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

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Saibu Femi; Salma Mhalla; Salome Hosch ORCID logo; Samar Kamal Kassim ORCID logo; Samar Metha; Sameh Trabelsi; Sara Hassan Agwa ORCID logo; Sarah Wambui Mwangi; Seydou Doumbia ORCID logo; Sheila Makiala-Mandanda; Sherihane Aryeetey; Shymaa S Ahmed ORCID logo; Side Mohamed Ahmed; Siham Elhamoumi; Sikhulile Moyo ORCID logo; Silvia Lutucuta; Simani Gaseitsiwe; Simbirie Jalloh; Soa Fy Andriamandimby ORCID logo; Sobajo Oguntope; Solène Grayo; Sonia Lekana-Douki ORCID logo; Sophie Prosolek; Soumeya Ouangraoua ORCID logo; Stephanie van Wyk; Stephen F Schaffner ORCID logo; Stephen Kanyerezi ORCID logo; Steve Ahuka-Mundeke; Steven Rudder; Sureshnee Pillay ORCID logo; Susan Nabadda; Sylvie Behillil ORCID logo; Sylvie L Budiaki ORCID logo; Sylvie van der Werf ORCID logo; Tapfumanei Mashe; Thabo Mohale ORCID logo; Thanh Le-Viet ORCID logo; Thirumalaisamy P Velavan ORCID logo; Tobias Schindler ORCID logo; Tongai G Maponga ORCID logo; Trevor Bedford ORCID logo; Ugochukwu J Anyaneji ORCID logo; Ugwu Chinedu ORCID logo; Upasana Ramphal ORCID logo; Uwem E George ORCID logo; Vincent Enouf ORCID logo; Vishvanath Nene; Vivianne Gorova; Wael H Roshdy ORCID logo; Wasim Abdul Karim; William K Ampofo; Wolfgang Preiser ORCID logo; Wonderful T Choga; Yahaya Ali Ahmed ORCID logo; Yajna Ramphal; Yaw Bediako ORCID logo; Yeshnee Naidoo; Yvan Butera ORCID logo; Zaydah R de Laurent ORCID logo; Africa Pathogen Genomics Initiative (Africa PGI)‡; Ahmed EO Ouma; Anne von Gottberg ORCID logo; George Githinji ORCID logo; Matshidiso Moeti; Oyewale Tomori ORCID logo; Pardis C Sabeti ORCID logo; Amadou A Sall; Samuel O Oyola; Yenew K Tebeje; Sofonias K Tessema; Tulio de Oliveira ORCID logo; Christian Happi ORCID logo; Richard Lessells ORCID logo; John Nkengasong; Eduan Wilkinson ORCID logo; (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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