HIV-1 variants in population-based national surveys in sub-Saharan Africa, 2015–2022

OBJECTIVE: To describe the distribution of HIV-1 variants in population-based national surveys conducted in sub-Saharan African countries between 2015 and 2022. DESIGN: Multicountry analysis. METHODS: Sixteen population-based national surveys, conducted between 2015 and 2022, were analyzed. Survey participants were eligible if HIV genotyping was successful. In most countries, people with HIV (PWH) with a recent infection, children with HIV younger than 18 months, and a country-specific selection of PWH with a non-recent infection were included. In Nigeria and South Africa, PWH were eligible when viral load >200 or >1000 RNA copies/ml, respectively. HIV-1 variants were identified using the REGA HIV-1 & 2 Automated Subtyping Tool version 3.0. The estimated distributions of HIV-1 variants for each survey were calculated as the percentage distribution. RESULTS: The sample size varied between 42 and 1434 PWH per country survey. Country distributions showed great variation, with a majority of CRF02_AG in Cameroon, Côte d'Ivoire and Nigeria; a majority of subtype A in Kenya, Rwanda, and Uganda; near equal proportions of subtype C (39%) and subtype A (37%) in Tanzania, and dominance of subtype C (>90%) in Ethiopia, Eswatini, Lesotho, Malawi, Namibia, South Africa, Zambia, and Zimbabwe. Recombinant viruses were mostly found in countries in West-Africa. CONCLUSIONS: The distribution of HIV-1 variants by country and region in sub-Saharan Africa showed important variation. HIV-1 diversity may need to be accounted for during the development of HIV diagnostic and viral load tests, vaccines, other prevention interventions, and treatment.