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

Wilkinson, EduanORCID logo; Giovanetti, MartaORCID logo; Tegally, HouriiyahORCID logo; San, James EORCID logo; Lessells, RichardORCID logo; Cuadros, Diego; Martin, Darren P; Rasmussen, David AORCID logo; Zekri, Abdel-Rahman NORCID logo; Sangare, Abdoul K; +292 more...Ouedraogo, Abdoul-Salam; Sesay, Abdul K; Priscilla, Abechi; Kemi, Adedotun-Sulaiman; Olubusuyi, Adewunmi MORCID logo; Oluwapelumi, Adeyemi OOORCID logo; Hammami, Adnène; Amuri, Adrienne AORCID logo; Sayed, Ahmad; Ouma, Ahmed EOORCID logo; Elargoubi, Aida; Ajayi, Nnennaya AORCID logo; Victoria, Ajogbasile F; Kazeem, Akano; George, Akpede; Trotter, Alexander J; Yahaya, Ali AORCID logo; Keita, Alpha K; Diallo, AmadouORCID logo; Kone, Amadou; Souissi, AmalORCID logo; Chtourou, Amel; Gutierrez, Ana VORCID logo; Page, Andrew JORCID logo; Vinze, Anika; Iranzadeh, Arash; Lambisia, ArnoldORCID logo; Ismail, ArshadORCID logo; Rosemary, AuduORCID logo; Sylverken, AugustinaORCID logo; Femi, AyoadeORCID logo; Ibrahimi, Azeddine; Marycelin, Baba; Oderinde, Bamidele S; Bolajoko, Bankole; Dhaala, Beatrice; Herring, Belinda L; Njanpop-Lafourcade, Berthe-Marie; Kleinhans, BronwynORCID logo; McInnis, Bronwyn; Tegomoh, Bryan; Brook, CaraORCID logo; Pratt, Catherine BORCID logo; Scheepers, CathrineORCID logo; Akoua-Koffi, Chantal G; Agoti, Charles N; Peyrefitte, Christophe; Daubenberger, ClaudiaORCID logo; Morang'a, Collins MORCID logo; Nokes, D JamesORCID logo; Amoako, Daniel GORCID logo; Bugembe, Daniel LORCID logo; Park, DannyORCID logo; Baker, David; Doolabh, Deelan; Ssemwanga, DeogratiusORCID logo; Tshiabuila, DerekORCID logo; Bassirou, DiarraORCID logo; Amuzu, Dominic SYORCID logo; Goedhals, Dominique; Omuoyo, Donwilliams O; Maruapula, Dorcas; Foster-Nyarko, EbenezerORCID logo; Lusamaki, Eddy KORCID logo; Simulundu, EdgarORCID logo; Ong'era, Edidah M; Ngabana, Edith N; Shumba, Edwin; El Fahime, ElmostafaORCID logo; Lokilo, EmmanuelORCID logo; Mukantwari, EnathaORCID logo; Philomena, Eromon; Belarbi, EssiaORCID logo; Simon-Loriere, EtienneORCID logo; 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Wiley, Michael RORCID logo; Youtchou, Mirabeau T; Ayekaba, Mitoha O; Abouelhoda, Mohamed; Seadawy, Mohamed G; Khalifa, Mohamed KORCID logo; Sekhele, Mooko; Ouadghiri, MounaORCID logo; Diagne, Moussa M; Mwenda, MulengaORCID logo; Allam, MushalORCID logo; Phan, My VTORCID logo; Abid, NabilORCID logo; Touil, Nadia; Rujeni, Nadine; Kharrat, NajlaORCID logo; Ismael, Nalia; Dia, Ndongo; Mabunda, Nedio; Hsiao, Nei-YuanORCID logo; Silochi, Nelson BORCID logo; Nsenga, Ngoy; Gumede, Nicksy; Mulder, NicolaORCID logo; Ndodo, Nnaemeka; Razanajatovo, Norosoa H; Iguosadolo, Nosamiefan; Judith, OguzieORCID logo; Kingsley, Ojide C; Sylvanus, Okogbenin; Peter, Okokhere; Femi, Oladiji; Idowu, Olawoye; Testimony, Olumade; Chukwuma, Omoruyi E; Ogah, Onwe E; Onwuamah, Chika KORCID logo; Cyril, OshomahORCID logo; Faye, OusmaneORCID logo; Tomori, OyewaleORCID logo; Ondoa, Pascale; Combe, Patrice; Semanda, PatrickORCID logo; Oluniyi, Paul EORCID logo; Arnaldo, PauloORCID logo; Quashie, Peter KORCID logo; Dussart, PhilippeORCID logo; Bester, Phillip A; Mbala, Placide K; Ayivor-Djanie, ReubenORCID logo; Njouom, Richard; Phillips, Richard OORCID logo; Gorman, Richmond; Kingsley, Robert A; Carr, Rosina AA; El Kabbaj, Saâd; Gargouri, Saba; Masmoudi, Saber; Sankhe, SafietouORCID logo; Lawal, Salako B; Kassim, SamarORCID logo; Trabelsi, Sameh; Metha, Samar; Kammoun, Sami; Lemriss, SanaâORCID logo; Agwa, Sara HAORCID logo; Calvignac-Spencer, SébastienORCID logo; Schaffner, Stephen FORCID logo; Doumbia, SeydouORCID logo; Mandanda, Sheila M; Aryeetey, Sherihane; Ahmed, Shymaa SORCID logo; Elhamoumi, Siham; Andriamandimby, Soafy; Tope, Sobajo; Lekana-Douki, Sonia; Prosolek, SophieORCID logo; Ouangraoua, SoumeyaORCID logo; Mundeke, Steve A; Rudder, Steven; Panji, SumirORCID logo; Pillay, SureshneeORCID logo; Engelbrecht, SusanORCID logo; Nabadda, Susan; Behillil, SylvieORCID logo; Budiaki, Sylvie L; van der Werf, SylvieORCID logo; Mashe, Tapfumanei; Aanniz, Tarik; Mohale, ThaboORCID logo; Le-Viet, ThanhORCID logo; Schindler, TobiasORCID logo; Anyaneji, Ugochukwu JORCID logo; Chinedu, UgwuORCID logo; Ramphal, UpasanaORCID logo; Jessica, Uwanibe; George, UwemORCID logo; Fonseca, VagnerORCID logo; Enouf, VincentORCID logo; Gorova, Vivianne; Roshdy, Wael HORCID logo; Ampofo, William K; Preiser, WolfgangORCID logo; Choga, Wonderful T; Bediako, YawORCID logo; Naidoo, YeshneeORCID logo; Butera, Yvan; de Laurent, Zaydah RORCID logo; Sall, Amadou A; Rebai, Ahmed; von Gottberg, AnneORCID logo; Kouriba, BouremaORCID logo; Williamson, CarolynORCID logo; Bridges, Daniel JORCID logo; Chikwe, Ihekweazu; Bhiman, Jinal NORCID logo; Mine, Madisa; Cotten, MatthewORCID logo; Moyo, SikhulileORCID logo; Gaseitsiwe, Simani; Saasa, NgondaORCID logo; Sabeti, Pardis CORCID logo; 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 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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