Genomics of SARS-CoV-2 in Botswana

Sikhulile Moyo of the Botswana Harvard AIDS Institute will expand the country’s genomic surveillance capacity to identify circulating SARS-CoV-2 variants and track their transmission routes and dynamics to inform the public pandemic response. Botswana has one of the highest global burdens of HIV and the associated immunosuppression may prolong SARS CoV-2 replication thereby increasing the probability of viral mutation and emergence of new variants. However, there is insufficient sequencing capacity to track these variants. They will increase national capacity by improving infrastructure, optimizing workflows, and providing training, as well as establishing a sampling framework and surveillance strategy. This will enable the temporal and spatial monitoring of circulating SARS-CoV-2 viral lineages across Botswana. They will also identify any associations between circulating viral variants and HIV infection, and study the risk of infection to specific SARS-CoV-2 variants among vaccinated people.