Background: Identifying the transmitted virus and elucidating its biological properties is likely to be instrumental in HIV-1 vaccine development

Methods: We developed a mathematical model of random viral evolution, and together with phylogenetic tree construction, used it to analyze 3440 complete single genome amplified HIV-1 env sequences from 102 clade B subjects. The median number of env sequences analyzed per subject per time point was 26 (range 10 to 202).

Results: Maximum within-patient env diversity ranged from 0.08% to 6.63% and segregated into 2 groups with a mean of 0.20% (range 0.08 to 0.47%) in 81 subjects and a mean of 2.76% (range 0.86 to 6.63%) in 21 others (p = 10 to 7). In 98 of the 102 subjects, a set (or sets) of identical or near identical env sequences formed the core of discreet viral lineages, each reflecting the progeny of a transmitted virus. The model predicts, and sequences confirmed, that viral env genes evolving from individual transmitted viruses generally exhibit a Poisson distribution of mutations and star-like phylogeny, which coalesces to an inferred consensus sequence at or near the moment of transmission. Instances where sequence diversity deviated from model predictions could be explained by APOBEC mediated G-to-A hypermutation, immune selection, early stochastic mutations, or transmission of closely related viruses. Altogether, the analyses indicated that 78 of 102 (77%) subjects had been infected by a single virus, and 24 (23%) others by 2 to 5 (median = 2) viruses. In no subject was there evidence of a genetic bottleneck in virus diversification between transmission and peak viremia. Transmitted Env mediated CD4 and CCR5-dependent cell entry and were neutralized by 1 or more broadly reactive human monoclonal anti-Env antibodies in concentrations typical for primary viruses.

Conclusions: Transmitted HIV-1 env, and sequences evolving from them, were identified in 98 of 102 subjects. We found low multiplicity of infection, limited env evolution preceding peak viremia, and exposure of conserved neutralization epitopes on transmitted Env. These findings provide new insight into HIV-1 transmission events and suggest that vaccine-induced neutralizing antibodies or cellular responses, if they could be elicited in sufficient titers and breadth, may constrain HIV-1 replication in this setting.