Elite controllers, who control HIV infection in the absence of antiretroviral therapy, may hold the key to developing a cure. While this control effectively prevents high-level viremia and disease progression, the latent viral reservoirs persist in these individuals. In a recently described nonhuman primate model of elite control, pigtail macaques (PTMs) are infected with a variant of SIVmac239 (termed ?GY) containing a 2 amino acid deletion in a conserved Env trafficking motif. After inoculation into PTMs, this virus produces high-level viremia, but is typically controlled to undetectable levels by host cellular immune responses in the absence of neutralizing antibodies. Animals remain clinically well for months-to-years. Because this phenotype resembles elite control of HIV in humans, we are investigating how the latent reservoir persists in this unique context.
We studied 4 male PTMs infected with ?GY for >5 yrs. 3 maintained undetectable levels of plasma viral RNA (<15 copies/ml; elite controllers), while 1 exhibited low viral blips (>15 to <4300 copies/ml; partial controller). We used the SIV intact proviral DNA assay (IPDA) to measure the number of intact proviruses in blood and lymph nodes, 151 and 163 weeks post-infection, respectively, and developed a novel assay for full-length sequencing of SIV proviruses to analyze how individual proviruses persist.
The number of intact proviruses was ~1 log lower in all 4 ?GY-infected PTMs compared to SIVmac251-infected rhesus macaques on ART for 60 weeks (A. Bender et al. 2019). Intact proviruses from the partial controller contained mutations flanking the ?GY mutation shown to confer improved fitness in vivo, as well as canonical and novel CTL escape mutations in immunodominant Gag and Tat epitopes restricted by MHC-I Mane-A*084, shared by these animals. In contrast, sequences from ?GY-elite controllers were markedly conserved relative to the ?GY inoculum, showing minimal evolution.
The smaller reservoirs of ?GY-elite controllers relative to those of ART-treated noncontrollers is similar to reservoir sizes of human elite controllers compared to those of ART-treated noncontrollers (A. Kwaa et al. 2020). The presence of CTL escape mutations in the partial controller demonstrates that the CTL response can be a potent driver of virus evolution in reservoirs. In contrast, the minimal sequence changes in proviruses from ?GY-elite controllers suggest a marked restriction of productive replication.