Compartmentalization of HIV-1 within the Female Genital Tract Is Due to Monotypic and Low-Diversity Variants Not Distinct Viral Populations

Abstract

BackgroundCompartmentalization of HIV-1 between the genital tract and blood was noted in half of 57 women included in 12 studies primarily using cell-free virus. To further understand differences between genital tract and blood viruses of women with chronic HIV-1 infection cell-free and cell-associated virus populations were sequenced from these tissues, reasoning that integrated viral DNA includes variants archived from earlier in infection, and provides a greater array of genotypes for comparisons.Methodology/Principal FindingsMultiple sequences from single-genome-amplification of HIV-1 RNA and DNA from the genital tract and blood of each woman were compared in a cross-sectional study. Maximum likelihood phylogenies were evaluated for evidence of compartmentalization using four statistical tests. Genital tract and blood HIV-1 appears compartmentalized in 7/13 women by ≥2 statistical analyses. These subjects' phylograms were characterized by low diversity genital-specific viral clades interspersed between clades containing both genital and blood sequences. Many of the genital-specific clades contained monotypic HIV-1 sequences. In 2/7 women, HIV-1 populations were significantly compartmentalized across all four statistical tests; both had low diversity genital tract-only clades. Collapsing monotypic variants into a single sequence diminished the prevalence and extent of compartmentalization. Viral sequences did not demonstrate tissue-specific signature amino acid residues, differential immune selection, or co-receptor usage.Conclusions/SignificanceIn women with chronic HIV-1 infection multiple identical sequences suggest proliferation of HIV-1-infected cells, and low diversity tissue-specific phylogenetic clades are consistent with bursts of viral replication. These monotypic and tissue-specific viruses provide statistical support for compartmentalization of HIV-1 between the female genital tract and blood. However, the intermingling of these clades with clades comprised of both genital and blood sequences and the absence of tissue-specific genetic features suggests compartmentalization between blood and genital tract may be due to viral replication and proliferation of infected cells, and questions whether HIV-1 in the female genital tract is distinct from blood.

Role of donor genital tract HIV-1 diversity in the transmission bottleneck

“…† Storey and Tibshirani (25) q value from SM P value, shown in bold, where q < 0.05. (18) for seminal PL and consistent with other studies that have investigated the relationship between blood and genital viral populations (5,(17)(18)(19)(20)(21). If transmission were a stochastic sampling of the donor GT virus population, the most common viral variants in the donor GT should have the greatest opportunity to interact with the recipient genital mucosa and be favored for transmission.…”

“…Recent studies have begun to answer the question of whether viral variants are sequestered in the genital tissue (17)(18)(19)(20)(21)(22) and show that distinct genetic lineages can propagate there. Here, we studied the genetic relationship of viruses in the blood and genital fluids from the chronically infected donor partners of eight Rwandan and Zambian transmission pairs and show that although distinct viral subpopulations are present in the GT, the transmitting founder variant did not originate from the predominant sampled population.…”

Origin and Evolution of HIV-1 in Breast Milk Determined by Single-Genome Amplification and Sequencing

“…Each of the subjects with evidence of significant compartmentalization by both tests had a large number of identical or nearly identical sequences in milk (Table 3), which could contribute to an overestimation of potential compartmentalization (6,7,15). Therefore, the identical sequences within the same compartment were removed from the data set subjected to the SM and S nn analyses for all subjects.…”

“…Divergent mucosal immune responses may shape compartmentspecific viruses, as described for anatomic compartments such as semen and cervicovaginal fluid (2,6,9,11,21,22,37). Early investigations of whether breast milk virus variants were compartmentalized from those in plasma were contradictory (5,16).…”

HIV-1 Pathogenesis: The Virus

“…Several studies have reported compartmentalization of viral sequences in the FMTwithin at least a subset of subjects (Poss et al 1998;Kemal et al 2003;Adal et al 2005;Andreoletti et al 2007). More recently, this compartmentalization was interpreted to be largely the result of clonal amplification (Bull et al 2009). There is a need for both longitudinal analysis of viral populations within the genital tract, and an examination of the impact of concurrent localized bacterial infections with attendant inflammation.…”