While HIV-1 transmission in humans occurs most frequently through mucosal exposure, the present study was undertaken using rhesus monkeys infected by intravenous inoculation of SIV using artificial means to collect longitudinal semen samples. Although infection by this virus and route therefore does not model mucosal HIV-1 acquisition, the present findings have important ramifications for the understanding of early events leading to infection of the male genital tract, and semen as a source of transmitted virus. Low-risk sexual transmission of HIV-1 usually results in an infection initiated by a very limited number of founder viruses 
. These viruses very rapidly appear in the blood after the transmission event, presumably as a consequence of the larger number of target cells in the blood than in the genital tract. In the periphery, HIV or SIV rapidly replicates to high levels and any subsequent virus diversification is likely a consequence of differences in virus replication in these compartments, independent of how infection was initiated.
During peak SIV replication we found little evidence for genetic segregation of virus between the semen and blood of infected rhesus monkeys. Instead, we observed an equilibration of SIV between these compartments manifested as closely related clusters of intermixed virus sequences derived from the semen or blood. As we applied SGA technology to generate all sequences 
, the large numbers of identical sequences observed at peak virus replication are not likely to be a methodologic artifact. Moreover, since the SIV population size in the semen during peak virus replication was high, error as a result of re-sampling seems unlikely 
Based on the phylogenetic relationship among virus in the semen at peak replication, significant amounts of virus appear to be derived as a result of clonal expansion of infected cells. The homeostatic proliferation of SIV infected cells trafficking from the blood into genital tissues is a plausible means of producing the oligoclonal “bursts” of virus observed in ejaculate. These findings account for the magnitude and delay in peak semen viremia relative to the blood that has been reported in acutely HIV-1 infected patients 
. Moreover, the influx of large numbers of SIV-infected cells into genital tissues make it unlikely that a specific virus amino acid “signature” could be a determinant of early viral tropism in the male genital tract 
, consistent with our inability to identify SIV Env amino acids that were significantly enriched in the seminal plasma. However, our analysis did not span a sufficient period of time to determine the presence of semen signatures during chronic infection 
Mechanistically, the high-level of virus present in the blood during early infection results in a “wave” or spillover of cell-free and cell-associated virus into the male genital tract, equilibrating virus between the two compartments. Host control of SIV replication results in a receding “tide” of virus as virologic set point is achieved. When peak virus replication is reduced to levels below the threshold required for intra-compartment gene flow, free virus or infected cells may be effectively “trapped” within the genital tissues at “low tide.” Continued replication of virus in the male genital tract, in the absence (or reduced rate) of inter-compartment gene flow would then account for the localized diversification of virus variants in the genital tissues.
In fact, we observed less env
diversification in the genital tract than in the blood of these monkeys. This finding is consistent with the lower level of SIV replication in the genital tract than in the blood at 16 weeks following infection. Moreover, the difference in virus diversification in these two anatomic compartments was particularly evident in the vaccinated monkeys after challenge (i.e., 3 of the 4 compartmentalized monkeys), consistent with the low-level virus replication in the male genital tract after set point 
. Vaccine-elicited immune responses and alterations in target cells in the genital tract may have also contributed to the observed effects.
Although the male genital tract is generally considered to be an immune privileged compartment, inflammatory conditions present during acute SIV infection may facilitate the infiltration of both free virus and infected cells. Over time, differences between the blood and the genital tract, as a result of restrictions in gene flow would foster local replication in the genital tract leading to the compartmentalization observed at set point. Inflammation is a likely cause for the trafficking of cells from the peripheral circulation into the genital compartment, and may explain the observations of intermittent viral shedding in the semen of chronically HIV-infected men as a result of bacterial or viral infection of the male genital tract 
. We did not determine if genital tract infections were present in any of the animals in this study.
These apparent differences in selective pressure between the blood and male genital tract should also be considered in light of the reduced effective SIV population size in the genital tract as virus set point is achieved. Virus populations of reduced size and altered genotype relative to the blood may contribute to the described genetic bottleneck associated with HIV-1 transmission, highlighted by several investigators 
. This bottleneck is manifested by the acquisition of HIV-1 variants in newly infected individuals that are not highly represented in the peripheral blood of the already infected, transmitting partner. The findings in the present study, despite limitations in experimental infection route and virus dose, suggest an alternative explanation for these observations. Thus, the early compartmentalization of virus in the male genital tract, vis-à-vis restrictions in virus gene flow, may account for the transmission of distinct viral quasispecies that are not represented in the blood of the already-infected individual at the time of transmission.