Defining the human immunodeficiency virus type 1 transmission genetic bottleneck in a region with multiple circulating subtypes and recombinant forms

Abstract The Mbeya region of Tanzania has a genetically complex HIV epidemic with multiple subtypes and recombinant forms circulating, together with a high frequency of dual infections with more than one subtype. This study aimed to determine whether this impacted the HIV-1 transmission bottleneck. A total of 210 env sequences from 22 participants were generated from recently infected women from Mbeya using the single genome amplification approach. Participants were infected with subtypes C ( n  = 9), A ( n  = 4), or D ( n  = 1), and recombinants AC ( n  = 4), CD ( n  = 2), AD ( n  = 1), or ACD ( n  = 1). Sixteen participants (73%) were infected with a single variant; five (23%) with multiple variants; and one (4%) was dually infected. Thus the frequency of single variant infections was similar to cohorts located in genetically restricted subtype B or C epidemics, suggesting that multiple circulating subtypes and unique recombinant forms do not have a significant impact on the transmission bottleneck.