Background:  The molecular basis of HIV-1 transmission in men who have sex with men (MSM) is not well described. Prior work with heterosexual infections in 5 different clinical cohorts suggest that a single virus is responsible for transmission in approximately 80 to 90% of cases. To further understand transmission and the genetic diversity of transmitted viruses in MSM, we examined viral sequences in 21 acutely infected individuals and 5 epidemiological-linked sexual partners. Subjects engaged in unprotected insertive and receptive anal intercourse.

Methods:  We derived 1246 complete Env sequences from 31 individuals by single genome amplification (SGA):  200 3’(vif, vpu, tat, rev, env, nef, U3, and R) and 5’(U5, gag and pol) sequences were derived from peripheral blood mononuclear cells (PBMC) and plasma at different time-points from a single subject, FMS. Uncloned amplicons were sequenced and analyzed phylogenetically and mathematically by a model of random virus evolution.

Results:  Maximum within-patient env diversity ranged from 0.12 to 7.12%. Of 29 acutely infected subjects, 19 had evidence of productive infection by a single virus and 10 had infection by 2 to 10 closely or distinctly related viruses. Phylogenetic analysis on the env sequences confirmed the epidemiological-linkage of 5 donor-recipient pairs. Each set of recipient sequences originated from either acutely or chronically infected donors and formed a distinct monophyletic sub-cluster. Env nucleotide diversity between the transmitted virus(es) and the closest donor virus ranged from 0.078 to 0.27% and 0.9 to 1% for the acute-to-acute and chronic-to-acute transmissions, respectively. In subject FMS, all sequences generated from different genomic regions, from different time-points, and from different plasma vRNA and PBMC vDNA compartments coalesced to a single unambiguous transmitted virus sequence.

Conclusions:  We found that 35% of acutely infected individuals were infected by more than 1 virus. This contrasts with heterosexual infection where transmission of multiple viruses is less common (estimated at 10 to 20% frequency). The kinetics and patterns of virus diversification following transmission by AI is similar to that in heterosexual (primarily vaginal) transmission. SGA sequences of env-only, 3’ and 5’ (“half-half”), and full-length genomes from plasma vRNA and PBMC pro-viral DNA coalesce to the identical virus, supporting the phylogenetic and mathematical inference that such viruses are responsible for productive clinical infection.