, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Selvaraman Nagamani
- Advanced Computation and Data Sciences Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Hridoy Jyoti Mahanta
- Advanced Computation and Data Sciences Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Himakshi Sarma
- Advanced Computation and Data Sciences Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India
| | - Ravi Kumar Sahu
- Biological Sciences and Technology Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Prachurjya Dutta
- Biological Sciences and Technology Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India
| | - Sawlang Borsingh Wann
- Centre for Infectious Diseases, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Jatin Kalita
- Centre for Infectious Diseases, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - G Narahari Sastry
- Centre for Infectious Diseases, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India,Advanced Computation and Data Sciences Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India,Corresponding author. Advanced Computation and Data Sciences Division, CSIR–North East Institute of Science and Technology, Jorhat, Assam, 785006, India
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10
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Lyimo BM, Popkin-Hall ZR, Giesbrecht DJ, Mandara CI, Madebe RA, Bakari C, Pereus D, Seth MD, Ngamba RM, Mbwambo RB, MacInnis B, Mbwambo D, Garimo I, Chacky F, Aaron S, Lusasi A, Molteni F, Njau R, Cunningham JA, Lazaro S, Mohamed A, Juliano JJ, Bailey J, Ishengoma DS. Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa. Front Cell Infect Microbiol 2022; 12:757844. [PMID: 35909968 PMCID: PMC9326448 DOI: 10.3389/fcimb.2022.757844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/17/2022] [Indexed: 12/02/2022] Open
Abstract
Recent developments in molecular biology and genomics have revolutionized biology and medicine mainly in the developed world. The application of next generation sequencing (NGS) and CRISPR-Cas tools is now poised to support endemic countries in the detection, monitoring and control of endemic diseases and future epidemics, as well as with emerging and re-emerging pathogens. Most low and middle income countries (LMICs) with the highest burden of infectious diseases still largely lack the capacity to generate and perform bioinformatic analysis of genomic data. These countries have also not deployed tools based on CRISPR-Cas technologies. For LMICs including Tanzania, it is critical to focus not only on the process of generation and analysis of data generated using such tools, but also on the utilization of the findings for policy and decision making. Here we discuss the promise and challenges of NGS and CRISPR-Cas in the context of malaria as Africa moves towards malaria elimination. These innovative tools are urgently needed to strengthen the current diagnostic and surveillance systems. We discuss ongoing efforts to deploy these tools for malaria detection and molecular surveillance highlighting potential opportunities presented by these innovative technologies as well as challenges in adopting them. Their deployment will also offer an opportunity to broadly build in-country capacity in pathogen genomics and bioinformatics, and to effectively engage with multiple stakeholders as well as policy makers, overcoming current workforce and infrastructure challenges. Overall, these ongoing initiatives will build the malaria molecular surveillance capacity of African researchers and their institutions, and allow them to generate genomics data and perform bioinformatics analysis in-country in order to provide critical information that will be used for real-time policy and decision-making to support malaria elimination on the continent.
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Affiliation(s)
- Beatus M. Lyimo
- National Institute for Medical Research, Dar es Salaam, Tanzania
- School of Life Sciences and Bio-Engineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | | | - David J. Giesbrecht
- Pathology and Laboratory Medicine, Center for International Health Research, Brown University, Providence, RI, United States
| | | | - Rashid A. Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Misago D. Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | - Ruth B. Mbwambo
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Bronwyn MacInnis
- Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Infectious Disease and Microbiome Program, Broad Institute, Boston, MA, United States
| | | | - Issa Garimo
- National Malaria Control Programme, Dodoma, Tanzania
| | - Frank Chacky
- National Malaria Control Programme, Dodoma, Tanzania
| | | | | | | | - Ritha Njau
- World Health Organization, Country Office, Dar es Salaam, Tanzania
| | - Jane A. Cunningham
- Global Malaria Programme, World Health Organization, Headquarters, Geneva, Switzerland
| | - Samwel Lazaro
- National Malaria Control Programme, Dodoma, Tanzania
| | - Ally Mohamed
- National Malaria Control Programme, Dodoma, Tanzania
| | - Jonathan J. Juliano
- School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Jeffrey A. Bailey
- Pathology and Laboratory Medicine, Center for International Health Research, Brown University, Providence, RI, United States
| | - Deus S. Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
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11
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El-Attar EA, Helmy Elkaffas RM, Aglan SA, Naga IS, Nabil A, Abdallah HY. Genomics in Egypt: Current Status and Future Aspects. Front Genet 2022; 13:797465. [PMID: 35664315 PMCID: PMC9157251 DOI: 10.3389/fgene.2022.797465] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Egypt is the third most densely inhabited African country. Due to the economic burden and healthcare costs of overpopulation, genomic and genetic testing is a huge challenge. However, in the era of precision medicine, Egypt is taking a shift in approach from “one-size-fits all” to more personalized healthcare via advancing the practice of medical genetics and genomics across the country. This shift necessitates concrete knowledge of the Egyptian genome and related diseases to direct effective preventive, diagnostic and counseling services of prevalent genetic diseases in Egypt. Understanding disease molecular mechanisms will enhance the capacity for personalized interventions. From this perspective, we highlight research efforts and available services for rare genetic diseases, communicable diseases including the coronavirus 2019 disease (COVID19), and cancer. The current state of genetic services in Egypt including availability and access to genetic services is described. Drivers for applying genomics in Egypt are illustrated with a SWOT analysis of the current genetic/genomic services. Barriers to genetic service development in Egypt, whether economic, geographic, cultural or educational are discussed as well. The sensitive topic of communicating genomic results and its ethical considerations is also tackled. To understand disease pathogenesis, much can be gained through the advancement and integration of genomic technologies via clinical applications and research efforts in Egypt. Three main pillars of multidisciplinary collaboration for advancing genomics in Egypt are envisaged: resources, infrastructure and training. Finally, we highlight the recent national plan to establish a genome center that will aim to prepare a map of the Egyptian human genome to discover and accurately determine the genetic characteristics of various diseases. The Reference Genome Project for Egyptians and Ancient Egyptians will initialize a new genomics era in Egypt. We propose a multidisciplinary governance system in Egypt to support genomic medicine research efforts and integrate into the healthcare system whilst ensuring ethical conduct of data.
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Affiliation(s)
- Eman Ahmed El-Attar
- Chemical Pathology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
- *Correspondence: Eman Ahmed El-Attar,
| | | | - Sarah Ahmed Aglan
- Chemical Pathology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Iman S. Naga
- Department of Microbiology, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Amira Nabil
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Hoda Y. Abdallah
- Medical Genetics Unit, Histology and Cell Biology Department, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Center of Excellence in Molecular and Cellular Medicine, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
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12
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Murewanhema G, Dzinamarira T. The COVID-19 Pandemic: Public Health Responses in Sub-Saharan Africa. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19084448. [PMID: 35457314 PMCID: PMC9027442 DOI: 10.3390/ijerph19084448] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/06/2022] [Indexed: 11/16/2022]
Abstract
The World Health Organisation declared the ongoing COVID-19 global health challenge a pandemic in March 2020. Since then, countries across the globe have implemented different public health control strategies-including global vaccination programs-in attempts to mitigate the further transmission of severe acute respiratory syndrome coronavirus 2. However, to date, the virus has continued to spread rapidly despite these interventions. Countries across sub-Saharan Africa have implemented variable control strategies to combat the pandemic; however, despite the continent being among the least affected in terms of direct case burden, morbidity, and mortality, it has experienced marked socioeconomic disruption. Therefore, economic resuscitation is an urgent priority. The continent is vastly underrepresented in the body of scientific evidence due to limited research resources, testing capacity and genomic surveillance leading to empirical responses or responses guided by evidence from elsewhere. To inform the ongoing pandemic, and to prepare for the future, this Special Issue calls for manuscripts on global COVID-19 responses, and encourages researchers and stakeholders from resource-limited settings, particularly from sub-Saharan Africa, to share their COVID-19 public health responses. Areas to be covered include, but are not limited to, surveillance, case management, infection prevention and control, risk communication and community engagement, logistics, laboratory, ports of entry, and co-ordination. Manuscripts including primary research, viewpoints/perspectives, and comprehensive literature reviews are all welcome.
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Affiliation(s)
- Grant Murewanhema
- Unit of Obstetrics and Gynaecology, Department of Primary Health Care Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare P.O. Box MP167, Zimbabwe;
| | - Tafadzwa Dzinamarira
- ICAP at Columbia University, Harare P.O. Box MP167, Zimbabwe
- School of Health Systems & Public Health, University of Pretoria, Pretoria 0002, South Africa
- Correspondence:
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13
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Okoh OS, Nii-Trebi NI, Jakkari A, Olaniran TT, Senbadejo TY, Kafintu-kwashie AA, Dairo EO, Ganiyu TO, Akaninyene IE, Ezediuno LO, Adeosun IJ, Ockiya MA, Jimah EM, Spiro DJ, Oladipo EK, Trovão NS. Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa. iScience 2022; 25:103880. [PMID: 35156006 PMCID: PMC8817759 DOI: 10.1016/j.isci.2022.103880] [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: 08/03/2021] [Revised: 11/29/2021] [Accepted: 02/03/2022] [Indexed: 12/15/2022] Open
Abstract
There is a dearth of information on COVID-19 disease dynamics in Africa. To fill this gap, we investigated the epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in the continent. We retrieved 5229 complete genomes collected in 33 African countries from the GISAID database. We investigated the circulating diversity, reconstructed the viral evolutionary divergence and history, and studied the case and death trends in the continent. Almost a fifth (144/782, 18.4%) of Pango lineages found worldwide circulated in Africa, with five different lineages dominating over time. Phylogenetic analysis revealed that African viruses cluster more closely with those from Europe. We also identified two motifs that could function as integrin-binding sites and N-glycosylation domains. These results shed light on the epidemiological and evolutionary dynamics of the circulating viral diversity in Africa. They also emphasize the need to expand surveillance efforts in Africa to help inform and implement better public health measures.
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Affiliation(s)
| | - Nicholas Israel Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Abdulrokeeb Jakkari
- Department of Microbiology, Faculty of Science, Lagos State University, Ojo, Lagos, Nigeria
| | - Tosin Titus Olaniran
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Helix Biogen Institute, Ogbomoso, Nigeria
| | - Tosin Yetunde Senbadejo
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Anna Aba Kafintu-kwashie
- Department of Medical Microbiology, Clinical Virology Unit, University of Ghana Medical School, Accra, Ghana
| | - Emmanuel Oluwatobi Dairo
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Tajudeen Oladunni Ganiyu
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Ifiokakaninyene Ekpo Akaninyene
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Helix Biogen Institute, Ogbomoso, Nigeria
| | - Louis Odinakaose Ezediuno
- Department of Microbiology, Faculty of Life Sciences, University of Ilorin,1515 P.M.B, Ilorin, Nigeria
| | - Idowu Jesulayomi Adeosun
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun, Nigeria
- Division of Microbiology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield Pretoria 0028, South Africa
| | - Michael Asebake Ockiya
- Department of Animal Science, Niger Delta University, Wilberforce Island, Bayelsa, Nigeria
| | - Esther Moradeyo Jimah
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, University of Ilorin 1515, P.M.B, Ilorin, Nigeria
| | - David J. Spiro
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Elijah Kolawole Oladipo
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun, Nigeria
| | - Nídia S. Trovão
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
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14
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Harste HJ, Kiff G, Okeke IN, Adebiyi AO, Ravikumar KL, Nagaraj G, Ajiboye JJ, Osma Castro ECD, Herrera E, Aanensen DM. Good Financial Grant Practice: A Tool for Developing and Demonstrating Institutional Financial and Grant Management Capacity in Global Health. Clin Infect Dis 2021; 73:S275-S282. [PMID: 34850833 PMCID: PMC8634540 DOI: 10.1093/cid/ciab768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The administration and governance of grant funding across global health organizations presents enormous challenges. Meeting these challenges is crucial to ensuring that funds are used in the most effective way to improve health outcomes, in line with the United Nations' Sustainable Development Goal 3, "Ensure healthy lives and promote well-being for all at all ages." The Good Financial Grant Practice (GFGP) Standard (ARS 1651) is the world's first and, currently, only international standard for the financial governance and management of grant funding. Through consensus building and global harmonization between both low- and middle-income and high-income country players, the GFGP Standard has achieved a leveling impact: GFGP applies equally to, and can be implemented by, all types of organization, regardless of location, size, or whether they predominantly give or receive funding. GFGP can be used as a tool for addressing some of the challenges of the current funding model. Here, we describe our experiences and lessons learned from implementing GFGP across 4 diverse research institutions in India, Nigeria, Colombia, and the Philippines as part of our National Institute for Health Research Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance.
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Affiliation(s)
- Harry J Harste
- Oxford Big Data Institute, University of Oxford, Oxford, United Kingdom; Wellcome Genome Campus, Hinxton, United Kingdom
| | - Genevieve Kiff
- Oxford University Clinical Research Unit, Hanoi, Vietnam; African Academy of Sciences, Nairobi, Kenya
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Akindele O Adebiyi
- College Research and Innovation Management, College of Medicine, University of Ibadan, Nigeria
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Jolaade J Ajiboye
- Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Erik C D Osma Castro
- AGROSAVIA (Corporación Colombiana de Investigación Agropecuaria), Bogotá, Colombia
| | - Elmer Herrera
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute of Tropical Medicine, Manila, Philippines
| | - David M Aanensen
- Oxford Big Data Institute, University of Oxford, Oxford, United Kingdom; Wellcome Genome Campus, Hinxton, United Kingdom
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15
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Progress and challenges in virus genomic epidemiology. Trends Parasitol 2021; 37:1038-1049. [PMID: 34620561 DOI: 10.1016/j.pt.2021.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/18/2022]
Abstract
Genomic epidemiology, which links pathogen genomes with associated metadata to understand disease transmission, has become a key component of outbreak response. Decreasing costs of genome sequencing and increasing computational power provide opportunities to generate and analyse large viral genomic datasets that aim to uncover the spatial scales of transmission, the demographics contributing to transmission patterns, and to forecast epidemic trends. Emerging sources of genomic data and associated metadata provide new opportunities to further unravel transmission patterns. Key challenges include how to integrate genomic data with metadata from multiple sources, how to generate efficient computational algorithms to cope with large datasets, and how to establish sampling frameworks to enable robust conclusions.
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16
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Lane CR, Sherry NL, Porter AF, Duchene S, Horan K, Andersson P, Wilmot M, Turner A, Dougall S, Johnson SA, Sait M, Gonçalves da Silva A, Ballard SA, Hoang T, Stinear TP, Caly L, Sintchenko V, Graham R, McMahon J, Smith D, Leong LE, Meumann EM, Cooley L, Schwessinger B, Rawlinson W, van Hal SJ, Stephens N, Catton M, Looker C, Crouch S, Sutton B, Alpren C, Williamson DA, Seemann T, Howden BP. Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study. Lancet Public Health 2021; 6:e547-e556. [PMID: 34252365 PMCID: PMC8270762 DOI: 10.1016/s2468-2667(21)00133-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND A cornerstone of Australia's ability to control COVID-19 has been effective border control with an extensive supervised quarantine programme. However, a rapid recrudescence of COVID-19 was observed in the state of Victoria in June, 2020. We aim to describe the genomic findings that located the source of this second wave and show the role of genomic epidemiology in the successful elimination of COVID-19 for a second time in Australia. METHODS In this observational, genomic epidemiological study, we did genomic sequencing of all laboratory-confirmed cases of COVID-19 diagnosed in Victoria, Australia between Jan 25, 2020, and Jan 31, 2021. We did phylogenetic analyses, genomic cluster discovery, and integrated results with epidemiological data (detailed information on demographics, risk factors, and exposure) collected via interview by the Victorian Government Department of Health. Genomic transmission networks were used to group multiple genomic clusters when epidemiological and genomic data suggested they arose from a single importation event and diversified within Victoria. To identify transmission of emergent lineages between Victoria and other states or territories in Australia, all publicly available SARS-CoV-2 sequences uploaded before Feb 11, 2021, were obtained from the national sequence sharing programme AusTrakka, and epidemiological data were obtained from the submitting laboratories. We did phylodynamic analyses to estimate the growth rate, doubling time, and number of days from the first local infection to the collection of the first sequenced genome for the dominant local cluster, and compared our growth estimates to previously published estimates from a similar growth phase of lineage B.1.1.7 (also known as the Alpha variant) in the UK. FINDINGS Between Jan 25, 2020, and Jan 31, 2021, there were 20 451 laboratory-confirmed cases of COVID-19 in Victoria, Australia, of which 15 431 were submitted for sequencing, and 11 711 met all quality control metrics and were included in our analysis. We identified 595 genomic clusters, with a median of five cases per cluster (IQR 2-11). Overall, samples from 11 503 (98·2%) of 11 711 cases clustered with another sample in Victoria, either within a genomic cluster or transmission network. Genomic analysis revealed that 10 426 cases, including 10 416 (98·4%) of 10 584 locally acquired cases, diagnosed during the second wave (between June and October, 2020) were derived from a single incursion from hotel quarantine, with the outbreak lineage (transmission network G, lineage D.2) rapidly detected in other Australian states and territories. Phylodynamic analyses indicated that the epidemic growth rate of the outbreak lineage in Victoria during the initial growth phase (samples collected between June 4 and July 9, 2020; 47·4 putative transmission events, per branch, per year [1/years; 95% credible interval 26·0-85·0]), was similar to that of other reported variants, such as B.1.1.7 in the UK (mean approximately 71·5 1/years). Strict interventions were implemented, and the outbreak lineage has not been detected in Australia since Oct 29, 2020. Subsequent cases represented independent international or interstate introductions, with limited local spread. INTERPRETATION Our study highlights how rapid escalation of clonal outbreaks can occur from a single incursion. However, strict quarantine measures and decisive public health responses to emergent cases are effective, even with high epidemic growth rates. Real-time genomic surveillance can alter the way in which public health agencies view and respond to COVID-19 outbreaks. FUNDING The Victorian Government, the National Health and Medical Research Council Australia, and the Medical Research Future Fund.
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Affiliation(s)
- Courtney R Lane
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Norelle L Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ashleigh F Porter
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Patiyan Andersson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mathilda Wilmot
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Sally Dougall
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Sandra A Johnson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Michelle Sait
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Tuyet Hoang
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Timothy P Stinear
- Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Sydney, NSW, Australia; Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Rikki Graham
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - Jamie McMahon
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, QLD, Australia
| | - David Smith
- Department of Microbiology, PathWest Laboratory Medicine, QEII Medical Centre, Perth, WA, Australia; School of Medicine, University of Western Australia, Perth, WA, Australia
| | - Lex Ex Leong
- Public Health Laboratory, Microbiology and Infectious Diseases, SA Pathology, Adelaide, SA, Australia
| | - Ella M Meumann
- Territory Pathology, Royal Darwin Hospital, Darwin, NT, Australia; Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Louise Cooley
- Royal Hobart Hospital, Hobart, TAS, Australia; School of Medicine, University of Tasmania, Hobart, TAS, Australia
| | | | - William Rawlinson
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Sebastiaan J van Hal
- Department of Infectious Disease and Microbiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Nicola Stephens
- School of Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Mike Catton
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Clare Looker
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Simon Crouch
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Brett Sutton
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Charles Alpren
- Victorian Department of Health, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Doherty Applied Microbial Genomics, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
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17
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Gravagnuolo AM, Faqih L, Cronshaw C, Wynn J, Klapper P, Wigglesworth M. High throughput diagnostics and dynamic risk assessment of SARS-CoV-2 variants of concern. EBioMedicine 2021; 70:103540. [PMID: 34392145 PMCID: PMC8358312 DOI: 10.1016/j.ebiom.2021.103540] [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: 04/16/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The rise of new SARS-CoV-2 variants worldwide requires global molecular surveillance strategies to support public health control. Early detection and evaluation of their associated risk of spreading within the population are pivotal. METHODS Between April 2020 and February 2021, the UK Lighthouse Labs Network at Alderley Park tested more than eight million nose and throat swab samples for the presence of SARS-CoV-2, via PCR. The assay targeted three genomic regions of the virus: N, Orf1ab and S. Whole-genome next-generation sequencing was used to confirm positive PCR results. Positive results were mapped using the postal district origin of samples to allow real-time tracking of the spread of a new variant through the UK. FINDINGS In mid-November 2020, the assay identified an increasing number of S gene negative, N and Orf1ab positive samples. Whole-genome sequencing demonstrated that the loss of S gene detection was due to the appearance of a SARS-CoV-2 lineage (B.1.1.7) designated as Variant of concern (VOC) 202012/01. By the beginning of January 2021, the new SARS-CoV-2 VOC comprised 70% of daily positive samples tested at Alderley Park and ∼98% by the end of February 2021. INTERPRETATION The timeline view identified the rapid spread of the new SARS-CoV-2 variant across England during the first three weeks of December. Coupling high-throughput diagnostics and molecular surveillance was pivotal to the early detection of the spread of this variant. The availability of real-time tracking of an emerging variant is an important new tool to inform decision-making authorities for risk mitigation. In a respiratory pandemic, a tool for the timely response to the emergence and spread of a novel variant is vital, even more so when a variant is associated with the enhanced transmission, as has occurred with VOC 202012/01. FUNDING None.
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Affiliation(s)
- Alfredo Maria Gravagnuolo
- Medicines Discovery Catapult, Lighthouse Labs Network, Alderley Park, Mereside, Alderley Edge, Cheshire SK10 4TG, United Kingdom
| | - Layla Faqih
- Medicines Discovery Catapult, Lighthouse Labs Network, Alderley Park, Mereside, Alderley Edge, Cheshire SK10 4TG, United Kingdom
| | - Cara Cronshaw
- Department of Health and Social Care, 39 Victoria Street, London SW1H 0EU, United Kingdom
| | - Jacquelyn Wynn
- Medicines Discovery Catapult, Lighthouse Labs Network, Alderley Park, Mereside, Alderley Edge, Cheshire SK10 4TG, United Kingdom
| | - Paul Klapper
- Department of Health and Social Care, 39 Victoria Street, London SW1H 0EU, United Kingdom; The University of Manchester, Oxford Rd, Manchester M13 9PL, United Kingdom
| | - Mark Wigglesworth
- Medicines Discovery Catapult, Lighthouse Labs Network, Alderley Park, Mereside, Alderley Edge, Cheshire SK10 4TG, United Kingdom; Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Alderley Park, Mereside, Alderley Edge, Cheshire SK10 4TG, United Kingdom.
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18
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The Dual/Global Value of SARS-CoV-2 Genome Surveillance on Migrants Arriving to Europe via the Mediterranean Routes. Ann Glob Health 2021; 87:71. [PMID: 34327118 PMCID: PMC8300587 DOI: 10.5334/aogh.3425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite the pandemic, 34,154 migrants, refugees or asylum-seekers landed in Sicily (Italy) in 2020, representing the main point of entry by sea into Europe. The SARS-CoV-2 surveillance program among migrants arriving to Sicily via the Mediterranean Sea, made by the combination of clinical examination and molecular testing, has been integrated by full-genome sequencing strains using the NGS technology from the last week of February. To date, more than one hundred full-genome strains have been sequenced and 8 different lineages have been identified mostly belonging to the lineages B.1.1.7 and B.1.525. As global access to COVID-19 vaccines should be ensured, the need to provide more detailed information to inform policies and to drive the possible re-engineering of vaccines needed to deal with the challenge of new and future variants should be highlighted.
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19
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Kamp M, Krause A, Ramsay M. Has translational genomics come of age in Africa? Hum Mol Genet 2021; 30:R164-R173. [PMID: 34240178 DOI: 10.1093/hmg/ddab180] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/27/2021] [Accepted: 06/29/2021] [Indexed: 01/12/2023] Open
Abstract
The rapid increase in genomics research in Africa and the growing promise of precision public health begs the question of whether African genomics has come of age and is being translated into improved healthcare for Africans. An assessment of the continent's readiness suggests that genetic service delivery remains limited and extremely fragile. The paucity of data on mutation profiles for monogenic disorders and lack of large genome-wide association cohorts for complex traits in African populations is a significant barrier, coupled with extreme genetic variation across different regions and ethnic groups. Data from many different populations is essential to developing appropriate genetic services. Of the proposed genetic service delivery models currently used in Africa-Uncharacterized, Limited, Disease-focused, Emerging and Established-the first three best describe the situation in most African countries. Implementation is fraught with difficulties related to the scarcity of an appropriately skilled medical genetic workforce, limited infrastructure and processes, insufficient health funding and lack of political support, and overstretched health systems. There is a strong nucleus of determined and optimistic clinicians and scientists with a clear vision, and there is hope for innovative solutions and technological leapfrogging. However, a multi-dimensional approach with active interventions to stimulate genomic research, clinical genetics and overarching healthcare systems is needed to reduce genetic service inequalities and accelerate precision public health on the continent. Human and infrastructure capacity development, dedicated funding, political will and supporting legislation, and public education and awareness, are critical elements for success. Africa-relevant genomic and related health economics research remains imperative with an overarching need to translate knowledge into improved healthcare. Given the limited data and genetic services across most of Africa, the continent has not yet come of 'genomics' age.
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Affiliation(s)
- Michelle Kamp
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, The University of the Witwatersrand, National Health Laboratory Service, Johannesburg, 2193, South Africa.,Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, The University of the Witwatersrand, National Health Laboratory Service, Johannesburg, 2193, South Africa
| | - Michèle Ramsay
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, The University of the Witwatersrand, National Health Laboratory Service, Johannesburg, 2193, South Africa.,Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
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20
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van Reisen M, Oladipo F, Stokmans M, Mpezamihgo M, Folorunso S, Schultes E, Basajja M, Aktau A, Amare SY, Taye GT, Purnama Jati PH, Chindoza K, Wirtz M, Ghardallou M, van Stam G, Ayele W, Nalugala R, Abdullahi I, Osigwe O, Graybeal J, Medhanyie AA, Kawu AA, Liu F, Wolstencroft K, Flikkenschild E, Lin Y, Stocker J, Musen MA. Design of a FAIR digital data health infrastructure in Africa for COVID-19 reporting and research. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:e10050. [PMID: 34514430 PMCID: PMC8420285 DOI: 10.1002/ggn2.10050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 12/13/2022]
Abstract
The limited volume of COVID-19 data from Africa raises concerns for global genome research, which requires a diversity of genotypes for accurate disease prediction, including on the provenance of the new SARS-CoV-2 mutations. The Virus Outbreak Data Network (VODAN)-Africa studied the possibility of increasing the production of clinical data, finding concerns about data ownership, and the limited use of health data for quality treatment at point of care. To address this, VODAN Africa developed an architecture to record clinical health data and research data collected on the incidence of COVID-19, producing these as human- and machine-readable data objects in a distributed architecture of locally governed, linked, human- and machine-readable data. This architecture supports analytics at the point of care and-through data visiting, across facilities-for generic analytics. An algorithm was run across FAIR Data Points to visit the distributed data and produce aggregate findings. The FAIR data architecture is deployed in Uganda, Ethiopia, Liberia, Nigeria, Kenya, Somalia, Tanzania, Zimbabwe, and Tunisia.
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Affiliation(s)
- Mirjam van Reisen
- Leiden UniversityLeidenNetherlands
- Leiden University Medical Centre (LUMC)Leiden UniversityLeidenNetherlands
- Leiden Institute of Advanced Computer Science (LIACS)Leiden UniversityLeidenNetherlands
- Faculty of Humanities and Digital SciencesTilburg UniversityTilburgNetherlands
| | | | - Mia Stokmans
- Faculty of Humanities and Digital SciencesTilburg UniversityTilburgNetherlands
| | | | - Sakinat Folorunso
- Department of Computer ScienceOlabisi Onabanjo UniversityAgo IwoyeNigeria
| | | | - Mariam Basajja
- Leiden UniversityLeidenNetherlands
- Leiden Institute of Advanced Computer Science (LIACS)Leiden UniversityLeidenNetherlands
| | - Aliya Aktau
- Faculty of Humanities and Digital SciencesTilburg UniversityTilburgNetherlands
| | | | - Getu Tadele Taye
- Faculty of Humanities and Digital SciencesTilburg UniversityTilburgNetherlands
- Department of Health informatics, School of Public HealthMekelle UniversityMek'eleEthiopia
| | - Putu Hadi Purnama Jati
- Faculty of Humanities and Digital SciencesTilburg UniversityTilburgNetherlands
- Badan Pusat StatistikCentral JakartaIndonesia
| | - Kudakwashe Chindoza
- Faculty of Humanities and Digital SciencesTilburg UniversityTilburgNetherlands
- Department of Computer ScienceGreat Zimbabwe UniversityMasvingoZimbabwe
| | - Morgane Wirtz
- Faculty of Humanities and Digital SciencesTilburg UniversityTilburgNetherlands
| | | | | | - Wondimu Ayele
- Department of Biostatistics and Epidemiology, School of Public health College of Health SciencesAddis Ababa UniversityAddis AbabaEthiopia
| | | | | | | | - John Graybeal
- Stanford Center for Biomedical Informatics ResearchStanford UniversityStanfordCaliforniaUSA
| | - Araya Abrha Medhanyie
- Department of Reproductive health, School of Public HealthMekelle UniversityMek'eleEthiopia
| | | | | | | | - Erik Flikkenschild
- Leiden University Medical Centre (LUMC)Leiden UniversityLeidenNetherlands
| | - Yi Lin
- Leiden UniversityLeidenNetherlands
| | - Joëlle Stocker
- Department of GeosciencesUtrecht UniversityUtrechtNetherlands
| | - Mark A. Musen
- Stanford Center for Biomedical Informatics ResearchStanford UniversityStanfordCaliforniaUSA
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21
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Okoh OS, Nii-Trebi NI, Jakkari A, Olaniran TT, Senbadejo TY, Kafintu-kwashie AA, Dairo EO, Ganiyu TO, Akaninyene IE, Ezediuno LO, Adeosun IJ, Ockiya MA, Jimah EM, Spiro DJ, Oladipo EK, Trovão NS. Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.05.17.21257341. [PMID: 34031660 PMCID: PMC8142660 DOI: 10.1101/2021.05.17.21257341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
COVID-19 disease dynamics have been widely studied in different settings around the globe, but little is known about these patterns in the African continent. To investigate the epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa, more than 2400 complete genomes from 33 African countries were retrieved from the GISAID database and analyzed. We investigated their diversity using various clade and lineage nomenclature systems, reconstructed their evolutionary divergence and history using maximum likelihood inference methods, and studied the case and death trends in the continent. We also examined potential repeat patterns and motifs across the sequences. In this study, we show that after almost one year of the COVID-19 pandemic, only 143 out of the 782 Pango lineages found worldwide circulated in Africa, with five different lineages dominating in distinct periods of the pandemic. Analysis of the number of reported deaths in Africa also revealed large heterogeneity across the continent. Phylogenetic analysis revealed that African viruses cluster closely with those from all continents but more notably with viruses from Europe. However, the extent of viral diversity observed among African genomes is closest to that of the Oceania outbreak, most likely due to genomic under-surveillance in Africa. We also identified two motifs that could function as integrin-binding sites and N-glycosylation domains. These results shed light on the evolutionary dynamics of the circulating viral strains in Africa, elucidate the functions of protein motifs present in the genome sequences, and emphasize the need to expand genomic surveillance efforts in the continent to better understand the molecular, evolutionary, epidemiological, and spatiotemporal dynamics of the COVID-19 pandemic in Africa.
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Affiliation(s)
| | - Nicholas Israel Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Abdulrokeeb Jakkari
- Department of Microbiology, Faculty of Science, Lagos State University, Ojo, Lagos, Nigeria
| | - Tosin Titus Olaniran
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Helix Biogen Institute, Ogbomoso, Nigeria
| | - Tosin Yetunde Senbadejo
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Anna Aba Kafintu-kwashie
- Department of Medical Microbiology Clinical Virology unit, University of Ghana Medical School, Accra, Ghana
| | - Emmanuel Oluwatobi Dairo
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Tajudeen Oladunni Ganiyu
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Ifiokakaninyene Ekpo Akaninyene
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Helix Biogen Institute, Ogbomoso, Nigeria
| | | | - Idowu Jesulayomi Adeosun
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
| | - Michael Asebake Ockiya
- Department of Animal Science, Niger Delta University, Wilberforce Island, Bayelsa State, Nigeria
| | - Esther Moradeyo Jimah
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, University of Ilorin, Nigeria
| | - David J. Spiro
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Elijah Kolawole Oladipo
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
| | - Nídia S. Trovão
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
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22
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Boum Y, Bebell LM, Bisseck ACZK. Africa needs local solutions to face the COVID-19 pandemic. Lancet 2021; 397:1238-1240. [PMID: 33773113 PMCID: PMC7990475 DOI: 10.1016/s0140-6736(21)00719-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/30/2022]
Affiliation(s)
- Yap Boum
- Epicentre, Médecins Sans Frontières, Yaoundé BP 12069, Cameroon.
| | - Lisa M Bebell
- Massachusetts General Hospital Center for Global Health, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
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23
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Happi AN, Ugwu CA, Happi CT. Tracking the emergence of new SARS-CoV-2 variants in South Africa. Nat Med 2021; 27:372-373. [PMID: 33723453 DOI: 10.1038/s41591-021-01265-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Anise N Happi
- African Center of Excellence for Genomics of Infectious Disease, Redeemer's University, Ede, Nigeria
| | - Chinedu A Ugwu
- African Center of Excellence for Genomics of Infectious Disease, Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Christian T Happi
- African Center of Excellence for Genomics of Infectious Disease, Redeemer's University, Ede, Nigeria. .,Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria.
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24
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Genomic-informed pathogen surveillance in Africa: opportunities and challenges. THE LANCET. INFECTIOUS DISEASES 2021; 21:e281-e289. [PMID: 33587898 PMCID: PMC7906676 DOI: 10.1016/s1473-3099(20)30939-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/18/2020] [Accepted: 11/25/2020] [Indexed: 12/14/2022]
Abstract
The ongoing COVID-19 pandemic has highlighted the need to incorporate pathogen genomics for enhanced disease surveillance and outbreak management in Africa. The genomics of SARS-CoV-2 has been instrumental to the timely development of diagnostics and vaccines and in elucidating transmission dynamics. Global disease control programmes, including those for tuberculosis, malaria, HIV, foodborne pathogens, and antimicrobial resistance, also recommend genomics-based surveillance as an integral strategy towards control and elimination of these diseases. Despite the potential benefits, capacity remains low for many public health programmes in Africa. The COVID-19 pandemic presents an opportunity to reassess and strengthen surveillance systems and potentially integrate emerging technologies for preparedness of future epidemics and control of endemic diseases. We discuss opportunities and challenges for integrating pathogen genomics into public health surveillance systems in Africa. Improving accessibility through the creation of functional continent-wide networks, building multipathogen sequencing cores, training a critical mass of local experts, development of standards and policies to facilitate best practices for data sharing, and establishing a community of practice of genomics experts are all needed to use genomics for improved disease surveillance in Africa. Coordination and leadership are also crucial, which the Africa Centres for Disease Control and Prevention seeks to provide through its institute for pathogen genomics.
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Lu L, Lycett S, Ashworth J, Mutapi F, Woolhouse M. What are SARS-CoV-2 genomes from the WHO Africa region member states telling us? BMJ Glob Health 2021; 6:bmjgh-2020-004408. [PMID: 33419930 PMCID: PMC7798429 DOI: 10.1136/bmjgh-2020-004408] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022] Open
Affiliation(s)
- Lu Lu
- Usher Institute, Ashworth Laboratories, Kings Buildings, The University of Edinburgh, Edinburgh, UK
| | - Samantha Lycett
- The University of Edinburgh The Roslin Institute, Roslin, Midlothian, UK
| | - Jordan Ashworth
- Usher Institute, Ashworth Laboratories, Kings Buildings, The University of Edinburgh, Edinburgh, UK
| | - Francisca Mutapi
- Institute of Immunology & Infection Research, The University of Edinburgh School of Biological Sciences, Edinburgh, UK .,NIHR Global Health Research Unit Tackling Infections to Benefit Africa (TIBA), The University of Edinburgh, Edinburgh, UK
| | - Mark Woolhouse
- Usher Institute, Ashworth Laboratories, Kings Buildings, The University of Edinburgh, Edinburgh, UK.,NIHR Global Health Research Unit Tackling Infections to Benefit Africa (TIBA), The University of Edinburgh, Edinburgh, UK
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