Abstract
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.
| Original language | English |
|---|---|
| Pages (from-to) | 423-431 |
| Number of pages | 9 |
| Journal | Science |
| Volume | 374 |
| Issue number | 6566 |
| Early online date | 9 Sep 2021 |
| DOIs | |
| Publication status | Published - 22 Oct 2021 |
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A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. / Wilkinson, Eduan; Giovanetti, Marta; Tegally, Houriiyah; San, James E.; Lessells, Richard; Cuadros, Diego; Martin, Darren P.; Rasmussen, David A.; Zekri, Abdel Rahman N.; Sangare, Abdoul K.; Ouedraogo, Abdoul Salam; Sesay, Abdul K.; Priscilla, Abechi; Kemi, Adedotun Sulaiman; Olubusuyi, Adewunmi M.; Oluwapelumi, Adeyemi O. O.; Hammami, Adnène; Amuri, Adrienne A.; Sayed, Ahmad; Ouma, Ahmed E. O.; Elargoubi, Aida; Ajayi, Nnennaya A.; Victoria, Ajogbasile F.; Kazeem, Akano; George, Akpede; Trotter, Alexander J.; Yahaya, Ali A.; Keita, Alpha K.; Diallo, Amadou; Kone, Amadou; Souissi, Amal; Chtourou, Amel; Gutierrez, Ana V.; Page, Andrew J.; Vinze, Anika; Iranzadeh, Arash; Lambisia, Arnold; Ismail, Arshad; Rosemary, Audu; Sylverken, Augustina; Femi, Ayoade; Ibrahimi, Azeddine; Marycelin, Baba; Oderinde, Bamidele S.; Bolajoko, Bankole; Dhaala, Beatrice; Herring, Belinda L.; Njanpop-Lafourcade, Berthe Marie; Kleinhans, Bronwyn; McInnis, Bronwyn; Tegomoh, Bryan; Brook, Cara; Pratt, Catherine B.; Scheepers, Cathrine; Akoua-Koffi, Chantal G.; Agoti, Charles N.; Peyrefitte, Christophe; Daubenberger, Claudia; Morang’a, Collins M.; Nokes, D. James; Amoako, Daniel G.; Bugembe, Daniel L.; Park, Danny; Baker, David; Doolabh, Deelan; Ssemwanga, Deogratius; Tshiabuila, Derek; Bassirou, Diarra; Amuzu, Dominic S. Y.; Goedhals, Dominique; Omuoyo, Donwilliams O.; Maruapula, Dorcas; Foster-Nyarko, Ebenezer; Lusamaki, Eddy K.; Simulundu, Edgar; Ong’era, Edidah M.; Ngabana, Edith N.; Shumba, Edwin; El Fahime, Elmostafa; Lokilo, Emmanuel; Mukantwari, Enatha; Philomena, Eromon; Belarbi, Essia; Simon-Loriere, Etienne; Anoh, Etilé A.; Leendertz, Fabian; Ajili, Faida; Enoch, Fakayode O.; Wasfi, Fares; Abdelmoula, Fatma; Mosha, Fausta S.; Takawira, Faustinos T.; Derrar, Fawzi; Bouzid, Feriel; Onikepe, Folarin; Adeola, Fowotade; Muyembe, Francisca M.; Tanser, Frank; Dratibi, Fred A.; Mbunsu, Gabriel K.; Thilliez, Gaetan; Kay, Gemma L.; Githinji, George; van Zyl, Gert; Awandare, Gordon A.; Schubert, Grit; Maphalala, Gugu P.; Ranaivoson, Hafaliana C.; Lemriss, Hajar; Anise, Happi; Abe, Haruka; Karray, Hela H.; Nansumba, Hellen; Elgahzaly, Hesham A.; Gumbo, Hlanai; Smeti, Ibtihel; Ayed, Ikhlas B.; Odia, Ikponmwosa; Boubaker, Ilhem Boutiba Ben; Gaaloul, Imed; Gazy, Inbal; Mudau, Innocent; Ssewanyana, Isaac; Konstantinus, Iyaloo; Lekana-Douk, Jean B.; Makangara, Jean Claude C.; Tamfum, Jean Jacques M.; Heraud, Jean Michel; Shaffer, Jeffrey G.; Giandhari, Jennifer; Li, Jingjing; Yasuda, Jiro; Mends, Joana Q.; Kiconco, Jocelyn; Morobe, John M.; Gyapong, John O.; Okolie, Johnson C.; Kayiwa, John T.; Edwards, Johnathan A.; Gyamfi, Jones; Farah, Jouali; Nakaseegu, Joweria; Ngoi, Joyce M.; Namulondo, Joyce; Andeko, Julia C.; Lutwama, Julius J.; O’Grady, Justin; Siddle, Katherine; Adeyemi, Kayode T.; Tumedi, Kefentse A.; Said, Khadija M.; Hae-Young, Kim; Duedu, Kwabena O.; Belyamani, Lahcen; Fki-Berrajah, Lamia; Singh, Lavanya; Martins, Leonardo de O.; Tyers, Lynn; Ramuth, Magalutcheemee; Mastouri, Maha; Aouni, Mahjoub; el Hefnawi, Mahmoud; Matsheka, Maitshwarelo I.; Kebabonye, Malebogo; Diop, Mamadou; Turki, Manel; Paye, Marietou; Nyaga, Martin M.; Mareka, Mathabo; Damaris, Matoke Muhia; Mburu, Maureen W.; Mpina, Maximillian; Nwando, Mba; Owusu, Michael; Wiley, Michael R.; Youtchou, Mirabeau T.; Ayekaba, Mitoha O.; Abouelhoda, Mohamed; Seadawy, Mohamed G.; Khalifa, Mohamed K.; Sekhele, Mooko; Ouadghiri, Mouna; Diagne, Moussa M.; Mwenda, Mulenga; Allam, Mushal; Phan, My V.T.; Abid, Nabil; Touil, Nadia; Rujeni, Nadine; Kharrat, Najla; Ismael, Nalia; Dia, Ndongo; Mabunda, Nedio; Hsiao, Nei Yuan; Silochi, Nelson B.; Nsenga, Ngoy; Gumede, Nicksy; Mulder, Nicola; Ndodo, Nnaemeka; Razanajatovo, Norosoa H.; Iguosadolo, Nosamiefan; Judith, Oguzie; Kingsley, Ojide C.; Sylvanus, Okogbenin; Peter, Okokhere; Femi, Oladiji; Idowu, Olawoye; Testimony, Olumade; Chukwuma, Omoruyi E.; Ogah, Onwe E.; Onwuamah, Chika K.; Cyril, Oshomah; Faye, Ousmane; Tomori, Oyewale; Ondoa, Pascale; Combe, Patrice; Semanda, Patrick; Oluniyi, Paul E.; Arnaldo, Paulo; Quashie, Peter K.; Dussart, Philippe; Bester, Phillip A.; Mbala, Placide K.; Ayivor-Djanie, Reuben; Njouom, Richard; Phillips, Richard O.; Gorman, Richmond; Kingsley, Robert A.; Carr, Rosina A.A.; El Kabbaj, Saâd; Gargouri, Saba; Masmoudi, Saber; Sankhe, Safietou; Lawal, Salako B.; Kassim, Samar; Trabelsi, Sameh; Metha, Samar; Kammoun, Sami; Lemriss, Sanaâ; Agwa, Sara H.A.; Calvignac-Spencer, Sébastien; Schaffner, Stephen F.; Doumbia, Seydou; Mandanda, Sheila M.; Aryeetey, Sherihane; Ahmed, Shymaa S.; Elhamoumi, Siham; Andriamandimby, Soafy; Tope, Sobajo; Lekana-Douki, Sonia; Prosolek, Sophie; Ouangraoua, Soumeya; Mundeke, Steve A.; Rudder, Steven; Panji, Sumir; Pillay, Sureshnee; Engelbrecht, Susan; Nabadda, Susan; Behillil, Sylvie; Budiaki, Sylvie L.; van der Werf, Sylvie; Mashe, Tapfumanei; Aanniz, Tarik; Mohale, Thabo; Le-Viet, Thanh; Schindler, Tobias; Anyaneji, Ugochukwu J.; Chinedu, Ugwu; Ramphal, Upasana; Jessica, Uwanibe; George, Uwem; Fonseca, Vagner; Enouf, Vincent; Gorova, Vivianne; Roshdy, Wael H.; Ampofo, William K.; Preiser, Wolfgang; Choga, Wonderful T.; Bediako, Yaw; Naidoo, Yeshnee; Butera, Yvan; de Laurent, Zaydah R.; Sall, Amadou A.; Rebai, Ahmed; von Gottberg, Anne; Kouriba, Bourema; Williamson, Carolyn; Bridges, Daniel J.; Chikwe, Ihekweazu; Bhiman, Jinal N.; Mine, Madisa; Cotten, Matthew; Moyo, Sikhulile; Gaseitsiwe, Simani; Saasa, Ngonda; Sabeti, Pardis C.; Kaleebu, Pontiano; Tebeje, Yenew K.; Tessema, Sofonias K.; Happi, Christian; Nkengasong, John; de Oliveira, Tulio.
In: Science, Vol. 374, No. 6566, 22.10.2021, p. 423-431.Research output: Contribution to journal › Article › peer-review
TY - JOUR
T1 - A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
AU - Wilkinson, Eduan
AU - Giovanetti, Marta
AU - Tegally, Houriiyah
AU - San, James E.
AU - Lessells, Richard
AU - Cuadros, Diego
AU - Martin, Darren P.
AU - Rasmussen, David A.
AU - Zekri, Abdel Rahman N.
AU - Sangare, Abdoul K.
AU - Ouedraogo, Abdoul Salam
AU - Sesay, Abdul K.
AU - Priscilla, Abechi
AU - Kemi, Adedotun Sulaiman
AU - Olubusuyi, Adewunmi M.
AU - Oluwapelumi, Adeyemi O. O.
AU - Hammami, Adnène
AU - Amuri, Adrienne A.
AU - Sayed, Ahmad
AU - Ouma, Ahmed E. O.
AU - Elargoubi, Aida
AU - Ajayi, Nnennaya A.
AU - Victoria, Ajogbasile F.
AU - Kazeem, Akano
AU - George, Akpede
AU - Trotter, Alexander J.
AU - Yahaya, Ali A.
AU - Keita, Alpha K.
AU - Diallo, Amadou
AU - Kone, Amadou
AU - Souissi, Amal
AU - Chtourou, Amel
AU - Gutierrez, Ana V.
AU - Page, Andrew J.
AU - Vinze, Anika
AU - Iranzadeh, Arash
AU - Lambisia, Arnold
AU - Ismail, Arshad
AU - Rosemary, Audu
AU - Sylverken, Augustina
AU - Femi, Ayoade
AU - Ibrahimi, Azeddine
AU - Marycelin, Baba
AU - Oderinde, Bamidele S.
AU - Bolajoko, Bankole
AU - Dhaala, Beatrice
AU - Herring, Belinda L.
AU - Njanpop-Lafourcade, Berthe Marie
AU - Kleinhans, Bronwyn
AU - McInnis, Bronwyn
AU - Tegomoh, Bryan
AU - Brook, Cara
AU - Pratt, Catherine B.
AU - Scheepers, Cathrine
AU - Akoua-Koffi, Chantal G.
AU - Agoti, Charles N.
AU - Peyrefitte, Christophe
AU - Daubenberger, Claudia
AU - Morang’a, Collins M.
AU - Nokes, D. James
AU - Amoako, Daniel G.
AU - Bugembe, Daniel L.
AU - Park, Danny
AU - Baker, David
AU - Doolabh, Deelan
AU - Ssemwanga, Deogratius
AU - Tshiabuila, Derek
AU - Bassirou, Diarra
AU - Amuzu, Dominic S. Y.
AU - Goedhals, Dominique
AU - Omuoyo, Donwilliams O.
AU - Maruapula, Dorcas
AU - Foster-Nyarko, Ebenezer
AU - Lusamaki, Eddy K.
AU - Simulundu, Edgar
AU - Ong’era, Edidah M.
AU - Ngabana, Edith N.
AU - Shumba, Edwin
AU - El Fahime, Elmostafa
AU - Lokilo, Emmanuel
AU - Mukantwari, Enatha
AU - Philomena, Eromon
AU - Belarbi, Essia
AU - Simon-Loriere, Etienne
AU - Anoh, Etilé A.
AU - Leendertz, Fabian
AU - Ajili, Faida
AU - Enoch, Fakayode O.
AU - Wasfi, Fares
AU - Abdelmoula, Fatma
AU - Mosha, Fausta S.
AU - Takawira, Faustinos T.
AU - Derrar, Fawzi
AU - Bouzid, Feriel
AU - Onikepe, Folarin
AU - Adeola, Fowotade
AU - Muyembe, Francisca M.
AU - Tanser, Frank
AU - Dratibi, Fred A.
AU - Mbunsu, Gabriel K.
AU - Thilliez, Gaetan
AU - Kay, Gemma L.
AU - Githinji, George
AU - van Zyl, Gert
AU - Awandare, Gordon A.
AU - Schubert, Grit
AU - Maphalala, Gugu P.
AU - Ranaivoson, Hafaliana C.
AU - Lemriss, Hajar
AU - Anise, Happi
AU - Abe, Haruka
AU - Karray, Hela H.
AU - Nansumba, Hellen
AU - Elgahzaly, Hesham A.
AU - Gumbo, Hlanai
AU - Smeti, Ibtihel
AU - Ayed, Ikhlas B.
AU - Odia, Ikponmwosa
AU - Boubaker, Ilhem Boutiba Ben
AU - Gaaloul, Imed
AU - Gazy, Inbal
AU - Mudau, Innocent
AU - Ssewanyana, Isaac
AU - Konstantinus, Iyaloo
AU - Lekana-Douk, Jean B.
AU - Makangara, Jean Claude C.
AU - Tamfum, Jean Jacques M.
AU - Heraud, Jean Michel
AU - Shaffer, Jeffrey G.
AU - Giandhari, Jennifer
AU - Li, Jingjing
AU - Yasuda, Jiro
AU - Mends, Joana Q.
AU - Kiconco, Jocelyn
AU - Morobe, John M.
AU - Gyapong, John O.
AU - Okolie, Johnson C.
AU - Kayiwa, John T.
AU - Edwards, Johnathan A.
AU - Gyamfi, Jones
AU - Farah, Jouali
AU - Nakaseegu, Joweria
AU - Ngoi, Joyce M.
AU - Namulondo, Joyce
AU - Andeko, Julia C.
AU - Lutwama, Julius J.
AU - O’Grady, Justin
AU - Siddle, Katherine
AU - Adeyemi, Kayode T.
AU - Tumedi, Kefentse A.
AU - Said, Khadija M.
AU - Hae-Young, Kim
AU - Duedu, Kwabena O.
AU - Belyamani, Lahcen
AU - Fki-Berrajah, Lamia
AU - Singh, Lavanya
AU - Martins, Leonardo de O.
AU - Tyers, Lynn
AU - Ramuth, Magalutcheemee
AU - Mastouri, Maha
AU - Aouni, Mahjoub
AU - el Hefnawi, Mahmoud
AU - Matsheka, Maitshwarelo I.
AU - Kebabonye, Malebogo
AU - Diop, Mamadou
AU - Turki, Manel
AU - Paye, Marietou
AU - Nyaga, Martin M.
AU - Mareka, Mathabo
AU - Damaris, Matoke Muhia
AU - Mburu, Maureen W.
AU - Mpina, Maximillian
AU - Nwando, Mba
AU - Owusu, Michael
AU - Wiley, Michael R.
AU - Youtchou, Mirabeau T.
AU - Ayekaba, Mitoha O.
AU - Abouelhoda, Mohamed
AU - Seadawy, Mohamed G.
AU - Khalifa, Mohamed K.
AU - Sekhele, Mooko
AU - Ouadghiri, Mouna
AU - Diagne, Moussa M.
AU - Mwenda, Mulenga
AU - Allam, Mushal
AU - Phan, My V.T.
AU - Abid, Nabil
AU - Touil, Nadia
AU - Rujeni, Nadine
AU - Kharrat, Najla
AU - Ismael, Nalia
AU - Dia, Ndongo
AU - Mabunda, Nedio
AU - Hsiao, Nei Yuan
AU - Silochi, Nelson B.
AU - Nsenga, Ngoy
AU - Gumede, Nicksy
AU - Mulder, Nicola
AU - Ndodo, Nnaemeka
AU - Razanajatovo, Norosoa H.
AU - Iguosadolo, Nosamiefan
AU - Judith, Oguzie
AU - Kingsley, Ojide C.
AU - Sylvanus, Okogbenin
AU - Peter, Okokhere
AU - Femi, Oladiji
AU - Idowu, Olawoye
AU - Testimony, Olumade
AU - Chukwuma, Omoruyi E.
AU - Ogah, Onwe E.
AU - Onwuamah, Chika K.
AU - Cyril, Oshomah
AU - Faye, Ousmane
AU - Tomori, Oyewale
AU - Ondoa, Pascale
AU - Combe, Patrice
AU - Semanda, Patrick
AU - Oluniyi, Paul E.
AU - Arnaldo, Paulo
AU - Quashie, Peter K.
AU - Dussart, Philippe
AU - Bester, Phillip A.
AU - Mbala, Placide K.
AU - Ayivor-Djanie, Reuben
AU - Njouom, Richard
AU - Phillips, Richard O.
AU - Gorman, Richmond
AU - Kingsley, Robert A.
AU - Carr, Rosina A.A.
AU - El Kabbaj, Saâd
AU - Gargouri, Saba
AU - Masmoudi, Saber
AU - Sankhe, Safietou
AU - Lawal, Salako B.
AU - Kassim, Samar
AU - Trabelsi, Sameh
AU - Metha, Samar
AU - Kammoun, Sami
AU - Lemriss, Sanaâ
AU - Agwa, Sara H.A.
AU - Calvignac-Spencer, Sébastien
AU - Schaffner, Stephen F.
AU - Doumbia, Seydou
AU - Mandanda, Sheila M.
AU - Aryeetey, Sherihane
AU - Ahmed, Shymaa S.
AU - Elhamoumi, Siham
AU - Andriamandimby, Soafy
AU - Tope, Sobajo
AU - Lekana-Douki, Sonia
AU - Prosolek, Sophie
AU - Ouangraoua, Soumeya
AU - Mundeke, Steve A.
AU - Rudder, Steven
AU - Panji, Sumir
AU - Pillay, Sureshnee
AU - Engelbrecht, Susan
AU - Nabadda, Susan
AU - Behillil, Sylvie
AU - Budiaki, Sylvie L.
AU - van der Werf, Sylvie
AU - Mashe, Tapfumanei
AU - Aanniz, Tarik
AU - Mohale, Thabo
AU - Le-Viet, Thanh
AU - Schindler, Tobias
AU - Anyaneji, Ugochukwu J.
AU - Chinedu, Ugwu
AU - Ramphal, Upasana
AU - Jessica, Uwanibe
AU - George, Uwem
AU - Fonseca, Vagner
AU - Enouf, Vincent
AU - Gorova, Vivianne
AU - Roshdy, Wael H.
AU - Ampofo, William K.
AU - Preiser, Wolfgang
AU - Choga, Wonderful T.
AU - Bediako, Yaw
AU - Naidoo, Yeshnee
AU - Butera, Yvan
AU - de Laurent, Zaydah R.
AU - Sall, Amadou A.
AU - Rebai, Ahmed
AU - von Gottberg, Anne
AU - Kouriba, Bourema
AU - Williamson, Carolyn
AU - Bridges, Daniel J.
AU - Chikwe, Ihekweazu
AU - Bhiman, Jinal N.
AU - Mine, Madisa
AU - Cotten, Matthew
AU - Moyo, Sikhulile
AU - Gaseitsiwe, Simani
AU - Saasa, Ngonda
AU - Sabeti, Pardis C.
AU - Kaleebu, Pontiano
AU - Tebeje, Yenew K.
AU - Tessema, Sofonias K.
AU - Happi, Christian
AU - Nkengasong, John
AU - de Oliveira, Tulio
N1 - Funding Information: 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 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).
PY - 2021/10/22
Y1 - 2021/10/22
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85118485974&partnerID=8YFLogxK
U2 - 10.1126/science.abj4336
DO - 10.1126/science.abj4336
M3 - Article
C2 - 34672751
AN - SCOPUS:85118485974
VL - 374
SP - 423
EP - 431
JO - Science
JF - Science
SN - 0036-8075
IS - 6566
ER -