Conditional Immune Escape during Chronic Simian Immunodeficiency Virus Infection

Abstract

Anti-HIV CD8 T cells included in therapeutic treatments will need to target epitopes that do not accumulate escape mutations.Identifying the epitopes that do not accumulate variants but retain immunogenicity depends on both host major histocompatibility complex (MHC) genetics and the likelihood for an epitope to tolerate variation. We previously found that immune escape during acute SIV infection is conditional; the accumulation of mutations in T cell epitopes is limited, and the rate of accumulation depends on the number of epitopes being targeted. We have now tested the hypothesis that conditional immune escape extends into chronic SIV infection and that epitopes with a preserved wild-type sequence have the potential to elicit epitope-specific CD8 T cells. We deep sequenced simian immunodeficiency virus (SIV) from Mauritian cynomolgus macaques (MCMs) that were homozygous and heterozygous for the M3 MHC haplotype and had been infected with SIV for about 1 year. When interrogating variation within individual epitopes restricted by M3 MHC alleles, we found three categories of epitopes, which we called categories A, B, and C. Category B epitopes readily accumulated variants in M3-homozygous MCMs, but this was less common in M3-heterozygous MCMs. We then determined that chronic CD8 T cells specific for these epitopes were more likely preserved in the M3-heterozygous MCMs than M3-homozygous MCMs. We provide evidence that epitopes known to escape from chronic CD8 T cell responses in animals that are homozygous for a set of MHC alleles are preserved and retain immunogenicity in a host that is heterozygous for the same MHC alleles. IMPORTANCEAnti-HIV CD8 T cells that are part of therapeutic treatments will need to target epitopes that do not accumulate escape mutations. Defining these epitope sequences is a necessary precursor to designing approaches that enhance the functionality of CD8 T cells with the potential to control virus replication during chronic infection or after reactivation of latent virus. Using MHChomozygous and -heterozygous Mauritian cynomolgus macaques, we have now obtained evidence that epitopes known to escape from chronic CD8 T cell responses in animals that are MHC homozygous are preserved and retain immunogenicity in a host that is heterozygous for the same MHC alleles. Importantly, our findings support the conditional immune escape hypothesis, such that the potential to present a greater number of CD8 T cell epitopes within a single animal can delay immune escape in targeted epitopes. As a result, certain epitope sequences can retain immunogenicity into chronic infection.

Acute-phase CD4+ T cell responses targeting invariant viral regions are associated with control of live-attenuated simian immunodeficiency virus

“…We engineered a variant of SIVmac239Δnef with point mutations in eight CD8+ T cell epitopes restricted by MHC class I molecules expressed by the M3 haplotype (Figure 1a). All eight epitopes are highly immunogenic and accumulate high frequency escape mutations in response to immunodominant CD8+ T cell responses elicited during infection with either SIVmac239 or SIVmac239Δnef (16, 26, 27). For each epitope, we used sequence data from nine M3/M3 MCMs chronically infected with SIVmac239 to identify common variants in the replicating virus population (26).…”

“…When we examined the sequences from virus populations isolated during post-peak infection (weeks 7–9), four of the six new regions remained nearly identical to the inoculum, while Gag 57–71 CG15 and Env 329–347 VG19 had accumulated high-frequency mutations (Figure 4b, right). To determine whether these 4 apparently invariant regions can accumulate mutations during pathogenic SIV infection, we examined variant accumulation in these 4 regions in virus populations isolated and sequenced from 9 M3/M3 MCMs who had been infected with SIVmac239 for ∼52 weeks for a previous study by our group (Figure 4c) (26). In 3 of these regions, we found that 70–99% of sequences (median=97%) matched wild type SIVmac239 in all nine animals.…”

Heterologous Protection against Asian Zika Virus Challenge in Rhesus Macaques

“…Virus populations replicating in plasma were sequenced using methods similar to those described previously [26]. Viral RNA was isolated from 500 μl of plasma using the QIAamp MinElute Viral RNA isolation kit, according to manufacturer’s protocol.…”

Vaccination with Live Attenuated Simian Immunodeficiency Virus (SIV) Protects from Mucosal, but Not Necessarily Intravenous, Challenge with a Minimally Heterologous SIV

“…Fresh PBMCs (peripheral blood mononuclear cells) were subjected immediately to an gamma interferon (IFN-␥) enzyme-linked immunosorbent spot (ELISPOT) assay, as previously described (12). Briefly, a precoated monkey IFN-␥ ELISPOTplus plate (Mabtech, Mariemont, OH) was blocked, and peptides corresponding to each of the wild-type epitope sequences were added to each well at a final concentration of 1 M. Peptides were tested in duplicate.…”

“…Genome-wide deep sequencing of replicating virus populations from animals cy0381, cy0348, and cy0382 at necropsy was performed as previously described (12). Briefly, circulating plasma vRNA was isolated with the MinElute virus spin kit (Qiagen).…”