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BACKGROUND: Phylogenetic mapping of HIV-1 lineages circulating across defined geographical locations is promising for better understanding HIV transmission networks to design optimal prevention interventions. METHODS: We obtained near full-length HIV-1 genome sequences from people living with HIV (PLWH), including participants on antiretroviral treatment in the Botswana Combination Prevention Project, conducted in 30 Botswana communities in 2013-2018. Phylogenetic relationships among viral sequences were estimated by maximum likelihood. RESULTS: We obtained 6078 near full-length HIV-1C genome sequences from 6075 PLWH. We identified 984 phylogenetically distinct HIV-1 lineages (molecular HIV clusters) circulating in Botswana by mid-2018, with 2-27 members per cluster. Of these, dyads accounted for 62%, approximately 32% (n = 316) were found in single communities, and 68% (n = 668) were spread across multiple communities. Men in clusters were approximately 3 years older than women (median age 42 years, vs 39 years; P 

Original publication




Journal article


J Infect Dis

Publication Date





1670 - 1680


Botswana, HIV-1 clusters, transmission network, viral lineages, Adolescent, Adult, Antirheumatic Agents, Botswana, Diagnostic Tests, Routine, Female, Genome, Viral, Genotype, HIV Infections, HIV-1, Humans, Male, Middle Aged, Phylogeny, Research Design, Sequence Alignment, Young Adult