The evolving SARS-CoV-2 epidemic in Africa: insights from rapidly expanding genomic surveillance. Tegally, H., San, J. E, Cotten, M., Tegomoh, B., Mboowa, G., Martin, D. P, Baxter, C., Moir, M., Lambisia, A., Diallo, A., Amoako, D. G, Diagne, M. M, Sisay, A., Zekri, A. N, Barakat, A., Gueye, A. S., Sangare, A. K, Ouedraogo, A., Sow, A., Musa, A. O, Sesay, A. K, Lagare, A., Kemi, A., Abar, A. E., Johnson, A. A, Fowotade, A., Olubusuyi, A. M, Oluwapelumi, A. O, Amuri, A. A, Juru, A., Ramadan, A. M., Kandeil, A., Mostafa, A., Rebai, A., Sayed, A., Kazeem, A., Balde, A., Christoffels, A., Trotter, A. J, Campbell, A., Keita, A. K., Kone, A., Bouzid, A., Souissi, A., Agweyu, A., Gutierrez, A. V, Page, A. J, Yadouleton, A., Vinze, A., Happi, A. N, Chouikha, A., Iranzadeh, A., Maharaj, A., Batchi-Bouyou, A. L., Ismail, A., Sylverken, A., Goba, A., Femi, A., Sijuwola, A. E., Ibrahimi, A., Marycelin, B., Salako, B. L., Oderinde, B. S, Bolajoko, B., Dhaala, B., Herring, B. L, Tsofa, B., Mvula, B., Njanpop-Lafourcade, B., Marondera, B. T, Khaireh, B. A., Kouriba, B., Adu, B., Pool, B., McInnis, B., Brook, C., Williamson, C., Anscombe, C., Pratt, C. B, Scheepers, C., Akoua-Koffi, C. G, Agoti, C. N, Loucoubar, C., Onwuamah, C. K., Ihekweazu, C., Malaka, C. N., Peyrefitte, C., Omoruyi, C. E., Rafaï, C. D., Morang'a, C. M, Nokes, D J., Lule, D. B., Bridges, D. J, Mukadi-Bamuleka, D., Park, D., Baker, D., Doolabh, D., Ssemwanga, D., Tshiabuila, D., Bassirou, D., Amuzu, D. S Y, Goedhals, D., Grant, D. S, Omuoyo, D. O, Maruapula, D., Wanjohi, D. W., Foster-Nyarko, E., Lusamaki, E. K, Simulundu, E., Ong'era, E. M, Ngabana, E. N, Abworo, E. O, Otieno, E., Shumba, E., Barasa, E., Ahmed, E. B., Kampira, E., Fahime, E. E., Lokilo, E., Mukantwari, E., Cyril, E., Philomena, E., Belarbi, E., Simon-Loriere, E., Anoh, E. A, Leendertz, F., Taweh, F. M, Wasfi, F., Abdelmoula, F., Takawira, F. T, Derrar, F., Ajogbasile, F. V, Treurnicht, F., Onikepe, F., Ntoumi, F., Muyembe, F. M, Ngiambudulu, F., Zongo Ragomzingba, F. E., Dratibi, F. A., Iyanu, F., Mbunsu, G. K, Thilliez, G., Kay, G. L, Akpede, G. O, George, U. E, van Zyl, G., Awandare, G. A, Schubert, G., Maphalala, G. P, Ranaivoson, H. C, Lemriss, H., Omunakwe, H. E, Onywera, H., Abe, H., Karray, H., Nansumba, H., Triki, H., Adje Kadjo, H. A., Elgahzaly, H., Gumbo, H., Mathieu, H., Kavunga-Membo, H., Smeti, I., Olawoye, I. B, Adetifa, I., Odia, I., Boubaker, I. B., Ssewanyana, I., Wurie, I., Konstantinus, I. S, Afiwa Halatoko, J. W., Ayei, J., Sonoo, J., Lekana-Douki, J. B., Makangara, J. C, Tamfum, J. M, Heraud, J., Shaffer, J. G, Giandhari, J., Musyoki, J., Uwanibe, J. N, Bhiman, J. N, Yasuda, J., Morais, J., Mends, J. Q, Kiconco, J., Sandi, J. D., Huddleston, J., Odoom, J. K., Morobe, J. M, Gyapong, J. O, Kayiwa, J. T, Okolie, J. C, Xavier, J. S., Gyamfi, J., Kofi Bonney, J. H., Nyandwi, J., Everatt, J., Farah, J., Nakaseegu, J., Ngoi, J. M, Namulondo, J., Oguzie, J. U, Andeko, J. C, Lutwama, J. J, O'Grady, J., Siddle, K. J, Victoir, K., Adeyemi, K. T, Tumedi, K. A, Carvalho, K. S., Mohammed, K. S., Musonda, K. G, Duedu, K. O, Belyamani, L., Fki-Berrajah, L., Singh, L., Biscornet, L., de Oliveira Martins , L., Chabuka, L., Olubayo, L., Deng, L. L., Ochola-Oyier, L. I., Mine, M., Ramuth, M., Mastouri, M., ElHefnawi, M., Mbanne, M., Matsheka, M. I, Kebabonye, M., Diop, M., Momoh, M., Lima Mendonça, M. d. L., Venter, M., Paye, M. F, Faye, M., Nyaga, M. M, Mareka, M., Damaris, M., Mburu, M. W, Mpina, M., Claujens Chastel, M. M., Owusu, M., Wiley, M. R, Tatfeng, M. Y., Ayekaba, M. O., Abouelhoda, M., Beloufa, M. A., Seadawy, M. G, Khalifa, M. K, Dellagi, M. K., Matobo, M. M., Kane, M., Ouadghiri, M., Salou, M., Mbulawa, M. B, Saibu, M. F., Mwenda, M., Kaba, M., Phan, M. V T, Abid, N., Touil, N., Rujeni, N., Ismael, N., Top, N. M., Dia, N., Mabunda, N., Hsiao, N., Silochi, N. B., Saasa, N., Bbosa, N., Murunga, N., Gumede, N., Wolter, N., Sitharam, N., Ndodo, N., Ajayi, N. A, Tordo, N., Mbhele, N., Razanajatovo, N. H, Iguosadolo, N., Mba, N., Kingsley, O. C, Sylvanus, O., Peter, O., Femi, O., Testimony, O., Ogunsanya, O. A., Fakayode, O., Ogah, O. E, Faye, O., Smith-Lawrence, P., Ondoa, P., Combe, P., Nabisubi, P., Semanda, P., Oluniyi, P. E, Arnaldo, P., Quashie, P. K., Bejon, P., Dussart, P., Bester, P. A, Mbala, P. K, Kaleebu, P., Abechi, P., El-Shesheny, R., Joseph, R., Aziz, R. K., Essomba, R. G., Ayivor-Djanie, R., Njouom, R., Phillips, R. O, Gorman, R., Kingsley, R. A, Audu, R., Carr, R. A A, Kabbaj, S. E., Gargouri, S., Masmoudi, S., Sankhe, S., Mohamed, S. I., Mhalla, S., Hosch, S., Kassim, S. K., Metha, S., Trabelsi, S., Lemriss, S., Agwa, S. H., Mwangi, S. W., Doumbia, S., Makiala-Mandanda, S., Aryeetey, S., Ahmed, S. S, Ahmed, S. M., Elhamoumi, S., Moyo, S., Lutucuta, S., Gaseitsiwe, S., Jalloh, S., Andriamandimby, S., Oguntope, S., Grayo, S., Lekana-Douki, S., Prosolek, S., Ouangraoua, S., van Wyk, S., Schaffner, S. F, Kanyerezi, S., Ahuka-Mundeke, S., Rudder, S., Pillay, S., Nabadda, S., Behillil, S., Budiaki, S. L, van der Werf, S., Mashe, T., Aanniz, T., Mohale, T., Le-Viet, T., Velavan, T. P, Schindler, T., Maponga, T., Bedford, T., Anyaneji, U. J, Chinedu, U., Ramphal, U., Enouf, V., Nene, V., Gorova, V., Roshdy, W. H, Karim, W. A., Ampofo, W. K, Preiser, W., Choga, W. T, Ahmed, Y. A., Ramphal, Y., Bediako, Y., Naidoo, Y., Butera, Y., de Laurent, Z. R, Ouma, A. E O, von Gottberg, A., Githinji, G., Moeti, M., Tomori, O., Sabeti, P. C, Sall, A. A, Oyola, S. O, Tebeje, Y. K, Tessema, S. K, de Oliveira, T., Happi, C., Lessells, R., Nkengasong, J., & Wilkinson, E. medRxiv, jan, 2022.
The evolving SARS-CoV-2 epidemic in Africa: insights from rapidly expanding genomic surveillance [link]Paper  doi  abstract   bibtex   
Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks.One-Sentence Summary Expanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.Competing Interest StatementWith the exception of Pardis Sabeti who is a co-founder of and consultant to Sherlock Biosciences and a Board Member of Danaher Corporation and who holds equity in the companies, we the authors have no conflicts of interest to declare.Funding StatementSequencing efforts in the African Union Member States were supported by the Africa Center for Disease Control (Africa CDC) - Africa Pathogen Genomics Initiative (Africa PGI), and the World Health Organization Regional Office for Africa (WHO AFRO) through the transfer of laboratory infrastructure, the provision of reagents and training. The Africa PGI is supported by the African Union, Centers for Disease Control and Prevention (CDC), Bill and Melinda Gates Foundation (BMGF), Illumina Inc, Oxford Nanopore Technologies (ONT) and other partners. In addition, all Institut Pasteur organizations and CERMES in Niger are part of the PEPAIR COVID-19-Afirica project which is funded by the French Ministry for European and Foreign Affairs. KRISP and CERI is furthermore supported in part by grants from the World Health Organization, the Abbott Pandemic Defense Coalition (APDC), the National Institute of Health USA (U01 AI151698) for the United World Antivirus Research Network (UWARN) and the INFORM Africa project through IHVN (U54 TW012041), H3BioNet Africa (Grant # 2020 HTH 062), the South African Department of Science and Innovation (SA DSI) and the South African Medical Research Council (SAMRC) under the BRICS JAF #2020/049. ILRI is also supported by the Ministry for Economic Cooperation and Federal Development of Germany (BMZ). Work conducted at ACEGID is made possible by support provided to ACEGID by a cohort of generous donors through TED's Audacious Project, including the ELMA Foundation, MacKenzie Scott, the Skoll Foundation, and Open Philanthropy. Work at ACEGID was also partly supported by grants from the National Institute of Allergy and Infectious Diseases (https://www.niaid.nih.gov), NIH-H3Africa (https://h3africa.org) (U01HG007480 and U54HG007480), the World Bank (projects ACE-019 and ACE-IMPACT), the Rockefeller Foundation (Grant #2021 HTH), the Africa CDC through the African Society of Laboratory Medicine [ASLM] (Grant #INV018978), the Wellcome Trust (Project 216619/Z/19/Z) and the Science for Africa Foundation. Sequencing efforts at the National Institute for Communicable Diseases (NICD) was also 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 United States Centers for Disease Control and Prevention (FAIN# U01IP001048; NU51IP000930); the South African Medical Research Council (SAMRC, project number 96838); the African Society of Laboratory Medicine (ASLM) and 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); and the UK Department of Health and Social Care and managed by the Fleming Fund and performed under the auspices of the SEQAFRICA project. Funding for sequencing efforts in Angola was supported through Projecto Bongola (N. 11/MESCTI/PDCT/2020) and OGE INIS (2020/2021). Botswana's sequencing efforts led by the Botswana Harvard AIDS Institute Partnership was supported by: Foundation for Innovative New Diagnostics(FINDdx); Bill and Melinda Gates Foundation, H3ABioNet [U41HG006941], Sub-Saharan African Network for TB/HIV Research Excellence (SANTHE) and Fogarty International Center (Grant # 5D43TW009610) . H3ABioNet is an initiative of the Human Health and Heredity in Africa Consortium (H3Africa) programme of the African Academy of Science (AAS). HHS/NIH/National Institute of Allergy and Infectious Diseases (NIAID) (5K24AI131928-04; 5K24AI131924-04); SANTHE is a DELTAS Africa Initiative [grant # DEL-15-006]. The DELTAS Africa Initiative is an independent funding scheme of the African Academy of Sciences (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 (NEPADAgency) with funding from the Wellcome Trust [grant #107752/Z/15/Z] and the United Kingdom (UK) government. From Brazil, Joicymara Santos Xavier was funded by Coordena'ao de Aperfei'oamento de Pessoal de Nivel Superior - Brazil (CAPES) - Finance Code 001. Sequencing efforts from Cote d'Ivoire were funded by the Robert Koch Institute and the German Federal Ministry of Education and Research (BMBF). Sequencing efforts in the Democratic Republic of the Congo were funded by the Bill & Melinda Gates Foundation under grant INV-018030 awarded to CBP 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, the US Centre for Disease Control and Prevention (US CDC), USAMRIID, IRD/Montepellier, UCLA and SACIDS FIND. Efforts from Egypt was funded by the Egyptian Ministry of Health (REF#), the Egyptian Academy for Scientific Research and Technology (ASRT) JESOR project #3046 (Center for Genome and Microbiome Research), the Cairo University anti COVID-19 fund and the Science and Technology Development Fund (STDF), Project ID: 41907. 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. 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 JP21jm0110013) and a grant from AMED (grant number JP21wm0225003). CIRMF (Gabon) is funded by the Gabonese Government and TOTAL Energy inc. CIRMF is a member of CANTAM supported by EDCTP. The work at WACCBIP (Ghana) was funded by a grant from the Rockefeller Foundation (2021 HTH 006), an Institut de Recherche pour le Developpement (IRD) grant (ARIACOV), African Research Universities Alliance (ARUA) Vaccine Development Hubs grant with funds from Open Society Foundation, 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 World Bank African Centres of Excellence Impact grant (WACCBIP-NCDs: Awandare). In addition to the funding sources from ILRI, KEMRI (Kenyan) contributions to sequencing efforts was supported in part 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 (FCDO) and Wellcome (grant# 220985/Z/20/Z) and the Kenya Medical Research Institute Grant # KEMRI/COV/SPE/012. Contributions from Lesotho was supported by the Africa CDC, African Society for Laboratory Medicine (ALSM) and the South African National Institute for Communicable Diseases (SA NICD). Liberian efforts was funded by the Africa CDC through a subaward from the Bill and Melinda Gates Foundations (REF#), while efforts from Madagascar were funded by the French Ministry for Europe and Foreign Affairs through the REPAIR COVID-19-Africa project coordinated by the Pasteur International Network association. Sequencing from Malawi was supported by Wellcome Trust (REF#). Contributions from Mali was supported by Fogarty International Center and National Institute of Allergy and Infectious Diseases sections of the National Institutes of Health under Leidos-15X051, award numbers U2RTW010673 for the West African Center of Excellence for Global Health Bioinformatics Research Training and U19AI089696 and U19AI129387 for the West Africa International Center of Excellence for Malaria Research. Sequencing efforts from Morocco have been supported by Academie Hassan II of Science and Technology, Morocco. Funding for surveillance, sampling and testing in Madagascar: World Health Organization (WHO), the US Centers for Disease Control and Prevention (US CDC: Grant#U5/IP000812-05), the United States Agency for International Development (USAID: Cooperation Agreement 72068719CA00001), the Office of the Assistant Secretary for Preparedness and Response in the U.S. Department of Health and Human Services (DHHS: grant number IDSEP190051-01-0200). Funding for sequencing: Bill & Melinda Gates Foundation (GCE/ID OPP1211841), Chan Zuckerberg Biohub, and the Innovative Genomics Institute at UC Berkeley. Mozambique acknowledges support from the Mozambican Ministry of Health and the Bill and Melinda Gates Foundation (REF#). Namibian effo
@article{Tegally2022,
abstract = {Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks.One-Sentence Summary Expanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.Competing Interest StatementWith the exception of Pardis Sabeti who is a co-founder of and consultant to Sherlock Biosciences and a Board Member of Danaher Corporation and who holds equity in the companies, we the authors have no conflicts of interest to declare.Funding StatementSequencing efforts in the African Union Member States were supported by the Africa Center for Disease Control (Africa CDC) - Africa Pathogen Genomics Initiative (Africa PGI), and the World Health Organization Regional Office for Africa (WHO AFRO) through the transfer of laboratory infrastructure, the provision of reagents and training. The Africa PGI is supported by the African Union, Centers for Disease Control and Prevention (CDC), Bill and Melinda Gates Foundation (BMGF), Illumina Inc, Oxford Nanopore Technologies (ONT) and other partners. In addition, all Institut Pasteur organizations and CERMES in Niger are part of the PEPAIR COVID-19-Afirica project which is funded by the French Ministry for European and Foreign Affairs. KRISP and CERI is furthermore supported in part by grants from the World Health Organization, the Abbott Pandemic Defense Coalition (APDC), the National Institute of Health USA (U01 AI151698) for the United World Antivirus Research Network (UWARN) and the INFORM Africa project through IHVN (U54 TW012041), H3BioNet Africa (Grant {\#} 2020 HTH 062), the South African Department of Science and Innovation (SA DSI) and the South African Medical Research Council (SAMRC) under the BRICS JAF {\#}2020/049. ILRI is also supported by the Ministry for Economic Cooperation and Federal Development of Germany (BMZ). Work conducted at ACEGID is made possible by support provided to ACEGID by a cohort of generous donors through TED{\&}{\#}039;s Audacious Project, including the ELMA Foundation, MacKenzie Scott, the Skoll Foundation, and Open Philanthropy. Work at ACEGID was also partly supported by grants from the National Institute of Allergy and Infectious Diseases (https://www.niaid.nih.gov), NIH-H3Africa (https://h3africa.org) (U01HG007480 and U54HG007480), the World Bank (projects ACE-019 and ACE-IMPACT), the Rockefeller Foundation (Grant {\#}2021 HTH), the Africa CDC through the African Society of Laboratory Medicine [ASLM] (Grant {\#}INV018978), the Wellcome Trust (Project 216619/Z/19/Z) and the Science for Africa Foundation. Sequencing efforts at the National Institute for Communicable Diseases (NICD) was also 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 United States Centers for Disease Control and Prevention (FAIN{\#} U01IP001048; NU51IP000930); the South African Medical Research Council (SAMRC, project number 96838); the African Society of Laboratory Medicine (ASLM) and 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); and the UK Department of Health and Social Care and managed by the Fleming Fund and performed under the auspices of the SEQAFRICA project. Funding for sequencing efforts in Angola was supported through Projecto Bongola (N. 11/MESCTI/PDCT/2020) and OGE INIS (2020/2021). Botswana{\&}{\#}039;s sequencing efforts led by the Botswana Harvard AIDS Institute Partnership was supported by: Foundation for Innovative New Diagnostics(FINDdx); Bill and Melinda Gates Foundation, H3ABioNet [U41HG006941], Sub-Saharan African Network for TB/HIV Research Excellence (SANTHE) and Fogarty International Center (Grant {\#} 5D43TW009610) . H3ABioNet is an initiative of the Human Health and Heredity in Africa Consortium (H3Africa) programme of the African Academy of Science (AAS). HHS/NIH/National Institute of Allergy and Infectious Diseases (NIAID) (5K24AI131928-04; 5K24AI131924-04); SANTHE is a DELTAS Africa Initiative [grant {\#} DEL-15-006]. The DELTAS Africa Initiative is an independent funding scheme of the African Academy of Sciences (AAS){\&}{\#}039;s Alliance for Accelerating Excellence in Science in Africa (AESA) and supported by the New Partnership for Africa{\&}{\#}039;s Development Planning and Coordinating Agency (NEPADAgency) with funding from the Wellcome Trust [grant {\#}107752/Z/15/Z] and the United Kingdom (UK) government. From Brazil, Joicymara Santos Xavier was funded by Coordena{\&}{\#}039;ao de Aperfei{\&}{\#}039;oamento de Pessoal de Nivel Superior - Brazil (CAPES) - Finance Code 001. Sequencing efforts from Cote d{\&}{\#}039;Ivoire were funded by the Robert Koch Institute and the German Federal Ministry of Education and Research (BMBF). Sequencing efforts in the Democratic Republic of the Congo were funded by the Bill {\&}amp; Melinda Gates Foundation under grant INV-018030 awarded to CBP 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, the US Centre for Disease Control and Prevention (US CDC), USAMRIID, IRD/Montepellier, UCLA and SACIDS FIND. Efforts from Egypt was funded by the Egyptian Ministry of Health (REF{\#}), the Egyptian Academy for Scientific Research and Technology (ASRT) JESOR project {\#}3046 (Center for Genome and Microbiome Research), the Cairo University anti COVID-19 fund and the Science and Technology Development Fund (STDF), Project ID: 41907. 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. 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 JP21jm0110013) and a grant from AMED (grant number JP21wm0225003). CIRMF (Gabon) is funded by the Gabonese Government and TOTAL Energy inc. CIRMF is a member of CANTAM supported by EDCTP. The work at WACCBIP (Ghana) was funded by a grant from the Rockefeller Foundation (2021 HTH 006), an Institut de Recherche pour le Developpement (IRD) grant (ARIACOV), African Research Universities Alliance (ARUA) Vaccine Development Hubs grant with funds from Open Society Foundation, 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 World Bank African Centres of Excellence Impact grant (WACCBIP-NCDs: Awandare). In addition to the funding sources from ILRI, KEMRI (Kenyan) contributions to sequencing efforts was supported in part 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 (FCDO) and Wellcome (grant{\#} 220985/Z/20/Z) and the Kenya Medical Research Institute Grant {\#} KEMRI/COV/SPE/012. Contributions from Lesotho was supported by the Africa CDC, African Society for Laboratory Medicine (ALSM) and the South African National Institute for Communicable Diseases (SA NICD). Liberian efforts was funded by the Africa CDC through a subaward from the Bill and Melinda Gates Foundations (REF{\#}), while efforts from Madagascar were funded by the French Ministry for Europe and Foreign Affairs through the REPAIR COVID-19-Africa project coordinated by the Pasteur International Network association. Sequencing from Malawi was supported by Wellcome Trust (REF{\#}). Contributions from Mali was supported by Fogarty International Center and National Institute of Allergy and Infectious Diseases sections of the National Institutes of Health under Leidos-15X051, award numbers U2RTW010673 for the West African Center of Excellence for Global Health Bioinformatics Research Training and U19AI089696 and U19AI129387 for the West Africa International Center of Excellence for Malaria Research. Sequencing efforts from Morocco have been supported by Academie Hassan II of Science and Technology, Morocco. Funding for surveillance, sampling and testing in Madagascar: World Health Organization (WHO), the US Centers for Disease Control and Prevention (US CDC: Grant{\#}U5/IP000812-05), the United States Agency for International Development (USAID: Cooperation Agreement 72068719CA00001), the Office of the Assistant Secretary for Preparedness and Response in the U.S. Department of Health and Human Services (DHHS: grant number IDSEP190051-01-0200). Funding for sequencing: Bill {\&}amp; Melinda Gates Foundation (GCE/ID OPP1211841), Chan Zuckerberg Biohub, and the Innovative Genomics Institute at UC Berkeley. Mozambique acknowledges support from the Mozambican Ministry of Health and the Bill and Melinda Gates Foundation (REF{\#}). Namibian effo},
author = {Tegally, Houriiyah and San, James E and Cotten, Matthew and Tegomoh, Bryan and Mboowa, Gerald and Martin, Darren P and Baxter, Cheryl and Moir, Monika and Lambisia, Arnold and Diallo, Amadou and Amoako, Daniel G and Diagne, Moussa M and Sisay, Abay and Zekri, Abdel-Rahman N and Barakat, Abdelhamid and Gueye, Abdou Salam and Sangare, Abdoul K and Ouedraogo, Abdoul-Salam and Sow, Abdourahmane and Musa, Abdualmoniem O and Sesay, Abdul K and Lagare, Adamou and Kemi, Adedotun-Sulaiman and Abar, Aden Elmi and Johnson, Adeniji A and Fowotade, Adeola and Olubusuyi, Adewumi M and Oluwapelumi, Adeyemi O and Amuri, Adrienne A and Juru, Agnes and Ramadan, Ahmad Mabrouk and Kandeil, Ahmed and Mostafa, Ahmed and Rebai, Ahmed and Sayed, Ahmed and Kazeem, Akano and Balde, Aladje and Christoffels, Alan and Trotter, Alexander J and Campbell, Allan and Keita, Alpha Kabinet and Kone, Amadou and Bouzid, Amal and Souissi, Amal and Agweyu, Ambrose and Gutierrez, Ana V and Page, Andrew J and Yadouleton, Anges and Vinze, Anika and Happi, Anise N and Chouikha, Anissa and Iranzadeh, Arash and Maharaj, Arisha and Batchi-Bouyou, Armel Landry and Ismail, Arshad and Sylverken, Augustina and Goba, Augustine and Femi, Ayoade and Sijuwola, Ayotunde Elijah and Ibrahimi, Azeddine and Marycelin, Baba and Salako, Babatunde Lawal and Oderinde, Bamidele S and Bolajoko, Bankole and Dhaala, Beatrice and Herring, Belinda L and Tsofa, Benjamin and Mvula, Bernard and Njanpop-Lafourcade, Berthe-Marie and Marondera, Blessing T and Khaireh, Bouh Abdi and Kouriba, Bourema and Adu, Bright and Pool, Brigitte and McInnis, Bronwyn and Brook, Cara and Williamson, Carolyn and Anscombe, Catherine and Pratt, Catherine B and Scheepers, Cathrine and Akoua-Koffi, Chantal G and Agoti, Charles N and Loucoubar, Cheikh and Onwuamah, Chika Kingsley and Ihekweazu, Chikwe and Malaka, Christian No{\"{e}}l and Peyrefitte, Christophe and Omoruyi, Chukwuma Ewean and Rafa{\"{i}}, Clotaire Donatien and Morang'a, Collins M and Nokes, D James and Lule, Daniel Bugembe and Bridges, Daniel J and Mukadi-Bamuleka, Daniel and Park, Danny and Baker, David and Doolabh, Deelan and Ssemwanga, Deogratius and Tshiabuila, Derek and Bassirou, Diarra and Amuzu, Dominic S Y and Goedhals, Dominique and Grant, Donald S and Omuoyo, Donwilliams O and Maruapula, Dorcas and Wanjohi, Dorcas Waruguru and Foster-Nyarko, Ebenezer and Lusamaki, Eddy K and Simulundu, Edgar and Ong'era, Edidah M and Ngabana, Edith N and Abworo, Edward O and Otieno, Edward and Shumba, Edwin and Barasa, Edwine and Ahmed, El Bara and Kampira, Elizabeth and Fahime, Elmostafa El and Lokilo, Emmanuel and Mukantwari, Enatha and Cyril, Erameh and Philomena, Eromon and Belarbi, Essia and Simon-Loriere, Etienne and Anoh, Etil{\'{e}} A and Leendertz, Fabian and Taweh, Fahn M and Wasfi, Fares and Abdelmoula, Fatma and Takawira, Faustinos T and Derrar, Fawzi and Ajogbasile, Fehintola V and Treurnicht, Florette and Onikepe, Folarin and Ntoumi, Francine and Muyembe, Francisca M and Ngiambudulu, Francisco and {Zongo Ragomzingba}, Frank Edgard and Dratibi, Fred Athanasius and Iyanu, Fred-Akintunwa and Mbunsu, Gabriel K and Thilliez, Gaetan and Kay, Gemma L and Akpede, George O and George, Uwem E and van Zyl, Gert and Awandare, Gordon A and Schubert, Grit and Maphalala, Gugu P and Ranaivoson, Hafaliana C and Lemriss, Hajar and Omunakwe, Hannah E and Onywera, Harris and Abe, Haruka and Karray, Hela and Nansumba, Hellen and Triki, Henda and {Adje Kadjo}, Herve Alb{\'{e}}ric and Elgahzaly, Hesham and Gumbo, Hlanai and Mathieu, Hota and Kavunga-Membo, Hugo and Smeti, Ibtihel and Olawoye, Idowu B and Adetifa, Ifedayo and Odia, Ikponmwosa and Boubaker, Ilhem Boutiba-Ben and Ssewanyana, Isaac and Wurie, Isatta and Konstantinus, Iyaloo S and {Afiwa Halatoko}, Jacqueline Wemboo and Ayei, James and Sonoo, Janaki and Lekana-Douki, Jean Bernard and Makangara, Jean-Claude C and Tamfum, Jean-Jacques M and Heraud, Jean-Michel and Shaffer, Jeffrey G and Giandhari, Jennifer and Musyoki, Jennifer and Uwanibe, Jessica N and Bhiman, Jinal N and Yasuda, Jiro and Morais, Joana and Mends, Joana Q and Kiconco, Jocelyn and Sandi, John Demby and Huddleston, John and Odoom, John Kofi and Morobe, John M and Gyapong, John O and Kayiwa, John T and Okolie, Johnson C and Xavier, Joicymara Santos and Gyamfi, Jones and {Kofi Bonney}, Joseph Humphrey and Nyandwi, Joseph and Everatt, Josie and Farah, Jouali and Nakaseegu, Joweria and Ngoi, Joyce M and Namulondo, Joyce and Oguzie, Judith U and Andeko, Julia C and Lutwama, Julius J and O'Grady, Justin and Siddle, Katherine J and Victoir, Kathleen and Adeyemi, Kayode T and Tumedi, Kefentse A and Carvalho, Kevin Sanders and Mohammed, Khadija Said and Musonda, Kunda G and Duedu, Kwabena O and Belyamani, Lahcen and Fki-Berrajah, Lamia and Singh, Lavanya and Biscornet, Leon and {de Oliveira Martins}, Leonardo and Chabuka, Lucious and Olubayo, Luicer and Deng, Lul Lojok and Ochola-Oyier, Lynette Isabella and Mine, Madisa and Ramuth, Magalutcheemee and Mastouri, Maha and ElHefnawi, Mahmoud and Mbanne, Maimouna and Matsheka, Maitshwarelo I and Kebabonye, Malebogo and Diop, Mamadou and Momoh, Mambu and {Lima Mendon{\c{c}}a}, Maria da Luz and Venter, Marietjie and Paye, Marietou F and Faye, Martin and Nyaga, Martin M and Mareka, Mathabo and Damaris, Matoke-Muhia and Mburu, Maureen W and Mpina, Maximillian and {Claujens Chastel}, Mfoutou Mapanguy and Owusu, Michael and Wiley, Michael R and Tatfeng, Mirabeau Youtchou and Ayekaba, Mitoha Ondo'o and Abouelhoda, Mohamed and Beloufa, Mohamed Amine and Seadawy, Mohamed G and Khalifa, Mohamed K and Dellagi, Mohammed Koussai and Matobo, Mooko Marethabile and Kane, Mouhamed and Ouadghiri, Mouna and Salou, Mounerou and Mbulawa, Mphaphi B and Saibu, Mudashiru Femi and Mwenda, Mulenga and Kaba, Muluken and Phan, My V T and Abid, Nabil and Touil, Nadia and Rujeni, Nadine and Ismael, Nalia and Top, Ndeye Marieme and Dia, Ndongo and Mabunda, N{\'{e}}dio and Hsiao, Nei-yuan and Silochi, Nelson Boric{\'{o}} and Saasa, Ngonda and Bbosa, Nicholas and Murunga, Nickson and Gumede, Nicksy and Wolter, Nicole and Sitharam, Nikita and Ndodo, Nnaemeka and Ajayi, Nnennaya A and Tordo, No{\"{e}}l and Mbhele, Nokuzola and Razanajatovo, Norosoa H and Iguosadolo, Nosamiefan and Mba, Nwando and Kingsley, Ojide C and Sylvanus, Okogbenin and Peter, Okokhere and Femi, Oladiji and Testimony, Olumade and Ogunsanya, Olusola Akinola and Fakayode, Oluwatosin and Ogah, Onwe E and Faye, Ousmane and Smith-Lawrence, Pamela and Ondoa, Pascale and Combe, Patrice and Nabisubi, Patricia and Semanda, Patrick and Oluniyi, Paul E and Arnaldo, Paulo and Quashie, Peter Kojo and Bejon, Philip and Dussart, Philippe and Bester, Phillip A and Mbala, Placide K and Kaleebu, Pontiano and Abechi, Priscilla and El-Shesheny, Rabeh and Joseph, Rageema and Aziz, Ramy Karam and Essomba, Ren{\'{e}} Ghislain and Ayivor-Djanie, Reuben and Njouom, Richard and Phillips, Richard O and Gorman, Richmond and Kingsley, Robert A and Audu, Rosemary and Carr, Rosina A A and Kabbaj, Sa{\^{a}}d El and Gargouri, Saba and Masmoudi, Saber and Sankhe, Safietou and Mohamed, Sahra Isse and Mhalla, Salma and Hosch, Salome and Kassim, Samar Kamal and Metha, Samar and Trabelsi, Sameh and Lemriss, Sana{\^{a}} and Agwa, Sara Hassan and Mwangi, Sarah Wambui and Doumbia, Seydou and Makiala-Mandanda, Sheila and Aryeetey, Sherihane and Ahmed, Shymaa S and Ahmed, Sidi Mohamed and Elhamoumi, Siham and Moyo, Sikhulile and Lutucuta, Silvia and Gaseitsiwe, Simani and Jalloh, Simbirie and Andriamandimby, Soafy and Oguntope, Sobajo and Grayo, Sol{\`{e}}ne and Lekana-Douki, Sonia and Prosolek, Sophie and Ouangraoua, Soumeya and van Wyk, Stephanie and Schaffner, Stephen F and Kanyerezi, Stephen and Ahuka-Mundeke, Steve and Rudder, Steven and Pillay, Sureshnee and Nabadda, Susan and Behillil, Sylvie and Budiaki, Sylvie L and van der Werf, Sylvie and Mashe, Tapfumanei and Aanniz, Tarik and Mohale, Thabo and Le-Viet, Thanh and Velavan, Thirumalaisamy P and Schindler, Tobias and Maponga, Tongai and Bedford, Trevor and Anyaneji, Ugochukwu J and Chinedu, Ugwu and Ramphal, Upasana and Enouf, Vincent and Nene, Vishvanath and Gorova, Vivianne and Roshdy, Wael H and Karim, Wasim Abdul and Ampofo, William K and Preiser, Wolfgang and Choga, Wonderful T and Ahmed, Yahaya Ali and Ramphal, Yajna and Bediako, Yaw and Naidoo, Yeshnee and Butera, Yvan and de Laurent, Zaydah R and Ouma, Ahmed E O and von Gottberg, Anne and Githinji, George and Moeti, Matshidiso and Tomori, Oyewale and Sabeti, Pardis C and Sall, Amadou A and Oyola, Samuel O and Tebeje, Yenew K and Tessema, Sofonias K and de Oliveira, Tulio and Happi, Christian and Lessells, Richard and Nkengasong, John and Wilkinson, Eduan},
doi = {10.1101/2022.04.17.22273906},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Tegally et al. - 2022 - The evolving SARS-CoV-2 epidemic in Africa insights from rapidly expanding genomic surveillance.pdf:pdf},
journal = {medRxiv},
keywords = {OA,fund{\_}ack,original},
mendeley-tags = {OA,fund{\_}ack,original},
month = {jan},
pages = {2022.04.17.22273906},
title = {{The evolving SARS-CoV-2 epidemic in Africa: insights from rapidly expanding genomic surveillance}},
url = {http://medrxiv.org/content/early/2022/04/20/2022.04.17.22273906.abstract},
year = {2022}
}
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