article · Science
Substantial investment in SARS-CoV-2 sequencing across Africa has expanded domestic genomic capacity, generating more than 100,000 genomes to monitor the pandemic. Expanding national facilities has enabled more countries to conduct sequencing locally, leading to faster turnaround times and more regular routine disease monitoring. Analysis of these genomic data reveals that the epidemic has been heterogeneous across the continent, with distinct patterns in how variants of concern, including Alpha, Beta, Delta, and Omicron, dispersed. Although low testing proportions remain an operational constraint, tracking these viral lineages illustrates the value of regional genomic infrastructure. Sustained funding and resource allocation for diagnostics and sequencing remain essential to track ongoing viral evolution. Long-term support for these capabilities will strengthen preparedness and response systems across Africa against both existing and emerging infectious disease threats.
Building local genomic sequencing capacity allows public health authorities to detect and track dangerous viral variants much more rapidly. While low testing levels present challenges, routine surveillance within African countries improves response times during outbreaks. Sustaining these diagnostic platforms ensures that national health systems are better prepared to address future infectious disease emergencies and ongoing health threats across the continent.
The findings highlight practical applications for local diagnostic platforms and genomic surveillance infrastructure. These tools are actively applied and tested within public health and disease monitoring systems across multiple countries. Potential users include national health agencies, diagnostic laboratories, and surveillance programmes seeking rapid pathogen identification. Continued expansion could drive opportunities for suppliers of sequencing consumables, diagnostic hardware, and laboratory services supporting long-term pathogen surveillance networks.
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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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DOI: 10.1126/science.abq5358
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