Background
While antiretroviral therapy (ART) effectively suppresses HIV/SIV plasma viremia, it does not eradicate the virus. Understanding antiviral responses and transcriptional dynamics under ART suppression, including changes elicited by incompletely resolved viremia, are crucial to developing effective cure strategies. The simian immunodeficiency virus (SIV) macaque model offers a highly controlled system capable of characterizing these effects in both blood and sites of viral persistence, such as lymphoid tissues.
Methods
A cohort of 24 rhesus macaques was infected with SIVmac239M, with ART initiation (TDF/FTC/DTG) on day 9 post-infection. Longitudinal samples were collected from blood and lymphoid tissues for 70 weeks-post-infection (WPI), paired with plasma viral load (pVL) and cell-associated viral load (caVL). To assess ART-specific effects, samples were also collected from six uninfected macaques administered ART for six weeks. We performed single-cell RNA sequencing (scRNA-Seq) on all samples, with changes evaluated using pseudobulk contrast analysis.
Results
We identified a core gene program, comprised primarily of interferon (IFN) associated genes, strongly correlated with viral levels (pVL and caVL) in blood and lymphoid tissues. While this signature scaled with caVL in most tissues, the relationship is damped in mesenteric lymph node, suggesting a uniquely immunosuppressive environment that could enhance viral persistence. IFN signatures decayed rapidly after ART initiation, although remained elevated in lymphoid tissues as late as 66 WPI, despite undetectable plasma viremia. Finally, we demonstrate sustained ART-suppressed SIV elicits broad transcriptional alterations to all immune subsets, including enhanced TGFβ signaling, which are not present during acute infection. These changes are not reversed after 30 days of ART release.
Conclusions
Our data demonstrate that ART-suppressed SIV continues to alter the immune system, despite undetectable plasma viremia. These changes are heterogeneous across subjects, include altered TGFβ signaling, and have implications for HIV/SIV curative therapies that rely on immune control. Gut-associated lymphoid tissue exhibits unique tolerance to viral replication, which could enhance viral persistence.