In these investigations we applied a battery of computational techniques to paired semen- and blood-derived HIV-1 env
sequences, which confirmed previous reports that HIV within the genital tract is different from that within the bloodstream (10
). This study extends those observations with findings important to the understanding of how HIV adapts to the male genital tract. First, the male genital tract can function as a viral compartment, but the extent of compartmentalization differs between individuals and within individuals over time. Second, there are discordant selective pressures operating in the male genital tract and blood. Third, semen-derived viruses share a genetic signature across individuals due to tissue-specific selective pressures that are common across hosts.
Viral compartments are characterized by a restriction of gene flow between cells or tissues, usually identified by phylogenetic analysis (29
). In this study, viral compartmentalization between blood and the male genital tract was identified in 6 out of 12 individuals, and another individual demonstrated compartmentalization of virus only at the earliest sampling times. Viral migration between blood plasma and the male genital tract was minimal and infrequent in these individuals, which reinforces the concept that a significant fraction of virus shed in semen is produced locally in the male genital tract. Furthermore, there was a lower genetic diversity and rate of molecular evolution in seminal sequences, probably reflecting a lower effective population size within the male genital tract. This lower effective population size may contribute to the genetic bottleneck associated with HIV-1 transmission. We cannot exclude the possibility, however, that sampling issues contributed to this phenomenon; the efficiency of RNA extraction and reverse transcription-PCR may be lower in semen than plasma, increasing the potential for resampling.
The degree of compartmentalization varied among individuals and also within individuals over time. This may explain the observations of intermittent viral shedding in the semen of HIV-infected men (15
) and the increased viral shedding when the urethra is inflamed by concomitant bacterial or viral infection (40
). Local inflammation is a likely explanation for increased trafficking of HIV from the circulation to the genital compartment. Future studies examining the relationship between sexually transmitted infections and seminal viral loads may provide valuable insight into viral adaptation and dynamics within the male genital tract. This understanding could be crucial in the development of methods to interrupt HIV transmission such as vaccines, microbicides, and antiretroviral suppression.
Seeding of genital tissues occurs very early in infection before the development of any anti-HIV immune response (13
). Once the host mounts an anti-HIV immune response, it most likely varies in strength and nature between compartments (29
). We investigated the degree of selection on the virus within the two compartments and found that there was greater positive selection on virus in the blood than virus in the male genital tract. In six out of the seven individuals with compartmentalized virus, there were highly significant differences in env
glycosylation but not in a consistent direction. While this reinforces the theory that virus is produced locally in the male genital tract and responds to local humoral immunity, it does not explain the recent reports that HIV transmission through heterosexual exposure involves viruses with fewer envelope glycans (11
Since cellular tropism may also play a role in viral compartmentalization and adaptation to the male genital tract, we investigated the coreceptor usage of viruses in blood and semen. It is provocative that in all individuals who harbored CXCR4-using viruses, these viruses were underrepresented in the genital tract. Selection favoring R5 variants in the male genital tract may explain the observation that newly infected individuals are disproportionately infected with CCR5-using viruses (54
Although HIV within the male genital tract is often different from that within the bloodstream (10
), the initially infecting virus (founding virus) and the individual's immune responses determine viral genetics more than tissue of origin (29
). Therefore, it has been difficult to determine if semen-derived virus shares common genetic characteristics among individuals (10
). Using machine learning techniques, we have found that semen-derived HIV-1 has a strong genetic signature among individuals with compartmentalized virus. The signature comprises several positions across C2-V3; however, the residue at position 464 appears to be the most critical in determining viral tropism to the male genital tract. This particular position, to the best of our knowledge, has not previously been reported within the context of tissue tropism or viral compartmentalization. Nevertheless, this classification trial presents convincing evidence that the male genital tract environment selects for similar, predictable genetic changes in env
The male genital tract has been characterized as a reservoir (43
), a compartment (10
), and a drug sanctuary (45
). All have significant implications for preventing the transmission of HIV by using various theoretical methods such as microbicides, vaccines, or antiretroviral therapy (2
). Our investigations uniquely detail the viral compartmentalization dynamics and differing selection pressures between the blood and male genital tract and document a specific genetic signature of virus compartmentalized in the male genital tract. Taken together, these data offer important insights into the adaptation of HIV to the male genital tract, which may be valuable in the rational design of an effective vaccine.