Background: There is a genetic bottleneck during the transmission of HIV-1 at mucosal surfaces. A greater understanding of the transmitted viral sequences may provide key insight into ongoing vaccine design efforts.

Methods: Single genome amplification (SGA) followed by direct DNA sequencing of full-length env amplicons was performed for 32 subjects with acute/early subtype C HIV-1 and 34 subjects with chronic subtype C HIV-1 infection. In addition, 3 subtype B transmission pairs were identified, and single genome amplification-derived full-length env amplicons were generated from blood plasma and semen followed by DNA sequencing and detailed phylogenetic analyses.

Results: A total of 1474 full-length env amplicons were determined from the acute and chronic cohorts. All patients with chronic HIV-1 infection had heterogeneous env populations. In contrast, the majority of acute infections (27 of 32) were homogeneous and derived from a single transmitted variant. When compared to subjects with chronic infection, subjects with acute infection had fewer glycosylation sites in the V1-V2 variable loops as well as outside the V1-V2 variable loops. In regard to the 3 subtype B transmission pairs, phylogenetic linkage was confirmed. Heterogeneous env populations were detected in blood and semen of each donor. In contrast, each recipient was found to have extremely homogeneous env populations. Several subsets of seminal env sequences were selectively amplified within the donors, comprising approximately 50% of the total population. In contrast, no amplicons were duplicated within blood plasma of the donor.

Conclusions: We found a single HIV-1 variant transmitted in 84% of acute infections with subtype C. Acute infection sequences have fewer total glycosylation sites. In addition, env sequences generated from seminal plasma intermingled with viral sequences in peripheral blood, indicating that sequences in the seminal plasma are continually replenished from peripheral sources. However, the homogeneous nature of approximately 50% of the sequences in the seminal plasma indicates a selective amplification of a subset of these sequences within the genital tract. Genotypic and phenotypic analyses of these amplified env variants may provide further insight into the biological properties of the transmitted virus, and have further implications for HIV-1 vaccine design.