The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Tegally, HORCID logo; San, JEORCID logo; Cotten, MORCID logo; Moir, MORCID logo; Tegomoh, B; Mboowa, GORCID logo; Martin, DP; Baxter, CORCID logo; Lambisia, AWORCID logo; Diallo, AORCID logo; +392 more...Amoako, DGORCID logo; Diagne, MM; Sisay, AORCID logo; Zekri, ANORCID logo; Gueye, AS; Sangare, AK; Ouedraogo, A; Sow, A; Musa, AOORCID logo; Sesay, AK; Abias, AG; Elzagheid, AIORCID logo; Lagare, A; Kemi, A; Abar, AE; Johnson, AA; Fowotade, A; Oluwapelumi, AOORCID logo; Amuri, AAORCID logo; Juru, A; Kandeil, AORCID logo; Mostafa, AORCID logo; Rebai, AORCID logo; Sayed, A; Kazeem, A; Balde, A; Christoffels, AORCID logo; Trotter, AJORCID logo; Campbell, AORCID logo; Keita, AK; Kone, A; Bouzid, A; Souissi, AORCID logo; Agweyu, AORCID logo; Naguib, A; Gutierrez, AVORCID logo; Nkeshimana, A; Page, AJORCID logo; Yadouleton, AORCID logo; Vinze, A; Happi, AN; Chouikha, AORCID logo; Iranzadeh, A; Maharaj, A; Batchi-Bouyou, AL; Ismail, AORCID logo; Sylverken, AAORCID logo; Goba, A; Femi, AORCID logo; 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Semanda, PORCID logo; Oluniyi, PEORCID logo; Arnaldo, PORCID logo; Quashie, PKORCID logo; Okokhere, PO; Bejon, PORCID logo; Dussart, PORCID logo; Bester, PA; Mbala, PK; Kaleebu, P; Abechi, P; El-Shesheny, RORCID logo; Joseph, R; Aziz, RK; Essomba, RG; Ayivor-Djanie, RORCID logo; Njouom, R; Phillips, ROORCID logo; Gorman, R; Kingsley, RA; Neto Rodrigues, RMD; Audu, RAORCID logo; Carr, RAORCID logo; Gargouri, S; Masmoudi, S; Bootsma, S; Sankhe, SORCID logo; Mohamed, SI; Femi, S; Mhalla, S; Hosch, SORCID logo; Kassim, SKORCID logo; Metha, S; Trabelsi, S; Agwa, SHORCID logo; Mwangi, SW; Doumbia, SORCID logo; Makiala-Mandanda, S; Aryeetey, S; Ahmed, SSORCID logo; Ahmed, SM; Elhamoumi, S; Moyo, SORCID logo; Lutucuta, S; Gaseitsiwe, S; Jalloh, S; Andriamandimby, SFORCID logo; Oguntope, S; Grayo, S; Lekana-Douki, SORCID logo; Prosolek, S; Ouangraoua, SORCID logo; van Wyk, S; Schaffner, SFORCID logo; Kanyerezi, SORCID logo; Ahuka-Mundeke, S; Rudder, S; Pillay, SORCID logo; Nabadda, S; Behillil, SORCID logo; Budiaki, SLORCID logo; van der Werf, SORCID logo; Mashe, T; Mohale, TORCID logo; Le-Viet, TORCID logo; Velavan, TPORCID logo; Schindler, TORCID logo; Maponga, TGORCID logo; Bedford, TORCID logo; Anyaneji, UJORCID logo; Chinedu, UORCID logo; Ramphal, UORCID logo; George, UEORCID logo; Enouf, VORCID logo; Nene, V; Gorova, V; Roshdy, WHORCID logo; Karim, WA; Ampofo, WK; Preiser, WORCID logo; Choga, WT; Ahmed, YAORCID logo; Ramphal, Y; Bediako, YORCID logo; Naidoo, Y; Butera, YORCID logo; de Laurent, ZRORCID logo; Africa Pathogen Genomics Initiative (Africa PGI)‡; Ouma, AE; von Gottberg, AORCID logo; Githinji, GORCID logo; Moeti, M; Tomori, OORCID logo; Sabeti, PCORCID logo; Sall, AA; Oyola, SO; Tebeje, YK; Tessema, SK; de Oliveira, TORCID logo; Happi, CORCID logo; Lessells, RORCID logo; Nkengasong, J; Wilkinson, EORCID logo and (2022) The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. Science, 378 (6615). eabq5358-. ISSN 0036-8075 DOI: 10.1126/science.abq5358
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Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

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