SARS-CoV-2 Evolution in an HIV-Endemic Setting: A Genomic Epidemiology Study from Botswana

In a highly treated and vaccinated population, HIV infection did not fundamentally alter SARS-CoV-2 evolutionary trajectories at the population level. However, subtle clustering among HIV-positive hosts suggests possible host-specific effects, underscoring the importance of continued genomic surveillance integrating host immunologic and clinical data to detect early signals of viral adaptation.