Abstract

The progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. Here, 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 following 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.

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Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science

Cite as

Wilkinson, E., Giovanetti, M., Tegally, H., San, J., Lessells, R., Cuadros, D., Martin, D., Rasmussen, D., Zekri, A., Sangare, A., Ouedraogo, A., Sesay, A., Priscilla, A., Kemi, A., Olubusuyi, A., Oluwapelumi, A., Hammami, A., Amuri, A., Sayed, A., Ouma, A., Elargoubi, A., Anthony, A., Victoria, A., Kazeem, A., George, A., Trotter, A., Yahaya, A., Keita, A., Diallo, A., Kone, A., Souissi, A., Chtourou, A., Gutierrez, A., Page, A., Vinze, A., Iranzadeh, A., Lambisia, A., Ismail, A., Rosemary, A., Sylverken, A., Femi, A., Ibrahimi, A., Marycelin, B., Oderinde, B., Bolajoko, B., Dhaala, B., Herring, B., Njanpop-Lafourcade, B., Kleinhans, B., McInnis, B., Tegomoh, B., Brook, C., Pratt, C., Scheepers, C., Akoua-Koffi, C., Agoti, C., Peyrefitte, C., Daubenberger, C., Morang'a, C., Nokes, D., Amoako, D., Bugembe, D., Park, D., Baker, D., Doolabh, D., Ssemwanga, D., Tshiabuila, D., Bassirou, D., Amuzu, D., Goedhals, D., Omuoyo, D., Maruapula, D., Foster-Nyarko, E., Lusamaki, E., Simulundu, E., Ong'era, E., Ngabana, E., Shumba, E., Fahime, E., Lokilo, E., Mukantwari, E., Philomena, E., Belarbi, E., Simon-Loriere, E., Anoh, E., Leendertz, F., Ajili, F., Enoch, F., Wasfi, F., Abdelmoula, F., Mosha, F., Takawira, F., Derrar, F., Bouzid, F., Onikepe, F., Adeola, F., Muyembe, F., Tanser, F., Dratibi, F., Mbunsu, G., Thilliez, G., Kay, G., Githinji, G., van Zyl, G., Awandare, G., Schubert, G., Maphalala, G., Ranaivoson, H., Lemriss, H., Anise, H., Abe, H., Karray, H., Nansumba, H., Elgahzaly, H., Gumbo, H., Smeti, I., Ayed, I., Odia, I., Boubaker, I., Gaaloul, I., Gazy, I., Mudau, I., Ssewanyana, I., Konstantinus, I., Lekana-Douk, J., Makangara, J., Tamfum, J., Heraud, J., Shaffer, J., Giandhari, J., Li, J., Yasuda, J., Mends, J., Kiconco, J., Morobe, J., Gyapong, J., Okolie, J., Kayiwa, J., Edwards, J., Gyamfi, J., Farah, J., Nakaseegu, J., Ngoi, J., Namulondo, J., Andeko, J., Lutwama, J., O'Grady, J., Siddle, K., Adeyemi, K., Tumedi, K., Said, K., Hae-Young, K., Duedu, K., Belyamani, L., Fki-Berrajah, L., Singh, L., de O Martins, L., Tyers, L., Ramuth, M., Mastouri, M., Aouni, M., el Hefnawi, M., Matsheka, M., Kebabonye, M., Diop, M., Turki, M., Paye, M., Nyaga, M., Mareka, M., Damaris, M., Mburu, M., Mpina, M., Nwando, M., Owusu, M., Wiley, M., Youtchou, M., Ayekaba, M., Abouelhoda, M., Seadawy, M., Khalifa, M., Sekhele, M., Ouadghiri, M., Diagne, M., Mwenda, M., Allam, M., Phan, M., Abid, N., Touil, N., Rujeni, N., Kharrat, N., Ismael, N., Dia, N., Mabunda, N., Hsiao, N., Silochi, N., Nsenga, N., Gumede, N., Mulder, N., Ndodo, N., Razanajatovo, N., Iguosadolo, N., Judith, O., Kingsley, O., Sylvanus, O., Peter, O., Femi, O., Idowu, O., Testimony, O., Chukwuma, O., Ogah, O., Chika, O., Cyril, O., Faye, O., Tomori, O., Ondoa, P., Combe, P., Semanda, P., Oluniyi, P., Arnaldo, P., Quashie, P., Dussart, P., Bester, P., Mbala, P., Ayivor-Djanie, R., Njouom, R., Phillips, R., Gorman, R., Kingsley, R., Carr, R., Kabbaj, S., Gargouri, S., Masmoudi, S., Sankhe, S., Lawal, S., Kassim, S., Trabelsi, S., Metha, S., Kammoun, S., Lemriss, S., Agwa, S., Calvignac-Spencer, S., Schaffner, S., Doumbia, S., Mandanda, S., Aryeetey, S., Ahmed, S., Elhamoumi, S., Andriamandimby, S., Tope, S., Lekana-Douki, S., Prosolek, S., Ouangraoua, S., Mundeke, S., Rudder, S., Panji, S., Pillay, S., Engelbrecht, S., Nabadda, S., Behillil, S., Budiaki, S., van der Werf, S., Mashe, T., Aanniz, T., Mohale, T., Le-Viet, T., Schindler, T., Anyaneji, U., Chinedu, U., Ramphal, U., Jessica, U., George, U., Fonseca, V., Enouf, V., Gorova, V., Roshdy, W., Ampofo, W., Preiser, W., Choga, W., Bediako, Y., Naidoo, Y., Butera, Y., de Laurent, Z., Sall, A., Rebai, A., von Gottberg, A., Kouriba, B., Williamson, C., Bridges, D., Chikwe, I., Bhiman, J., Mine, M., Cotten, M., Moyo, S., Gaseitsiwe, S., Saasa, N., Sabeti, P., Kaleebu, P., Tebeje, Y., Tessema, S., Happi, C., Nkengasong, J. & De Oliveira, T. 2021, 'A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa', Science, 374, pp. 423-431. http://dx.doi.org/10.1126/science.abj4336

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Last updated: 16 June 2022
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