Background
Among people living with HIV (PLWH) receiving long-term antiretroviral therapy (LT-ART), the frequency of intact HIV-1 proviruses varies considerably, likely reflecting differences in immune pressure on the reservoir cell pool. Characterizing reservoir dynamics in individuals with exceptionally low reservoir under ART may provide critical insights for reservoir reduction and HIV cure strategies. In this study, we examined reservoir features in 11 participants from the LoViReT cohort whose reservoir sizes fell within the lowest 10% of a large ART-treated cohort (n=892).
Methods
The LoViReT cohort includes PLWH under ART with undetectable viremia for ≥3 years.
Using FLIP-seq (Full-Length Individual Proviral Sequencing) and MIP-seq (Matched Integration site and Proviral sequencing), we quantified intact and defective proviruses, mapped integration sites within the host genome, and analyzed reservoir dynamics. Samples were collected at three timepoints: before ART initiation, 5-11 years post-ART, and 15-28 years post-ART.
Results
In these 11 participants, we identified 1,721 individual proviral genomes (128 intact and 1,593 defective). Median frequencies of intact proviruses were 0.015 and 0.022 HIV-1 DNA copies/million PBMCs at 5–11 and 15–28 years, respectively. In contrast, unselected ART-treated individuals with similar treatment durations showed frequencies of 2.17 and 0.56 HIV-1 DNA copies/million PBMCs, respectively, while elite controllers (ECs) exhibit 0.17, notably higher than LoViReT participants. Longitudinal analysis revealed a half-life of 16.6 months for intact proviruses in LoViReT participants, compared to a reported half-life of ~44 months in the literature for PLWH under ART, suggesting stronger immune-mediated clearance of reservoir cells. Supporting this perspective, we observed a significant higher proportion of clonally expanded proviruses integrated in heterochromatin regions after ART, in comparison with the control cohort. Additionally, viral sequence analysis showed low proviral diversity pre- and post-ART, in combination with a lower proportion of CTL escape mutations, similarly to ECs.
Conclusions
These study participants exhibit a pronounced decline of their HIV-1 reservoir, associated with features typically observed in ECs and longer-treated individuals. These findings suggest the presence of more effective immune responses targeting the reservoir cell pool. The immunological mechanisms driving this enhanced clearance are currently under investigation.