If strategies currently in development succeed in eradicating HIV reservoirs in peripheral blood and lymphoid tissues, residual sources of virus may remain in anatomic compartments, including the genital tract. To design effective eradication strategies, it is crucial to determine to what extent compartmentalized HIV reservoirs contribute to viral rebound after antiretroviral therapy (ART) interruption.
Paired blood and semen samples were collected from 12 individuals enrolled in a randomized, double-blind, placebo-controlled clinical trial of HIV-MAG DNA vaccine prime, rVSVN4CT1gag booster vaccine in people living with HIV (PLWH) who began ART during acute or early infection (NCT01859325). At the first available time-points following viral rebound, we sequenced HIV-1 env (C2-V3), gag (p24), and pol (reverse transcriptase) regions amplified from cell-free HIV RNA in blood and seminal plasma using the MiSeq Illumina platform. Comprehensive sequence and phylogenetic analyses were performed to look for evidence of viral compartmentalization (Fst test), diversity (Shannon entropy measures) and unique viral subpopulations in seminal plasma as compared with blood plasma.
Vaccine had no effect on kinetics and magnitude of HIV RNA rebound in blood plasma (Sneller et al, STM 2017). Compared to blood, HIV RNA rebound in semen occurred significantly later (median of 66 vs 42 days post ART interruption) and reached lower levels (164 vs 16,224 copies/ml). Paired sequence data were available for 5 participants. All presented compartmentalized viral rebound between blood and semen (Fst, p≤0.05 for all genes). Phylogenetic analysis confirmed the presence of compartment-specific monophyletic HIV RNA populations in at least one HIV region in 3 out of the 5 participants in longitudinal time-points, suggesting that rebound originated within genital compartment rather than migrating from blood (Figure 1 panel A). Interestingly, despite early ART start, genetic diversity after adjusting for variant frequency was higher in semen compared to blood in all three coding regions (Significant for gag and pol (<0.01) but not in env (p=0.06)), Figure 1 panel B.
HIV reservoirs in the genital compartment might contribute to viral rebound in PLWH interrupting ART. Higher diversity in the genital compartment illustrates viral compartmentalization and distinct evolutionary dynamics. Reservoirs in all anatomic compartments need to be actively targeted to achieve a complete functional cure.