Background:  Previous studies of the HIV variants in the plasma and peripheral mononuclear blood cells (PMBC) of epidemiologically linked donor and recipient pairs demonstrated that despite a heterogeneous quasispecies in the chronically infected donor, the recipient sequences detected soon after seroconversion represented a relatively homogeneous population that was derived from a single genetic variant within the donor. This finding suggests that an acute genetic bottleneck occurs during the transmission process. We hypothesized that at least part of this genetic restriction could be occurring in the genital compartment of the donor.  

Methods:  A unique cohort of cohabitating HIV-1 discordant couples in Lusaka, Zambia was followed prospectively. Despite intervention methods, a small percentage of the uninfected partners seroconverted; blood and genital fluid samples were obtained from both consenting partners at the time of seroconversion to investigate the nature of the variant virus transmitted.  To determine the level of viral heterogeneity in donor genital fluids of a previously characterized linked transmission pair, viral variants present in the donor vaginal fluids at the time of transmission were amplified and sequenced. Viral DNA and RNA were isolated from vaginal swabs and amplified directly (DNA) or following reverse transcription (RNA), using an end-point dilution approach to amplify single genomes.

Results:  Successful extraction and amplification of viral RNA and DNA from 3 of 5 donor vaginal swabs allowed for sequence comparison of variants found in donor blood (PBMC and plasma) and genital fluids (DNA and RNA) to those in the recipient’s blood. Phylogenetic analysis of the donor-derived envelope sequences (V1-V4) from this initial 3 pairs did not reveal evidence of a genetic bottle neck within the donor genital compartment that was the source of the newly infecting virus

Conclusions:  These initial studies do not support the hypothesis that genetic restriction in the genital tissue is the basis for the extreme genetic bottleneck observed during transmission in HIV discordant couples. Because heterosexual transmission of HIV-1 is the predominant mode of transmission worldwide and non-subtype B viruses prevail in many developing countries, this study directly addresses critical questions about which stage in HIV transmission genetic bottlenecks occur—novel information that will be relevant to the development of vaccines and microbicides.