The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Houriiyah Tegally; James E San; Matthew Cotten; Monika Moir; Bryan Tegomoh; Gerald Mboowa; Darren P Martin; Cheryl Baxter; Arnold W Lambisia; Amadou Diallo; Daniel G Amoako; Moussa M Diagne; Abay Sisay; Abdel-Rahman N Zekri; Abdou Salam Gueye; Abdoul K Sangare; Abdoul-Salam Ouedraogo; Abdourahmane Sow; Abdualmoniem O Musa; Abdul K Sesay; Abe G Abias; Adam I Elzagheid; Adamou Lagare; Adedotun-Sulaiman Kemi; Aden Elmi Abar; Adeniji A Johnson; Adeola Fowotade; Adeyemi O Oluwapelumi; Adrienne A Amuri; Agnes Juru; Ahmed Kandeil; Ahmed Mostafa; Ahmed Rebai; Ahmed Sayed; Akano Kazeem; Aladje Balde; Alan Christoffels; Alexander J Trotter; Allan Campbell; Alpha K Keita; Amadou Kone; Amal Bouzid; Amal Souissi; Ambrose Agweyu; Amel Naguib; Ana V Gutierrez; Anatole Nkeshimana; Andrew J Page; Anges Yadouleton; Anika Vinze; Anise N Happi; Anissa Chouikha; Arash Iranzadeh; Arisha Maharaj; Armel L Batchi-Bouyou; Arshad Ismail; Augustina A Sylverken; Augustine Goba; Ayoade Femi; Ayotunde E Sijuwola; Baba Marycelin; Babatunde L Salako; Bamidele S Oderinde; Bankole Bolajoko; Bassirou Diarra; Belinda L Herring; Benjamin Tsofa; Bernard Lekana-Douki; Bernard Mvula; Berthe-Marie Njanpop-Lafourcade; Blessing T Marondera; Bouh Abdi Khaireh; Bourema Kouriba; Bright Adu; Brigitte Pool; Bronwyn McInnis; Cara Brook; Carolyn Williamson; Cassien Nduwimana; Catherine Anscombe; Catherine B Pratt; Cathrine Scheepers; Chantal G Akoua-Koffi; Charles N Agoti; Chastel M Mapanguy; Cheikh Loucoubar; Chika K Onwuamah; Chikwe Ihekweazu; Christian N Malaka; Christophe Peyrefitte; Chukwa Grace; Chukwuma E Omoruyi; Clotaire D Rafaï; Collins M Morang'a; Cyril Erameh; Daniel B Lule; Daniel J Bridges; Daniel Mukadi-Bamuleka; Danny Park; David A Rasmussen; Africa Pathogen Genomics Initiative (Africa PGI)

doi:10.1126/science.abq5358

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The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

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The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Houriiyah Tegally, James E San, Matthew Cotten, Monika Moir, Bryan Tegomoh, Gerald Mboowa, Darren P Martin, Cheryl Baxter, Arnold W Lambisia, Amadou Diallo, …

Science (American Association for the Advancement of Science), Vol.378(6615), p.eabq5358

07/10/2022

DOI: https://doi.org/10.1126/science.abq5358

PMID: 36108049

Résumé

Africa - epidemiology

COVID-19 - epidemiology

COVID-19 - virology

Epidemiological Monitoring

Genomics

Humans

Pandemics

SARS-CoV-2 - genetics

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

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Titre: The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
Créateurs - sans rôle: Houriiyah Tegally - KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
James E San - KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
Matthew Cotten - MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
Monika Moir - Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
Bryan Tegomoh - CDC Foundation, Atlanta, Georgia, Nebraska Department of Health and Human Services, Lincoln, NE, USA
Gerald Mboowa - Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
Darren P Martin - Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
Cheryl Baxter - Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
Arnold W Lambisia - KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
Amadou Diallo - Institut Pasteur de Dakar
Daniel G Amoako - School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
Moussa M Diagne - Institut Pasteur de Dakar
Abay Sisay - Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
Abdel-Rahman N Zekri - Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
Abdou Salam Gueye - World Health Organization, Africa Region, Brazzaville, Republic of the Congo
Abdoul K Sangare - Centre d'Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
Abdoul-Salam Ouedraogo - Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
Abdourahmane Sow - West African Health Organisation, Bobo-Dioulasso, Burkina Faso
Abdualmoniem O Musa - General Administration of Laboratories and Blood Banks, Ministry of Health, Kassala State, Sudan
Abdul K Sesay - MRC Unit the Gambia
Abe G Abias - National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
Adam I Elzagheid - Libyan Biotechnology Research Center, Tripoli, Libya
Adamou Lagare - Center for Medical and Sanitary Research (CERMES), Niamey, Niger
Adedotun-Sulaiman Kemi - Nigerian Institute of Medical Research
Aden Elmi Abar - Laboratoire de la Caisse Nationale de Sécurité Sociale, Djibouti, Republic of Djibouti
Adeniji A Johnson - Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
Adeola Fowotade - Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
Adeyemi O Oluwapelumi - The Pirbright Institute, Woking, UK
Adrienne A Amuri - Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
Agnes Juru - National Microbiology Reference Laboratory, Harare, Zimbabwe
Ahmed Kandeil - Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
Ahmed Mostafa - Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
Ahmed Rebai - Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
Ahmed Sayed - Genomics and Epigenomics Program, Research Department CCHE57357, Cairo, Egypt
Akano Kazeem - Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
Aladje Balde - University Jean Piaget in Guinea-Bissau, Bissau, Guinea-Bissau
Alan Christoffels - SAMRC Bioinformatics Unit, SA Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
Alexander J Trotter - Quadram Institute
Allan Campbell - Central Public Health Reference Laboratories, Freetown, Sierra Leone
Alpha K Keita - TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier University, 34090, Montpellier, France
Amadou Kone - University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
Amal Bouzid - Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
Amal Souissi - Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
Ambrose Agweyu - KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
Amel Naguib - Central Public Health Laboratories (CPHL), Cairo, Egypt
Ana V Gutierrez - Quadram Institute Bioscience, Norwich, UK
Anatole Nkeshimana - National Institute of Public Health, Bujumbura, Burundi
Andrew J Page - Quadram Institute Bioscience, Norwich, UK
Anges Yadouleton - Laboratoire des Fièvres Hémorragiques Virales du Benin, Cotonou, Benin
Anika Vinze - Broad Institute
Anise N Happi - African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Anissa Chouikha - Research Laboratory "Virus, Vectors and Hosts: One Health Apporach and Technological Innovation for a Better Health", LR20IPT02, Pasteur Institute, Tunis 1002, Tunisia
Arash Iranzadeh - University of Cape Town
Arisha Maharaj - Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
Armel L Batchi-Bouyou - Marien Ngouabi, Brazzaville, Republic of the Congo
Arshad Ismail - National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
Augustina A Sylverken - Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
Augustine Goba - Ministry of Health and Sanitation, Freetown, Sierra Leone
Ayoade Femi - Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
Ayotunde E Sijuwola - African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Baba Marycelin - Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Borno State, Nigeria
Babatunde L Salako - Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
Bamidele S Oderinde - University of Maiduguri
Bankole Bolajoko - Redeemer's University
Bassirou Diarra - University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
Belinda L Herring - World Health Organization, Africa Region, Brazzaville, Republic of the Congo
Benjamin Tsofa - KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
Bernard Lekana-Douki - Département de Parasitologie-Mycologie Université des Sciences de la Santé (USS), Libreville, Gabon
Bernard Mvula - National HIV Reference Laboratory, Community Health Sciences Unit, Ministry of Health, Lilongwe, Malawi
Berthe-Marie Njanpop-Lafourcade - World Health Organization, Africa Region, Brazzaville, Republic of the Congo
Blessing T Marondera - African Society for Laboratory Medicine, Addis Ababa, Ethiopia
Bouh Abdi Khaireh - Africa CDC, Rapid Responder, Team Djibouti, Djibouti, Djibouti
Bourema Kouriba - Centre d'Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
Bright Adu - Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
Brigitte Pool - Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health Seychelles, Victoria, Seychelles
Bronwyn McInnis - Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
Cara Brook - Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
Carolyn Williamson - National Health Laboratory Service (NHLS), Cape Town, South Africa
Cassien Nduwimana - National Institute of Public Health, Bujumbura, Burundi
Catherine Anscombe - Liverpool School of Tropical Medicine, Liverpool, UK
Catherine B Pratt - University of Nebraska Medical Center (UNMC), Omaha, NE, USA
Cathrine Scheepers - University of the Witwatersrand
Chantal G Akoua-Koffi - UFR Sciences Médicales, Universite Alassane Ouattara, Bouaké, Côte d'Ivoire
Charles N Agoti - Pwani University
Chastel M Mapanguy - Faculty of Science and Techniques, University Marien Ngouabi, Brazzaville, Republic of the Congo
Cheikh Loucoubar - Institut Pasteur de Dakar
Chika K Onwuamah - Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
Chikwe Ihekweazu - Nigeria Centre for Disease Control
Christian N Malaka - Laboratoire des Arbovirus, Fièvres Hémorragiques virales, Virus Emergents et Zoonoses, Institut Pasteur de Bangui, Bangui, Central African Republic
Christophe Peyrefitte - Institut Pasteur de Dakar
Chukwa Grace - Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
Chukwuma E Omoruyi - Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
Clotaire D Rafaï - Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
Collins M Morang'a - West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
Cyril Erameh - Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
Daniel B Lule - MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
Daniel J Bridges - PATH, Lusaka, Zambia
Daniel Mukadi-Bamuleka - Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
Danny Park - Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
David A Rasmussen - Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
Africa Pathogen Genomics Initiative (Africa PGI)
Détails de publication: Science (American Association for the Advancement of Science), Vol.378(6615), p.eabq5358
Note de subvention: MC_PC_20045 / Medical Research Council MC_UU_00027/1 / Medical Research Council K24 AI131924 / NIAID NIH HHS Wellcome Trust U01 HG007480 / NHGRI NIH HHS U2R TW010673 / FIC NIH HHS K24 AI131928 / NIAID NIH HHS MC_PC_20001 / Medical Research Council U19 AI089696 / NIAID NIH HHS U01 AI151812 / NIAID NIH HHS
Identifiants: 99148945509311
Unité académique: Recherches translationnelles sur le VIH et les Maladies Infect. Endém. émerg. - TransVIHMI
Langue: English
Type de ressource: Journal article