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Background:  Studies aimed at determining the infecting dose of HIV-1 in vivo and understanding viral diversification after infection have produced conflicting results. For this reason, we investigated and compared HIV-1 sequence variation in the pro-pol and env genes in plasma virus from 9 recently infected, treatment-naïve patients.

Methods:  Plasma samples were obtained from recent HIV-1 seroconverters within 5 months of infection. Individual HIV-1 pro-pol and env sequences were obtained by single-genome sequencing. We obtained 10 to 20 individual pro-pol and env sequences per sample. The pro-pol amplicons included the p6 region of gag and pro and the first 900 nucleotides of pol. Env amplicons included 900nt spanning the V1-V3 domains. We analyzed genetic diversity at single time points from 9 patients and serial time points from 3 patients over the first months to years of infection. The degree of variability within a virus population was measured by average pair-wise distance. Divergence from patient consensus and phylogenetic analyses were also performed for longitudinal samples.

Results:  The measurements of pol diversity in early post-infection samples revealed homogeneous virus populations with average pair-wise distances ranging from 0.04 to 0.5%, which averaged 5-fold less than the diversity measured in env in the same samples (0.2 to 1.1%). Of the early infection samples, 5 contained insertions in the V1/V2 loop and 8 of 9 samples showed sequence variation involving the gain or loss of glycosylation sites in env, while maintaining nearly homogeneous populations in pol. Phylogenetic analyses of serial samples showed changes in the population structure of env over intervals of 4 to 6 months until 2 to 3 years after infection. In contrast, only 1 change in population structure occurred in pol over the same 3-year period for 1 sample, ultimately reaching a diversity of 1%.

Conclusions:  Our analysis shows that the variable regions of env diversify rapidly after HIV-1 infection, whereas pol remains remarkably homogeneous. Prior studies have suggested that multiple variants of HIV-1 can be transmitted, based on substantial diversity in the V1/V2 or V3 domains of env in early infection. Our findings indicate that the early sequence diversity in env, including insertions in V1/V2, can result from transmission of a single variant followed by rapid evolution of divergent variants.

Keywords: early infection; diversity; pol and env