Background:  To help determine the selection of HIV-1 that occurs during sexual transmission, sequence analysis was performed on multiple clones of the entire envelope gene from both the incident and prevalent partners at the time of transmission.

Methods:  We sampled 10 monogamous partnership transmission pairs (5 male-to-female and 5 female-to-male) from the Rakai cohort at the transmitting time point that had been previously established as linked by direct sequencing of polymerase chain reaction (PCR) products from the gag, and gp41 regions were analyzed. All samples had viral loads < 10,000 copies/mL. Stored sera from the transmission time point were extracted from 20 subjects, and the gp160 gene was amplified by reverse transcriptase-nested PCR. The PCR product was cloned and 8 clones were sequenced. Gap-stripped unweighted nucleotide distances were calculated for all fragments (V1 to V5, C1 to C5, and gp41), and for the entire gp160. Additionally, these distances were determined between transmission pairs. Phylogenetic analysis was performed using PHYLIP on the entire gp160 based on envelope data from previously described full-length HIV-1 sequences from the Rakai Cohort. Statistical analysis comparing the differences in diversity in the incident time-point samples and the distance between transmitting pairs was performed using a student’s t-test incorporating a Bonferoni correction.

Results:  Biologic linkage was established between each transmission pair; however in none of the cases was the majority clone transmitted. The amount of variation between transmission pairs was greatest for female-to-male pairs in all regions except C4 and V5. The region with the least subject variation for the transmission pairs was C5, while the region with greatest variation was V4. The incident female subjects had a 4-fold greater variation in V3 region than the incidentally infected males (0.49% vs 2.00%, p < 0.05).

Conclusions:  These results demonstrate a potential difference in the selection of viral variants that occurs during male-to-female vs female-to-male transmission of HIV.

Keywords: Sexual transmission; gp160; Rakai Uganda