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

Africa Pathogen Genomics Initiative (Africa PGI)

    Research output: Contribution to journalArticlepeer-review

    55 Citations (SciVal)


    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.
    Original languageEnglish
    Article numbereabq5358
    Pages (from-to)eabq5358
    Issue number6615
    Publication statusPublished (VoR) - 7 Oct 2022


    FundersFunder number
    National Institute of Allergy and Infectious DiseasesK24AI131924


      • Africa/epidemiology *COVID-19/epidemiology/virology *Epidemiological Monitoring Genomics Humans *Pandemics *SARS-CoV-2/genetics


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