Figure 3.

Phylogenetic analyses of HIV env sequences from pre-ART and time of DS from genital tract. HIV SGA sequences from the blood and genital tract specimens collected pre-ART and during episodes of DS are shown for female participant 86 (A), and male participant 71 (B), whose DS specimens yielded multiple HIV RNA sequences after DNAse treatment. In both cases the HIV RNA sequences derived from cervical swab or seminal plasma during DS episodes were identical to sequences from pre-ART specimens and did not diverge from the most recent common ancestor of infection compared to sequences from pre-ART specimens; this suggests that a proliferating cell clone may have produced these virions. HIV DNA sequences derived from seminal cell pellet and cervicovaginal lavage collected at time of DS were monotypic in the female participant 86 and too few to assess from the male participant 71. All HIV RNA and DNA sequences from participant 86 samples were hypermutated and most likely were not replication competent. HIV RNA was detected in participant 71 plasma at a low level, a “blip” of 1.98 log₁₀ copies/mL, concurrent with detection of genital shedding, whereas in participant 86 plasma viral load was undetectable at the time of DS. Sequences were rooted using representative HIV-1 subtype B sequences from the GenBank database (clade B: B.US.83.RF, B.US.90.WEAU160, B.FR.83.HXB2, B.US.86.JRFL). Maximum likelihood trees were generated in DIVEIN with bootstrap values estimated by approximate likelihood ratio test. Bootstrap values ≥70 are indicated in red. Scale bars indicate number of substitutions per site. Abbreviations: ART, antiretroviral treatment; c/mL, copies/mL; CVL, cervicovaginal lavage; DS, discordant shedding; HIV, human immunodeficiency virus; mo, month after ART initiated; PBMC, peripheral blood mononuclear cells; SGA, single-genome amplification.