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. ORCID: https://orcid.org/0000-0002-0194-6485, 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 and de Oliveira, Tulio (2021) A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science, 374 (6566). pp. 423-431. ISSN 0036-8075

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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.

Item Type:	Article
Additional Information:	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). Publisher Copyright: © 2021 American Association for the Advancement of Science. All rights reserved.
Uncontrolled Keywords:	general ,/dk/atira/pure/subjectarea/asjc/1000
Faculty \ School:	Faculty of Science > School of Biological Sciences Faculty of Medicine and Health Sciences > Norwich Medical School
Related URLs:	http://www.scopus.com/inward/record.url?...
Depositing User:	LivePure Connector
Date Deposited:	04 Nov 2022 11:30
Last Modified:	17 May 2023 01:38
URI:	https://ueaeprints.uea.ac.uk/id/eprint/89616
DOI:	10.1126/science.abj4336

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