A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

Eduan Wilkinson; Marta Giovanetti; Houriiyah Tegally; James E. San; Richard Lessells; Diego Cuadros; Darren P. Martin; David A. Rasmussen; Abdel-Rahman Zekri; Abdoul Sangare; Abdoul-Salam Ouedraogo; Abdul Sesay; Abechi Priscilla; Adedotun-Sulaiman Kemi; Adewunmi Olubusuyi; Adeyemi Oluwapelumi; Adnène Hammami; Adrienne Amuri; Ahmad Sayed; Ahmed Ouma; Aida Elargoubi; Nnennaya Ajayi; Ajogbasile Victoria; Akano Kazeem; Akpede George; Alexander Trotter; Ali Yahaya; Alpha K. Keita; Amadou Diallo; Amadou Kone; Amal Souissi; Amel Chtourou; Ana Gutierrez; Andrew Page; Anika Vinze; Arash Iranzadeh; Arnold Lambisia; Arshad Ismail; Audu Rosemary; Augustina Sylverken; Ayoade Femi; Azeddine Ibrahimi; Baba Marycelin; Bamidele Oderinde; Bankole Bolajoko; Beatrice Dhaala; Belinda Herring; Berthe-Marie Njanpop-Lafourcade; Bronwyn Kleinhans; Bronwyn Mcinnis; Bryan Tegomoh; Cara Brook; Catherine Pratt; Cathrine Scheepers; Chantal Akoua-Koffi; Charles Agoti; Christophe Peyrefitte; Claudia Daubenberger; Collins Morang’a; D. James Nokes; Daniel Amoako; Daniel Bugembe; Danny Park; David Baker; Deelan Doolabh; Deogratius Ssemwanga; Derek Tshiabuila; Diarra Bassirou; Dominic Amuzu; Dominique Goedhals; Donwilliams Omuoyo; Dorcas Maruapula; Ebenezer Foster-Nyarko; Eddy Lusamaki; Edgar Simulundu; Edidah Ong’era; Edith Ngabana; Edwin Shumba; Elmostafa El Fahime; Emmanuel Lokilo; Enatha Mukantwari; Eromon Philomena; Essia Belarbi; Etienne Simon-Loriere; Etilé Anoh; Fabian Leendertz; Faida Ajili; Fakayode Enoch; Fares Wasfi; Fatma Abdelmoula; Fausta Mosha; Faustinos Takawira; Fawzi Derrar; Feriel Bouzid; Folarin Onikepe; Fowotade Adeola; Francisca Muyembe; Frank Tanser; Fred Dratibi; Gabriel Mbunsu; Gaetan Thilliez; Gemma Kay; George Githinji; Gert van Zyl; Gordon Awandare; Grit Schubert; Gugu Maphalala; Hafaliana Ranaivoson; Hajar Lemriss; Happi Anise; Haruka Abe; Hela Karray; Hellen Nansumba; Hesham Elgahzaly; Hlanai Gumbo; Ibtihel Smeti; Ikhlas Ayed; Ikponmwosa Odia; Ilhem Boutiba Ben Boubaker; Imed Gaaloul; Inbal Gazy; Innocent Mudau; Isaac Ssewanyana; Iyaloo Konstantinus; Jean Lekana-Douk; Jean-Claude Makangara; Jean-Jacques Tamfum; Jean-Michel Héraud; Jeffrey Shaffer; Jennifer Giandhari; Jingjing Li; Jiro Yasuda; Joana Mends; Jocelyn Kiconco; John Morobe; John Gyapong; Johnson Okolie; John Kayiwa; Johnathan Edwards; Jones Gyamfi; Jouali Farah; Joweria Nakaseegu; Joyce Ngoi; Joyce Namulondo; Julia Andeko; Julius Lutwama; Justin O’grady; Katherine Siddle; Kayode Adeyemi; Kefentse Tumedi; Khadija Said; Kim Hae-Young; Kwabena Duedu; Lahcen Belyamani; Lamia Fki-Berrajah; Lavanya Singh; Leonardo de O. Martins; Lynn Tyers; Magalutcheemee Ramuth; Maha Mastouri; Mahjoub Aouni; Mahmoud El Hefnawi; Maitshwarelo Matsheka; Malebogo Kebabonye; Mamadou Diop; Manel Turki; Marietou Paye; Martin Nyaga; Mathabo Mareka; Matoke-Muhia Damaris; Maureen Mburu; Maximillian Mpina; Mba Nwando; Michael Owusu; Michael Wiley; Mirabeau Youtchou; Mitoha Ayekaba; Mohamed Abouelhoda; Mohamed Seadawy; Mohamed Khalifa; Mooko Sekhele; Mouna Ouadghiri; Moussa M. Diagne; Mulenga Mwenda; Mushal Allam; My Phan; Nabil Abid; Nadia Touil; Nadine Rujeni; Najla Kharrat; Nalia Ismael; Ndongo Dia; Nedio Mabunda; Nei-Yuan Hsiao; Nelson Silochi; Ngoy Nsenga; Nicksy Gumede; Nicola Mulder; Nnaemeka Ndodo; Norosoa H Razanajatovo; Nosamiefan Iguosadolo; Oguzie Judith; Ojide Kingsley; Okogbenin Sylvanus; Okokhere Peter; Oladiji Femi; Olawoye Idowu; Olumade Testimony; Omoruyi Chukwuma; Onwe Ogah; Chika Onwuamah; Oshomah Cyril; Ousmane Faye; Oyewale Tomori; Pascale Ondoa; Patrice Combe; Patrick Semanda; Paul Oluniyi; Paulo Arnaldo; Peter Quashie; Philippe Dussart; Phillip Bester; Placide Mbala; Reuben Ayivor-Djanie; Richard Njouom; Richard Phillips; Richmond Gorman; Robert Kingsley; Rosina Carr; Saâd El Kabbaj; Saba Gargouri; Saber Masmoudi; Safietou Sankhe; Salako Lawal; Samar Kassim; Sameh Trabelsi; Samar Metha; Sami Kammoun; Sanaâ Lemriss; Sara Agwa; Sébastien Calvignac-Spencer; Stephen Schaffner; Seydou Doumbia; Sheila Mandanda; Sherihane Aryeetey; Shymaa Ahmed; Siham Elhamoumi; Soafy Andriamandimby; Sobajo Tope; Sonia Lekana-Douki; Sophie Prosolek; Soumeya Ouangraoua; Steve Mundeke; Steven Rudder; Sumir Panji; Sureshnee Pillay; Susan Engelbrecht; Susan Nabadda; Sylvie Behillil; Sylvie Budiaki; Sylvie van der Werf; Tapfumanei Mashe; Tarik Aanniz; Thabo Mohale; Thanh Le-Viet; Tobias Schindler; Ugochukwu Anyaneji; Ugwu Chinedu; Upasana Ramphal; Uwanibe Jessica; Uwem George; Vagner Fonseca; Vincent Enouf; Vivianne Gorova; Wael Roshdy; William Ampofo; Wolfgang Preiser; Wonderful Choga; Yaw Bediako; Yeshnee Naidoo; Yvan Butera; Zaydah de Laurent; Amadou A. Sall; Ahmed Rebai; Anne von Gottberg; Bourema Kouriba; Carolyn Williamson; Daniel Bridges; Ihekweazu Chikwe; Jinal Bhiman; Madisa Mine; Matthew Cotten; Sikhulile Moyo; Simani Gaseitsiwe; Ngonda Saasa; Pardis Sabeti; Pontiano Kaleebu; Yenew Tebeje; Sofonias Tessema; Christian Happi; John Nkengasong; Tulio de Oliveira

doi:10.1126/science.abj4336

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A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

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A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

Eduan Wilkinson, Marta Giovanetti, Houriiyah Tegally, James E. San, Richard Lessells, Diego Cuadros, Darren P. Martin, David A. Rasmussen, Abdel-Rahman Zekri, Abdoul Sangare, …

Science, Vol.374(6566), pp.423-431

22/10/2021

DOI: https://doi.org/10.1126/science.abj4336

PMCID: PMC7613315

PMID: 34672751

Abstract

SARS-CoV-2 across Africa The impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been hard to track in African countries, largely because of patchy data. Wilkinson et al . curated viral genomes collected in 2021 from several countries across the continent. Outbreaks during 2020 in each African country were initiated by imported cases, mostly from Europe. As the pandemic developed, case numbers in African countries were likely many times higher than reported, and subsequent waves of the pandemic appear to have been more severe. Consequently, high-transmission variants have emerged that have spread within the continent, and African countries must be included in global control efforts. —CA

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Title: A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
Creators - without role: Eduan Wilkinson - University of KwaZulu-Natal
Marta Giovanetti - Fundação Oswaldo Cruz
Houriiyah Tegally - University of KwaZulu-Natal
James E. San - University of KwaZulu-Natal
Richard Lessells - University of KwaZulu-Natal
Diego Cuadros - University of Cincinnati
Darren P. Martin - University of Cape Town
David A. Rasmussen - North Carolina State University
Abdel-Rahman Zekri
Abdoul Sangare
Abdoul-Salam Ouedraogo
Abdul Sesay - MRC Unit the Gambia
Abechi Priscilla
Adedotun-Sulaiman Kemi - Redeemer's University
Adewunmi Olubusuyi - University of Ibadan
Adeyemi Oluwapelumi
Adnène Hammami - University of Sfax
Adrienne Amuri
Ahmad Sayed - Children Cancer Hospital
Ahmed Ouma
Aida Elargoubi - University of Monastir
Nnennaya Ajayi - Federal Teaching Hospital Abakaliki
Ajogbasile Victoria - Redeemer's University
Akano Kazeem
Akpede George - Irrua Specialist Teaching Hospital
Alexander Trotter - Quadram Institute
Ali Yahaya
Alpha K. Keita - Université de Montpellier, Recherches translationnelles sur le VIH et les Maladies Infect. Endém. émerg. - TransVIHMI
Amadou Diallo - Institut Pasteur de Dakar
Amadou Kone - University of Bamako
Amal Souissi - Centre of Biotechnology of Sfax
Amel Chtourou - University of Sfax
Ana Gutierrez - Quadram Institute
Andrew Page - Quadram Institute
Anika Vinze - Broad Institute
Arash Iranzadeh - University of Cape Town
Arnold Lambisia - Kenya Medical Research Institute
Arshad Ismail - National Health Laboratory Service
Audu Rosemary
Augustina Sylverken - Charité - Universitätsmedizin Berlin
Ayoade Femi
Azeddine Ibrahimi - Mohammed V University
Baba Marycelin
Bamidele Oderinde - University of Maiduguri
Bankole Bolajoko - Redeemer's University
Beatrice Dhaala - Uganda Virus Research Institute
Belinda Herring - World Health Organization Regional Office for Africa
Berthe-Marie Njanpop-Lafourcade
Bronwyn Kleinhans - Stellenbosch University
Bronwyn Mcinnis - Cairo University
Bryan Tegomoh - Université de Yaoundé I
Cara Brook - University of Chicago
Catherine Pratt - University of Nebraska Medical Center
Cathrine Scheepers - University of the Witwatersrand
Chantal Akoua-Koffi
Charles Agoti - Pwani University
Christophe Peyrefitte - Institut Pasteur de Dakar
Claudia Daubenberger - Swiss Tropical and Public Health Institute
Collins Morang’a - University of Ghana
D. James Nokes - Kenya Medical Research Institute
Daniel Amoako - National Health Laboratory Service
Daniel Bugembe - Uganda Virus Research Institute
Danny Park
David Baker - Quadram Institute
Deelan Doolabh - Wellcome Centre for Infectious Diseases Research in Africa
Deogratius Ssemwanga - Uganda Virus Research Institute
Derek Tshiabuila - University of KwaZulu-Natal
Diarra Bassirou - Institut Pasteur de Dakar
Dominic Amuzu
Dominique Goedhals - National Health Laboratory Service
Donwilliams Omuoyo - Kenya Medical Research Institute
Dorcas Maruapula - Botswana Harvard AIDS Institute Partnership
Ebenezer Foster-Nyarko - Quadram Institute
Eddy Lusamaki
Edgar Simulundu - University of Zambia
Edidah Ong’era - Kenya Medical Research Institute
Edith Ngabana - University of Kinshasa
Edwin Shumba - African Society for Laboratory Medicine
Elmostafa El Fahime - National Centre for Nuclear Energy, Science and Technology
Emmanuel Lokilo - National Institute of Biomedical Research
Enatha Mukantwari
Eromon Philomena - Redeemer's University
Essia Belarbi - Robert Koch Institute
Etienne Simon-Loriere - Institut Pasteur
Etilé Anoh
Fabian Leendertz - Robert Koch Institute
Faida Ajili - Military Hospital of Tunis
Fakayode Enoch
Fares Wasfi
Fatma Abdelmoula - Centre of Biotechnology of Sfax
Fausta Mosha - World Health Organization Regional Office for Africa
Faustinos Takawira - National Blood Service Zimbabwe
Fawzi Derrar
Feriel Bouzid - Centre of Biotechnology of Sfax
Folarin Onikepe
Fowotade Adeola - University of Ibadan
Francisca Muyembe - University of Kinshasa
Frank Tanser - University of Lincoln
Fred Dratibi - World Health Organization Regional Office for Africa
Gabriel Mbunsu - University of Kinshasa
Gaetan Thilliez - Quadram Institute
Gemma Kay - Quadram Institute
George Githinji - Kenya Medical Research Institute
Gert van Zyl - Stellenbosch University
Gordon Awandare - University of Ghana
Grit Schubert - Robert Koch Institute
Gugu Maphalala - Ministry of Health
Hafaliana Ranaivoson - Institut Pasteur de Madagascar
Hajar Lemriss - Université Hassan 1er
Happi Anise
Haruka Abe - Nagasaki University
Hela Karray - University of Sfax
Hellen Nansumba
Hesham Elgahzaly - Ain Shams University
Hlanai Gumbo - National Blood Service Zimbabwe
Ibtihel Smeti - Centre of Biotechnology of Sfax
Ikhlas Ayed
Ikponmwosa Odia - Irrua Specialist Teaching Hospital
Ilhem Boutiba Ben Boubaker - Hôpital Charles-Nicolle
Imed Gaaloul - University of Monastir
Inbal Gazy - Hebrew University of Jerusalem
Innocent Mudau - Wellcome Centre for Infectious Diseases Research in Africa
Isaac Ssewanyana
Iyaloo Konstantinus - Namibia Institute of Pathology
Jean Lekana-Douk - Centre International de Recherches Médicales de Franceville
Jean-Claude Makangara
Jean-Jacques Tamfum
Jean-Michel Héraud - Institut Pasteur de Dakar
Jeffrey Shaffer - Tulane University
Jennifer Giandhari - University of KwaZulu-Natal
Jingjing Li - Drexel University
Jiro Yasuda - Nagasaki University
Joana Mends - University of Health and Allied Sciences
Jocelyn Kiconco - Uganda Virus Research Institute
John Morobe - Kenya Medical Research Institute
John Gyapong - University of Health and Allied Sciences
Johnson Okolie - Redeemer's University
John Kayiwa - Uganda Virus Research Institute
Johnathan Edwards - Emory University
Jones Gyamfi - University of Health and Allied Sciences
Jouali Farah
Joweria Nakaseegu - Uganda Virus Research Institute
Joyce Ngoi - University of Ghana
Joyce Namulondo - Uganda Virus Research Institute
Julia Andeko - Centre International de Recherches Médicales de Franceville
Julius Lutwama - Uganda Virus Research Institute
Justin O’grady - Quadram Institute
Katherine Siddle - Broad Institute
Kayode Adeyemi - Redeemer's University
Kefentse Tumedi - Botswana Institute for Technology Research and Innovation
Khadija Said
Kim Hae-Young
Kwabena Duedu - University of Health and Allied Sciences
Lahcen Belyamani - Mohammed V University
Lamia Fki-Berrajah - University of Sfax
Lavanya Singh - University of KwaZulu-Natal
Leonardo de O. Martins
Lynn Tyers - Wellcome Centre for Infectious Diseases Research in Africa
Magalutcheemee Ramuth - Ministry of Health and Quality of Life
Maha Mastouri - University of Monastir
Mahjoub Aouni - University of Monastir
Mahmoud El Hefnawi - National Research Centre
Maitshwarelo Matsheka - Botswana Institute for Technology Research and Innovation
Malebogo Kebabonye - Ministry of Health
Mamadou Diop - Institut Pasteur de Dakar
Manel Turki - University of Sfax
Marietou Paye - Broad Institute
Martin Nyaga - University of the Free State
Mathabo Mareka - National University of Lesotho
Matoke-Muhia Damaris
Maureen Mburu - Kenya Medical Research Institute
Maximillian Mpina
Mba Nwando
Michael Owusu - Kumasi Centre for Collaborative Research in Tropical Medicine
Michael Wiley - University of Nebraska Medical Center
Mirabeau Youtchou - Niger Delta University
Mitoha Ayekaba
Mohamed Abouelhoda - Cairo University
Mohamed Seadawy
Mohamed Khalifa - Children Cancer Hospital
Mooko Sekhele - National University of Lesotho
Mouna Ouadghiri - Mohammed V University
Moussa M. Diagne - Institut Pasteur de Dakar
Mulenga Mwenda
Mushal Allam - National Health Laboratory Service
My Phan
Nabil Abid - Manouba University
Nadia Touil - Mohammed V University
Nadine Rujeni - Rwanda Biomedical Center
Najla Kharrat - Centre of Biotechnology of Sfax
Nalia Ismael - Instituto Nacional de Saúde
Ndongo Dia - Institut Pasteur de Dakar
Nedio Mabunda - Instituto Nacional de Saúde
Nei-Yuan Hsiao
Nelson Silochi
Ngoy Nsenga - World Health Organization Regional Office for Africa
Nicksy Gumede - World Health Organization Regional Office for Africa
Nicola Mulder - University of Cape Town
Nnaemeka Ndodo - Nigeria Centre for Disease Control
Norosoa H Razanajatovo - Institut Pasteur de Madagascar
Nosamiefan Iguosadolo - Redeemer's University
Oguzie Judith
Ojide Kingsley - Federal Teaching Hospital Abakaliki
Okogbenin Sylvanus - Irrua Specialist Teaching Hospital
Okokhere Peter - Irrua Specialist Teaching Hospital
Oladiji Femi
Olawoye Idowu
Olumade Testimony
Omoruyi Chukwuma - University of Ibadan
Onwe Ogah - Federal Teaching Hospital Abakaliki
Chika Onwuamah - Nigerian Institute of Medical Research
Oshomah Cyril - Irrua Specialist Teaching Hospital
Ousmane Faye - Institut Pasteur de Dakar
Oyewale Tomori - Redeemer's University
Pascale Ondoa - African Society for Laboratory Medicine
Patrice Combe - Centre Hospitalier de Mayotte
Patrick Semanda
Paul Oluniyi - Redeemer's University
Paulo Arnaldo - Instituto Nacional de Saúde
Peter Quashie - University of Ghana
Philippe Dussart - Institut Pasteur de Madagascar
Phillip Bester - University of the Free State
Placide Mbala - University of Kinshasa
Reuben Ayivor-Djanie - University of Health and Allied Sciences
Richard Njouom - Centre Pasteur du Cameroun
Richard Phillips - Kwame Nkrumah University of Science and Technology
Richmond Gorman - Kwame Nkrumah University of Science and Technology
Robert Kingsley - Quadram Institute
Rosina Carr - University of Health and Allied Sciences
Saâd El Kabbaj - Laboratoire de Recherche et d’Analyses Médicales de la Fraternelle de la Gendarmerie Royale
Saba Gargouri - University of Sfax
Saber Masmoudi - Centre of Biotechnology of Sfax
Safietou Sankhe - Institut Pasteur de Dakar
Salako Lawal - Nigerian Institute of Medical Research
Samar Kassim - Ain Shams University
Sameh Trabelsi - Tunis El Manar University
Samar Metha - Broad Institute
Sami Kammoun - Hopital Universitaire Hedi Chaker
Sanaâ Lemriss - Laboratoire de Recherche et d’Analyses Médicales de la Fraternelle de la Gendarmerie Royale
Sara Agwa
Sébastien Calvignac-Spencer - Robert Koch Institute
Stephen Schaffner - Broad Institute
Seydou Doumbia - University of Bamako
Sheila Mandanda - University of Kinshasa
Sherihane Aryeetey - Central Laboratory For Agricultural Expert Systems
Shymaa Ahmed - Central Laboratory For Agricultural Expert Systems
Siham Elhamoumi - Broad Institute
Soafy Andriamandimby - Institut Pasteur de Madagascar
Sobajo Tope - Redeemer's University
Sonia Lekana-Douki - Centre International de Recherches Médicales de Franceville
Sophie Prosolek - Quadram Institute
Soumeya Ouangraoua - Centre Muraz
Steve Mundeke - University of Kinshasa
Steven Rudder - Quadram Institute
Sumir Panji - Wellcome Centre for Infectious Diseases Research in Africa
Sureshnee Pillay - University of KwaZulu-Natal
Susan Engelbrecht - Stellenbosch University
Susan Nabadda
Sylvie Behillil - Centre National de la Recherche Scientifique
Sylvie Budiaki - National University of Lesotho
Sylvie van der Werf - Institut Pasteur
Tapfumanei Mashe - National Blood Service Zimbabwe
Tarik Aanniz - Mohammed V University
Thabo Mohale - National Health Laboratory Service
Thanh Le-Viet - Quadram Institute
Tobias Schindler - Swiss Tropical and Public Health Institute
Ugochukwu Anyaneji - University of KwaZulu-Natal
Ugwu Chinedu
Upasana Ramphal - University of KwaZulu-Natal
Uwanibe Jessica - Redeemer's University
Uwem George - Redeemer's University
Vagner Fonseca - University of KwaZulu-Natal
Vincent Enouf - Université Paris Cité
Vivianne Gorova
Wael Roshdy - Central Laboratory For Agricultural Expert Systems
William Ampofo - University of Ghana
Wolfgang Preiser - Stellenbosch University
Wonderful Choga - Botswana Harvard AIDS Institute Partnership
Yaw Bediako - University of Ghana
Yeshnee Naidoo - University of KwaZulu-Natal
Yvan Butera - Rwanda Biomedical Center
Zaydah de Laurent - Kenya Medical Research Institute
Amadou A. Sall - Institut Pasteur de Dakar
Ahmed Rebai - Centre of Biotechnology of Sfax
Anne von Gottberg - National Health Laboratory Service
Bourema Kouriba - Nazi Boni University
Carolyn Williamson - Wellcome Centre for Infectious Diseases Research in Africa
Daniel Bridges
Ihekweazu Chikwe - Nigeria Centre for Disease Control
Jinal Bhiman - University of the Witwatersrand
Madisa Mine - Botswana Vaccine Institute
Matthew Cotten - Uganda Virus Research Institute
Sikhulile Moyo - Botswana Harvard AIDS Institute Partnership
Simani Gaseitsiwe - Botswana Harvard AIDS Institute Partnership
Ngonda Saasa - University of Zambia
Pardis Sabeti - Broad Institute
Pontiano Kaleebu - Uganda Virus Research Institute
Yenew Tebeje - Africa Centres for Disease Control and Prevention
Sofonias Tessema - Africa Centres for Disease Control and Prevention
Christian Happi - Redeemer's University
John Nkengasong - Africa Centres for Disease Control and Prevention
Tulio de Oliveira - Stellenbosch University
Publication Details: Science, Vol.374(6566), pp.423-431
Grant note: 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 Hédi 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 Côte 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 SARS-CoV-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).
Identifiers: 9936151209311
Academic Unit: Recherches translationnelles sur le VIH et les Maladies Infect. Endém. émerg. - TransVIHMI
Language: English
Resource Type: Journal article
Local Fields: hal-03772376