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

Wilkinson, EORCID logo; Giovanetti, MORCID logo; Tegally, HORCID logo; San, JEORCID logo; Lessells, RORCID logo; Cuadros, D; Martin, DP; Rasmussen, DAORCID logo; Zekri, ANORCID logo; Sangare, AK; +292 more...Ouedraogo, A; Sesay, AK; Priscilla, A; Kemi, A; Olubusuyi, AMORCID logo; Oluwapelumi, AOORCID logo; Hammami, A; Amuri, AAORCID logo; Sayed, A; Ouma, AEORCID logo; Elargoubi, A; Ajayi, NAORCID logo; Victoria, AF; Kazeem, A; George, A; Trotter, AJ; Yahaya, AAORCID logo; Keita, AK; Diallo, AORCID logo; Kone, A; Souissi, AORCID logo; Chtourou, A; Gutierrez, AVORCID logo; Page, AJORCID logo; Vinze, A; Iranzadeh, A; Lambisia, AORCID logo; Ismail, AORCID logo; Rosemary, AORCID logo; Sylverken, AORCID logo; Femi, AORCID logo; Ibrahimi, A; Marycelin, B; Oderinde, BS; Bolajoko, B; Dhaala, B; Herring, BL; Njanpop-Lafourcade, B; Kleinhans, BORCID logo; McInnis, B; Tegomoh, B; Brook, CORCID logo; Pratt, CBORCID logo; Scheepers, CORCID logo; Akoua-Koffi, CG; Agoti, CN; Peyrefitte, C; Daubenberger, CORCID logo; Morang'a, CMORCID logo; Nokes, DJORCID logo; Amoako, DGORCID logo; Bugembe, DLORCID logo; Park, DORCID logo; Baker, D; Doolabh, D; Ssemwanga, DORCID logo; Tshiabuila, DORCID logo; Bassirou, DORCID logo; Amuzu, DSORCID logo; Goedhals, D; Omuoyo, DO; Maruapula, D; Foster-Nyarko, EORCID logo; Lusamaki, EKORCID logo; Simulundu, EORCID logo; Ong'era, EM; Ngabana, EN; Shumba, E; El Fahime, EORCID logo; Lokilo, EORCID logo; Mukantwari, EORCID logo; Philomena, E; Belarbi, EORCID logo; Simon-Loriere, EORCID logo; Anoh, EAORCID logo; Leendertz, FORCID logo; Ajili, F; Enoch, FO; Wasfi, FORCID logo; Abdelmoula, F; Mosha, FS; Takawira, FT; Derrar, FORCID logo; Bouzid, FORCID logo; Onikepe, FORCID logo; Adeola, F; Muyembe, FM; Tanser, FORCID logo; Dratibi, FA; Mbunsu, GK; Thilliez, GORCID logo; Kay, GLORCID logo; Githinji, G; van Zyl, GORCID logo; Awandare, GA; Schubert, G; Maphalala, GP; Ranaivoson, HCORCID logo; Lemriss, HORCID logo; Anise, H; Abe, H; Karray, HHORCID logo; Nansumba, H; Elgahzaly, HA; Gumbo, H; Smeti, I; Ayed, IB; Odia, I; Ben Boubaker, IB; Gaaloul, I; Gazy, I; Mudau, I; Ssewanyana, I; Konstantinus, I; Lekana-Douk, JB; Makangara, JCORCID logo; Tamfum, JM; Heraud, JORCID logo; Shaffer, JGORCID logo; Giandhari, JORCID logo; Li, JORCID logo; Yasuda, JORCID logo; Mends, JQORCID logo; Kiconco, J; Morobe, JMORCID logo; Gyapong, JOORCID logo; Okolie, JC; Kayiwa, JT; Edwards, JAORCID logo; Gyamfi, JORCID logo; Farah, J; Nakaseegu, J; Ngoi, JM; Namulondo, J; Andeko, JC; Lutwama, JJORCID logo; O'Grady, J; Siddle, KORCID logo; Adeyemi, KT; Tumedi, KAORCID logo; Said, KMORCID logo; Hae-Young, KORCID logo; Duedu, KOORCID logo; Belyamani, L; Fki-Berrajah, L; Singh, LORCID logo; Martins, LdOORCID logo; Tyers, LORCID logo; Ramuth, MORCID logo; Mastouri, MORCID logo; Aouni, M; El Hefnawi, MORCID logo; Matsheka, MIORCID logo; Kebabonye, M; Diop, M; Turki, M; Paye, M; Nyaga, MM; Mareka, M; Damaris, MORCID logo; Mburu, MW; Mpina, MORCID logo; Nwando, M; Owusu, M; Wiley, MRORCID logo; Youtchou, MT; 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Calvignac-Spencer, SORCID logo; Schaffner, SFORCID logo; Doumbia, SORCID logo; Mandanda, SM; Aryeetey, S; Ahmed, SSORCID logo; Elhamoumi, S; Andriamandimby, S; Tope, S; Lekana-Douki, S; Prosolek, SORCID logo; Ouangraoua, SORCID logo; Mundeke, SA; Rudder, S; Panji, SORCID logo; Pillay, SORCID logo; Engelbrecht, SORCID logo; Nabadda, S; Behillil, SORCID logo; Budiaki, SL; van der Werf, SORCID logo; Mashe, T; Aanniz, T; Mohale, TORCID logo; Le-Viet, TORCID logo; Schindler, TORCID logo; Anyaneji, UJORCID logo; Chinedu, UORCID logo; Ramphal, UORCID logo; Jessica, U; George, UORCID logo; Fonseca, VORCID logo; Enouf, VORCID logo; Gorova, V; Roshdy, WHORCID logo; Ampofo, WK; Preiser, WORCID logo; Choga, WT; Bediako, YORCID logo; Naidoo, YORCID logo; Butera, Y; de Laurent, ZRORCID logo; Sall, AA; Rebai, A; von Gottberg, AORCID logo; Kouriba, BORCID logo; Williamson, CORCID logo; Bridges, DJORCID logo; Chikwe, I; Bhiman, JNORCID logo; Mine, M; Cotten, MORCID logo; Moyo, SORCID logo; Gaseitsiwe, S; Saasa, NORCID logo; Sabeti, PCORCID logo; Kaleebu, P; Tebeje, YK; Tessema, SK; Happi, C; Nkengasong, J; de Oliveira, T and (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 DOI: 10.1126/science.abj4336
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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.


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