Molecular Epidemiology of HIV in an African Epidemic with Declining HIV incidence but High Prevalence: A Longitudinal, Population-based Study in Uganda

The study analyzed HIV sequences and data from the Rakai Community Cohort Study from 1994 to 2019 in Uganda, where HIV incidence is declining despite high prevalence. Between December 2016 and May 2019, 474 out of 4,215 participants were newly diagnosed with HIV. Researchers identified 649 phylogenetic clusters and 673 geographic transmission chains. Most clusters were small with a median size of 2 to 3 individuals. Only 17.1% of new diagnoses had external origin, while 82.9% were linked to local chains. Mixed subtypes and recombinant chains had higher reproduction numbers (0.84) than single subtypes (0.55–0.63), but all were below one. The findings suggest that HIV transmission is fragmented across many slow-propagating lineages maintained by local clusters with occasional external introduction.