CD8ɑ+ cells suppress SIV replication without the development of mutations within MHC class-I-restricted epitopes during post-treatment control

Post-treatment control (PTC) is a rare phenomenon in which people living with HIV (PLWH) maintain viral control following antiretroviral treatment (ART) interruption. Characterizing virus populations present in PTCs may help elucidate mechanisms of immunologic control, but this is challenging without detectable plasma viremia. To model PTC, eight Mauritian cynomolgus macaques (MCMs) were infected with barcoded SIVmac239M and began an 8-month ART regimen 2 weeks post-infection (wpi). Six months following ART interruption, all MCMs were rechallenged with non-barcoded SIVmac239, followed by CD8α+ cell depletion 2 months later. Animals were grouped as viremic ( n = 5) or aviremic ( n = 3) based on the detection of plasma viremia between ART interruption and CD8ɑ+ cell depletion; all animals became viremic post-depletion. Barcode sequencing of plasma virus revealed that lineages with high pre-ART viral loads dominated the rebounding populations post-depletion and detectable rechallenge virus in two animals post-depletion. Additional sequencing of three CD8+ T-cell epitopes within plasma viruses identified point mutations only in viruses isolated from the viremic group post-depletion. A second cohort of 5 MCM who initiated ART 8 wpi was examined to identify the impact of the timing of ART initiation on viral epitope diversity and showed increased diversity prior to ART initiation and following ART interruption. These results suggest that early ART initiation is associated with reduced diversity within cytotoxic T lymphocyte (CTL) epitopes and a longer time to rebound, as well as highlight an important role of restricting the emergence of variant CTL epitopes in increasing the likelihood of PTC. IMPORTANCE While rare, a subset of PLWH, termed post-treatment controllers (PTCs), maintains viral control following antiretroviral treatment (ART) interruption. However, little is known about whether this control reflects a complete absence of viral replication or continual, subclinical replication. Here, we address a key knowledge gap regarding how viral populations change during CD8ɑ+ cell-mediated PTC of SIV. We utilized our Mauritian cynomolgus macaque model of HIV infection, in combination with barcoded SIVmac239M and deep sequencing, to characterize viral lineages and MHC-I-restricted CD8+ T-cell epitopes throughout the study. Our findings demonstrate that early ART initiation limits viral diversity, that pre-ART replication predicts post-ART reactivation, and that CD8ɑ+ cells can suppress viral replication without the emergence of mutations within CD8+ T-cell epitopes. These insights establish MCMs as a valuable model for dissecting mechanisms of durable ART-free viral control and highlight the potential of CD8-mediated immune control as a therapeutic target for HIV cure strategies.