Article (Scientific journals)
A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.
Wilkinson, Eduan; Giovanetti, Marta; Tegally, Houriiyah et al.
2021In Science, 374 (6566), p. 423-431
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Keywords :
Africa/epidemiology; COVID-19/epidemiology; COVID-19/transmission; COVID-19/virology; Genetic Variation; Humans; SARS-CoV-2/genetics; SARS-CoV-2/isolation & purification; Epidemiological Monitoring; Genomics; Pandemics; Africa; COVID-19; SARS-CoV-2; Multidisciplinary
Abstract :
[en] The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.
Disciplines :
Genetics & genetic processes
Author, co-author :
Wilkinson, Eduan ;  KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa ; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
Giovanetti, Marta ;  Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil ; Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
Tegally, Houriiyah ;  KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
San, James E ;  KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
Lessells, Richard ;  KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
Cuadros, Diego;  Department of Geography and GIS, University of Cincinnati, Cincinnati, OH, USA
Martin, Darren P;  Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa ; Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
Rasmussen, David A ;  Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA ; Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
Zekri, Abdel-Rahman N ;  Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt
Sangare, Abdoul K;  Centre d'Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
Ouedraogo, Abdoul-Salam;  Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
Sesay, Abdul K;  MRCG at LSHTM Genomics Lab, Fajara, Gambia
Priscilla, Abechi;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Kemi, Adedotun-Sulaiman;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Olubusuyi, Adewunmi M ;  Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
Oluwapelumi, Adeyemi O O ;  Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
Hammami, Adnène;  CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
Amuri, Adrienne A ;  Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo ; Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
Sayed, Ahmad;  Genomics Research Program, Children's Cancer Hospital, Cairo, Egypt
Ouma, Ahmed E O ;  Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
Elargoubi, Aida;  Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia ; Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
Ajayi, Nnennaya A ;  Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
Victoria, Ajogbasile F;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Kazeem, Akano;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
George, Akpede;  Irrua Specialist Teaching Hospital, Irrua, Nigeria
Trotter, Alexander J;  Quadram Institute Bioscience, Norwich, UK
Yahaya, Ali A ;  World Health Organization, Africa Region, Brazzaville Congo
Keita, Alpha K;  Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea ; TransVIHMI, Montpellier University/IRD/INSERM, Montpellier, France
Kone, Amadou;  Mali-University Clinical Research Center (UCRC), Bamako, Mali
Souissi, Amal ;  Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
Chtourou, Amel;  CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
Gutierrez, Ana V ;  Quadram Institute Bioscience, Norwich, UK
Page, Andrew J ;  Quadram Institute Bioscience, Norwich, UK
Vinze, Anika;  Broad Insitute of Harvard and MIT, Cambridge, MA, USA
Iranzadeh, Arash;  Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa ; Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
Lambisia, Arnold ;  KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
Ismail, Arshad ;  National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
Rosemary, Audu ;  The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
Sylverken, Augustina ;  Institute of Virology, Charité - Universitätsmedizin, Berlin, Germany
Femi, Ayoade ;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Ibrahimi, Azeddine;  Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
Marycelin, Baba;  Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
Oderinde, Bamidele S;  Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
Bolajoko, Bankole;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Dhaala, Beatrice;  MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
Herring, Belinda L;  World Health Organization, Africa Region, Brazzaville Congo
Njanpop-Lafourcade, Berthe-Marie;  World Health Organization, Africa Region, Brazzaville Congo
Kleinhans, Bronwyn ;  Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
McInnis, Bronwyn;  Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt
Tegomoh, Bryan;  The Biotechnology Center of the University of Yaoundé I, Cameroon and CDC Foundation, Yaounde, Cameroon
Brook, Cara ;  Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA ; Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
Pratt, Catherine B ;  University of Nebraska Medical Center (UNMC), Omaha, NE, USA
Scheepers, Cathrine ;  National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa ; Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
Akoua-Koffi, Chantal G;  CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d'Ivoire
Agoti, Charles N;  KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya ; School of Public Health, Pwani University, Kilifi, Kenya
Peyrefitte, Christophe;  Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
Daubenberger, Claudia ;  Swiss Tropical and Public Health Institute, Basel, Switzerland
Morang'a, Collins M ;  West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
Nokes, D James ;  KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya ; School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
Amoako, Daniel G ;  National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
Bugembe, Daniel L ;  MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
Park, Danny ;  Broad Insitute of Harvard and MIT, Cambridge, MA, USA
Baker, David;  Quadram Institute Bioscience, Norwich, UK
Doolabh, Deelan;  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
Ssemwanga, Deogratius ;  MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda ; Uganda Virus Research Institute, Entebbe, Uganda
Tshiabuila, Derek ;  KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
Bassirou, Diarra ;  Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
Amuzu, Dominic S Y ;  West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
Goedhals, Dominique;  Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
Omuoyo, Donwilliams O;  KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
Maruapula, Dorcas;  Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
Foster-Nyarko, Ebenezer;  Quadram Institute Bioscience, Norwich, UK
Lusamaki, Eddy K ;  Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo ; Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
Simulundu, Edgar ;  University of Zambia, School of Veterinary Medicine, Department of Disease Control, Lusaka, Zambia
Ong'era, Edidah M;  KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
Ngabana, Edith N;  Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo ; Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
Shumba, Edwin;  African Society for Laboratory Medicine, Addis Ababa, Ethiopia
El Fahime, Elmostafa ;  Functional Genomic Platform/National Centre for Scientific and Technical Research (CNRST), Rabat, Morocco
Lokilo, Emmanuel ;  Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
Mukantwari, Enatha ;  Rwanda National Reference Laboratory, Kigali, Rwanda
Philomena, Eromon;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Belarbi, Essia ;  Robert Koch-Institute, Berlin, Germany
Simon-Loriere, Etienne ;  G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Paris, France
Anoh, Etilé A ;  CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d'Ivoire
Leendertz, Fabian ;  Robert Koch-Institute, Berlin, Germany
Ajili, Faida;  Research Unit of Autoimmune Diseases UR17DN02, Military Hospital of Tunis, University of Tunis El Manar, Tunis, Tunisia
Enoch, Fakayode O;  Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
Wasfi, Fares ;  Laboratory of Clinical Virology, Institut Pasteur de Tunis, Tunis, Tunisia
Abdelmoula, Fatma;  Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia ; Faculty of Pharmacy of Monastir, Monastir, Tunisia
Mosha, Fausta S;  World Health Organization, Africa Region, Brazzaville Congo
Takawira, Faustinos T;  National Microbiology Reference Laboratory, Harare, Zimbabwe
Derrar, Fawzi ;  National Influenza Centre, Viral Respiratory Laboratory, Algiers, Algeria
Bouzid, Feriel ;  Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
Onikepe, Folarin ;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Adeola, Fowotade;  Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
Muyembe, Francisca M;  Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo ; Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
Tanser, Frank ;  Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK ; Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa ; Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
Dratibi, Fred A;  World Health Organization, Africa Region, Brazzaville Congo
Mbunsu, Gabriel K;  Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
Thilliez, Gaetan ;  Quadram Institute Bioscience, Norwich, UK
Kay, Gemma L ;  Quadram Institute Bioscience, Norwich, UK
Githinji, George;  KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya ; Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
van Zyl, Gert ;  Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa ; National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
Awandare, Gordon A;  West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
Schubert, Grit;  Robert Koch-Institute, Berlin, Germany
Maphalala, Gugu P;  Institution and Department, Ministry Of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
Ranaivoson, Hafaliana C ;  Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
Lemriss, Hajar ;  Laboratory of Health Sciences and Technologies, High Institute of Health Sciences, Hassan 1st University, Settat, Morocco
Anise, Happi;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Abe, Haruka;  Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
Karray, Hela H ;  CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
Nansumba, Hellen;  Central Public Health Laboratories (CPHL), Kampala, Uganda
Elgahzaly, Hesham A;  Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
Gumbo, Hlanai;  National Microbiology Reference Laboratory, Harare, Zimbabwe
Smeti, Ibtihel;  Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
Ayed, Ikhlas B;  Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
Odia, Ikponmwosa;  Irrua Specialist Teaching Hospital, Irrua, Nigeria
Ben Boubaker, Ilhem Boutiba;  Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, 1006 Tunis, Tunisia ; Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
Gaaloul, Imed;  Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
Gazy, Inbal;  Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel
Mudau, Innocent;  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
Ssewanyana, Isaac;  Central Public Health Laboratories (CPHL), Kampala, Uganda
Konstantinus, Iyaloo;  Namibia Institute of Pathology, Windhoek, Namibia
Lekana-Douk, Jean B;  Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
Makangara, Jean-Claude C ;  Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo ; Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
Tamfum, Jean-Jacques M;  Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo ; Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
Heraud, Jean-Michel ;  Virology Department, Institut Pasteur de Dakar, Dakar, Senegal ; Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
Shaffer, Jeffrey G ;  Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
Giandhari, Jennifer ;  KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
Li, Jingjing ;  Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, PA, USA
Yasuda, Jiro ;  Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
Mends, Joana Q ;  UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
Kiconco, Jocelyn;  Uganda Virus Research Institute, Entebbe, Uganda
Morobe, John M ;  KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
Gyapong, John O ;  UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
Okolie, Johnson C;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Kayiwa, John T;  MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
Edwards, Johnathan A ;  Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK ; Rollins School of Public Health, Emory University, Atlanta, GA, USA
Gyamfi, Jones ;  UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
Farah, Jouali;  Anoual Laboratory, Casablanca, Morocco
Nakaseegu, Joweria;  Uganda Virus Research Institute, Entebbe, Uganda
Ngoi, Joyce M;  West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
Namulondo, Joyce;  Uganda Virus Research Institute, Entebbe, Uganda
Andeko, Julia C;  Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
Lutwama, Julius J ;  MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
O'Grady, Justin;  Quadram Institute Bioscience, Norwich, UK
Siddle, Katherine ;  Broad Insitute of Harvard and MIT, Cambridge, MA, USA
Adeyemi, Kayode T;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Tumedi, Kefentse A ;  Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
Said, Khadija M ;  KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
Hae-Young, Kim ;  New York University Grossman School of Medicine, New York City, NY, USA
Duedu, Kwabena O ;  UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
Belyamani, Lahcen;  Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
Fki-Berrajah, Lamia;  CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
Singh, Lavanya ;  KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
Martins, Leonardo de O ;  Quadram Institute Bioscience, Norwich, UK
Tyers, Lynn ;  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
Ramuth, Magalutcheemee ;  Virology/Molecular Biology Department, Central Health Laboratory, Ministry of Health and Wellness, Mauritius
Mastouri, Maha ;  Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia ; Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
Aouni, Mahjoub;  Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
El Hefnawi, Mahmoud ;  Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo Egypt
Matsheka, Maitshwarelo I ;  Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
Kebabonye, Malebogo;  Ministry of Health and Wellness, Gaborone, Botswana
Diop, Mamadou;  Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
Turki, Manel;  Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
Paye, Marietou;  Broad Insitute of Harvard and MIT, Cambridge, MA, USA
Nyaga, Martin M;  Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
Mareka, Mathabo;  National Reference Laboratory Lesotho, Maseru, Lesotho
Damaris, Matoke-Muhia ;  Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
Mburu, Maureen W;  KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
Mpina, Maximillian ;  Swiss Tropical and Public Health Institute, Basel, Switzerland ; Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea ; Ifakara Health Institute, Dar-es-Salaam, Tanzania
Nwando, Mba;  Nigeria Centre for Disease Control, Abuja, Nigeria
Owusu, Michael;  Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
Wiley, Michael R ;  University of Nebraska Medical Center (UNMC), Omaha, NE, USA
Youtchou, Mirabeau T;  Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
Ayekaba, Mitoha O;  Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
Abouelhoda, Mohamed;  Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo 12613, Egypt ; King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
Seadawy, Mohamed G;  Biological Prevention Department, Main Chemical Laboratories, Egypt Army, Cairo, Egypt
Khalifa, Mohamed K ;  Genomics Research Program, Children's Cancer Hospital, Cairo, Egypt
Sekhele, Mooko;  National Reference Laboratory Lesotho, Maseru, Lesotho
Ouadghiri, Mouna ;  Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
Diagne, Moussa M;  Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
Mwenda, Mulenga ;  PATH, Lusaka, Zambia
Allam, Mushal ;  National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
Phan, My V T ;  MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
Abid, Nabil ;  Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia ; Department of Biotechnology, High Institute of Biotechnology of Sidi Thabet, University of Manouba, BP-66, 2020 Ariana-Tunis, Tunisia
Touil, Nadia;  Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
Rujeni, Nadine;  Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda ; School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
Kharrat, Najla ;  Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
Ismael, Nalia;  Instituto Nacional de Saude (INS), Maputo, Mozambique
Dia, Ndongo;  Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
Mabunda, Nedio;  Instituto Nacional de Saude (INS), Maputo, Mozambique
Hsiao, Nei-Yuan ;  Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa ; National Health Laboratory Service (NHLS), Cape Town, South Africa
Silochi, Nelson B ;  Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
Nsenga, Ngoy;  World Health Organization, Africa Region, Brazzaville Congo
Gumede, Nicksy;  World Health Organization, Africa Region, Brazzaville Congo
Mulder, Nicola ;  Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
Ndodo, Nnaemeka;  Nigeria Centre for Disease Control, Abuja, Nigeria
Razanajatovo, Norosoa H;  Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
Iguosadolo, Nosamiefan;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Judith, Oguzie ;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Kingsley, Ojide C;  Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
Sylvanus, Okogbenin;  Irrua Specialist Teaching Hospital, Irrua, Nigeria
Peter, Okokhere;  Irrua Specialist Teaching Hospital, Irrua, Nigeria
Femi, Oladiji;  Department of Epidemiology and Community Health, Faculty of Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
Idowu, Olawoye;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Testimony, Olumade;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Chukwuma, Omoruyi E;  Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
Ogah, Onwe E;  Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
Onwuamah, Chika K ;  The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria ; Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
Cyril, Oshomah ;  Irrua Specialist Teaching Hospital, Irrua, Nigeria
Tomori, Oyewale ;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Ondoa, Pascale;  African Society for Laboratory Medicine, Addis Ababa, Ethiopia
Combe, Patrice;  Mayotte Hospital Center, Mayotte, France
Semanda, Patrick ;  Central Public Health Laboratories (CPHL), Kampala, Uganda
Oluniyi, Paul E ;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Arnaldo, Paulo ;  Instituto Nacional de Saude (INS), Maputo, Mozambique
Quashie, Peter K ;  West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
Dussart, Philippe ;  Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
Bester, Phillip A;  Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
Mbala, Placide K;  Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo ; Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
Ayivor-Djanie, Reuben ;  UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
Njouom, Richard;  Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
Phillips, Richard O ;  Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
Gorman, Richmond;  Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
Kingsley, Robert A;  Quadram Institute Bioscience, Norwich, UK
Carr, Rosina A A;  UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
El Kabbaj, Saâd;  Laboratoire de Recherche et d'Analyses Médicales de la Gendarmerie Royale, Rabat, Morocco
Gargouri, Saba;  CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
Masmoudi, Saber;  Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
Sankhe, Safietou ;  Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
Lawal, Salako B;  The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
Kassim, Samar ;  Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
Trabelsi, Sameh;  Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
Metha, Samar;  Broad Insitute of Harvard and MIT, Cambridge, MA, USA
Kammoun, Sami;  CHU Hedi Chaker Sfax, Service de Pneumologie, Tunis, Tunisia
Lemriss, Sanaâ ;  Laboratoire de Recherche et d'Analyses Médicales de la Gendarmerie Royale, Rabat, Morocco
Agwa, Sara H A ;  Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
Calvignac-Spencer, Sébastien ;  Robert Koch-Institute, Berlin, Germany
Schaffner, Stephen F ;  Broad Insitute of Harvard and MIT, Cambridge, MA, USA
Doumbia, Seydou ;  Mali-University Clinical Research Center (UCRC), Bamako, Mali
Mandanda, Sheila M;  Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo ; Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
Aryeetey, Sherihane;  Central Public Health Laboratories (CPHL), Cairo, Egypt
Ahmed, Shymaa S ;  Central Public Health Laboratories (CPHL), Cairo, Egypt
Elhamoumi, Siham;  Broad Insitute of Harvard and MIT, Cambridge, MA, USA
Andriamandimby, Soafy;  Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
Tope, Sobajo;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Lekana-Douki, Sonia;  Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
Prosolek, Sophie ;  Quadram Institute Bioscience, Norwich, UK
Ouangraoua, Soumeya ;  Centre MURAZ, Ouagadougou, Burkina Faso ; National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
Mundeke, Steve A;  Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo ; Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
Rudder, Steven;  Quadram Institute Bioscience, Norwich, UK
Panji, Sumir ;  Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
Pillay, Sureshnee ;  KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
Engelbrecht, Susan ;  Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa ; National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
Nabadda, Susan;  Central Public Health Laboratories (CPHL), Kampala, Uganda
Behillil, Sylvie ;  National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
Budiaki, Sylvie L;  National Reference Laboratory Lesotho, Maseru, Lesotho
van der Werf, Sylvie ;  National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
Mashe, Tapfumanei;  National Microbiology Reference Laboratory, Harare, Zimbabwe
Aanniz, Tarik;  Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
Mohale, Thabo ;  National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
Le-Viet, Thanh ;  Quadram Institute Bioscience, Norwich, UK
Schindler, Tobias ;  Swiss Tropical and Public Health Institute, Basel, Switzerland ; Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
Anyaneji, Ugochukwu J ;  KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
Chinedu, Ugwu ;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Ramphal, Upasana ;  KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa ; Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa ; Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
Jessica, Uwanibe;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
George, Uwem ;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Fonseca, Vagner ;  KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa ; Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil ; Coordenação Geral de Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
Enouf, Vincent ;  National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
Gorova, Vivianne;  World Health Organization, WHO Lesotho, Maseru, Lesotho ; Med24 Medical Centre, Ruwa, Zimbabwe
Roshdy, Wael H ;  Central Public Health Laboratories (CPHL), Cairo, Egypt
Ampofo, William K;  West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
Preiser, Wolfgang ;  Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa ; National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
Choga, Wonderful T;  Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana ; Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
Bediako, Yaw ;  West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
Naidoo, Yeshnee ;  KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
Butera, Yvan  ;  Université de Liège - ULiège > GIGA ; Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda ; Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda ; Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
de Laurent, Zaydah R ;  KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
Sall, Amadou A;  Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
Rebai, Ahmed;  Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
von Gottberg, Anne ;  National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa ; School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
Kouriba, Bourema ;  Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
Williamson, Carolyn ;  Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa ; Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa ; National Health Laboratory Service (NHLS), Cape Town, South Africa
Bridges, Daniel J ;  PATH, Lusaka, Zambia
Chikwe, Ihekweazu;  Nigeria Centre for Disease Control, Abuja, Nigeria
Bhiman, Jinal N ;  National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa ; School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
Mine, Madisa;  National Health Laboratory, Gaborone, Botswana
Cotten, Matthew ;  MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda ; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
Moyo, Sikhulile ;  Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana ; Harvard T.H. Chan School of Public Health, Boston, MA, USA
Gaseitsiwe, Simani;  Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana ; Harvard T.H. Chan School of Public Health, Boston, MA, USA
Saasa, Ngonda ;  University of Zambia, School of Veterinary Medicine, Department of Disease Control, Lusaka, Zambia
Sabeti, Pardis C ;  Broad Insitute of Harvard and MIT, Cambridge, MA, USA
Kaleebu, Pontiano;  MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
Tebeje, Yenew K;  Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
Tessema, Sofonias K;  Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
Happi, Christian;  African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
Nkengasong, John;  Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
de Oliveira, Tulio;  KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa ; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa ; Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa ; Department of Global Health, University of Washington, Seattle, WA, USA
More authors (290 more) Less
Language :
English
Title :
A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.
Publication date :
22 October 2021
Journal title :
Science
ISSN :
0036-8075
eISSN :
1095-9203
Publisher :
American Association for the Advancement of Science, United States
Volume :
374
Issue :
6566
Pages :
423-431
Peer reviewed :
Peer Reviewed verified by ORBi
Funding text :
The University of Ghana (WACCBIP) team was funded by a Wellcome/African Academy of Sciences Developing Excellence in Leadership Training and Science (DELTAS) grant (DEL-15-007 and 107755/Z/15/Z: Awandare); National Institute of Health Research (NIHR) (17.63.91) grants using UK aid from the UK government for a global health research group for genomic surveillance of malaria in West Africa (Wellcome Sanger Institute, UK) and the global research unit for Tackling Infections to Benefit Africa (TIBA partnership, University of Edinburgh); and a World Bank African Centres of Excellent grant (WACCBIP-NCDs: Awandare). Project ADAGE PRFCOV19-GP2 (2020-2022) includes 40 researchers from the Center of Biotechnology of Sfax, the University of Sfax, the University of Monastir, the University Hospital H?di Chaker of Sfax, the Military Hospital of Tunis, and Dacima Consulting. Ministry of Higher Education and Scientific Research and Ministry of Health of the Republic of Tunisia. The Uganda contributions were funded by the UK Medical Research Council (MRC/UKRI) and the UK Department for International Development (DFID) under the MRC/ DFID concordat agreement (grant agreement number NC_PC_19060) and by the Wellcome, DFID?Wellcome Epidemic Preparedness?Coronavirus (grant agreement number 220977/Z/ 20/Z) awarded to M.C. Work from Quadram Institute Bioscience was funded by The Biotechnology and Biological Sciences Research Council Institute Strategic Programme Microbes in the Food Chain BB/ R012504/1 and its constituent projects BBS/E/F/000PR10348, BBS/E/F/000PR10349, BBS/E/F/000PR10351, and BBS/E/F/ 000PR10352 and by the Quadram Institute Bioscience BBSRC?funded Core Capability Grant (project number BB/CCG1860/1). The Africa Pathogen Genomics Initiative (Africa PGI) at the Africa CDC is supported by the Bill & Melinda Gates Foundation (INV018978 and INV018278), Illumina Inc, the US Centers for Disease Control and Prevention (CDC), and Oxford Nanopore Technologies. Sequences generated in Zambia through PATH were funded by the Bill & Melinda Gates Foundation. The findings and conclusions contained within are those of the authors and do not necessarily reflect positions or policies of the Bill & Melinda Gates Foundation. Funding for sequencing in C?te d?Ivoire, Burkina Faso, and part of the sequencing in the DRC was granted by the German Federal Ministry of Education and Research (BMBF). Sequencing efforts from Morocco have been supported by Academie Hassan II of Science and Technology, Morocco. Funding for surveillance, sampling, and testing in Madagasar was provided by the WHO, the CDC (grant U5/ IP000812-05), the US Agency for International Development (USAID; cooperation agreement 72068719CA00001), and the Office of the Assistant Secretary for Preparedness and Response in the US Department of Health and Human Services (DHHS; grant number IDSEP190051-01-0200). Funding for sequencing was provided by the Bill & Melinda Gates Foundation (GCE/ID OPP1211841), Chan Zuckerberg Biohub, and the Innovative Genomics Institute at UC Berkeley. The Botswana Harvard AIDS Institute was supported by the following funding: H3ABioNet through funding from the National Institutes of Health Common Fund (U41HG006941)?H3ABioNet is an initiative of the Human Health and Heredity in Africa Consortium (H3Africa) program of the African Academy of Science (AAS); DHHS?NIH?National Institute of Allergy and Infectious Diseases (NIAID) (5K24AI131928-04 and 5K24AI131924-04); Sub-Saharan African Network for TB/HIV Research Excellence (SANTHE); a DELTAS Africa Initiative (grant DEL-15-0060?the DELTAS Africa Initiative is an independent funding scheme of the AAS?s Alliance for Accelerating Excellence in Science in Africa (AESA) and supported by the New Partnership for Africa?s Development Planning and Coordinating Agency (NEPAD Agency) with funding from the Wellcome Trust [grant 107752/Z/15/Z] and the UK government; and the South African Medical Research Council (SAMRC) and the Department of Technology and Innovation as part of the Network for Genomic Surveillance in South Africa (NGS-SA) and the Stellenbosch University Faculty of Medicine & Health Sciences, Strategic Equipment Fund. D.P.M. is funded by the Wellcome Trust (Wellcome Trust grant 222574/Z/21/Z). Sequencing activities at the NICD were supported by a conditional grant from the South African National Department of Health as part of the emergency COVID-19 response; a cooperative agreement between the National Institute for Communicable Diseases of the National Health Laboratory Service and the U.S. Centers for Disease Control and Prevention (grant number 5 U01IP001048-05-00); the African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention through a sub-award from the Bill and Melinda Gates Foundation grant number INV-018978; the UK Foreign, Commonwealth and Development Office and Wellcome (Grant no 221003/Z/20/Z); the South African Medical Research Council (Reference number SHIPNCD 76756); the UK Department of Health and Social Care, managed by the Fleming Fund and performed under the auspices of the SEQAFRICA project. Furthermore, pandemic surveillance in South Africa and Senegal was supported in part through NIH grant U01 AI151698 for the United World Antiviral Research Network (UWARN). Support for pandemic surveillance from the Tulio de Oliveira group to other African countries is funded by the Rockefeller Foundation. Sequencing efforts in the DRC were funded by the Bill & Melinda Gates Foundation under grant INV-018030 awarded to C.B.P. and further supported by funding from the Africa CDC through the ASLM (African Society of Laboratory Medicine) for Accelerating SARSCoV-2 Genomic Surveillance in Africa. Sequencing efforts in Rwanda were commissioned by the NIHR Global Health Research program (16/ 136/33) using UK aid from the UK government (funding to E.M. and N. R. through TIBA partnership) and additional funds from the government of Rwanda through RBC/National Reference Laboratory in collaboration with the Belgian Development Agency (ENABEL) for additional genomic sequencing at GIGA Research Institute?Liege/ Belgium. The sequencing effort in Equatorial Guinea was supported by a public-private partnership, the Bioko Island Malaria Elimination Project, composed of the government of Equatorial Guinea Ministries of Mines and Hydrocarbons, and Health and Social Welfare, Marathon EG Production Limited, Noble Energy, Atlantic Methanol Production Company, and EG LNG. Sample collection and typing in Mali were supported by Fondation Merieux?France, and sequence efforts have been supported by the Enable and Enhance Initiative of the German Federal Government?s Security Cooperation against Biological Threats in the G5 Sahel Region. The Nigeria work was made possible by support from Flu Lab and a cohort of generous donors through TED?s Audacious Project, including the ELMA Foundation, MacKenzie Scott, the Skoll Foundation, and Open Philanthropy. Further Nigeria funding came from grants from the NIAID (www.niaid.nih. gov), NIH-H3Africa (https://h3africa.org) (U01HG007480 and U54HG007480), and the World Bank grant (worldbank.org) (ACE IMPACT project) to C.H. Analysis for the Gabon strains was supported by the Science and Technology Research Partnership for Sustainable Development (SATREPS), Japan International Cooperation Agency (JICA), and Japan Agency for Medical Research and Development (AMED) (grant number JP20jm0110013) and a grant from AMED (grant number JP20wm0225003). Sequencing at KEMRI-Wellcome Trust Research Programme site in Kenya was supported by the National Institute for Health Research (NIHR) (project references 17/ 63/82 and 16/136/33), using UK aid from the UK Government to support global health research, and the UK Foreign, Commonwealth and Development Office and Wellcome Trust (grant# 102975; 220985).
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