High Frequency of Transmitted HIV-1 Gag HLA Class I-Driven Immune Escape Variants but Minimal Immune Selection over the First Year of Clade C Infection

Abstract

In chronic HIV infection, CD8+ T cell responses to Gag are associated with lower viral loads, but longitudinal studies of HLA-restricted CD8+ T cell-driven selection pressure in Gag from the time of acute infection are limited. In this study we examined Gag sequence evolution over the first year of infection in 22 patients identified prior to seroconversion. A total of 310 and 337 full-length Gag sequences from the earliest available samples (median = 14 days after infection [Fiebig stage I/II]) and at one-year post infection respectively were generated. Six of 22 (27%) individuals were infected with multiple variants. There was a trend towards early intra-patient viral sequence diversity correlating with viral load set point (p = 0.07, r = 0.39). At 14 days post infection, 59.7% of Gag CTL epitopes contained non-consensus polymorphisms and over half of these (35.3%) comprised of previously described CTL escape variants. Consensus and variant CTL epitope proportions were equally distributed irrespective of the selecting host HLA allele and most epitopes remained unchanged over 12 months post infection. These data suggest that intrapatient diversity during acute infection is an indicator of disease outcome. In this setting, there is a high rate of transmitted CTL escape variants and limited immune selection in Gag during the first year of infection. These data have relevance for vaccine strategies designed to elicit effective CD8+ T cell immune responses.

Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity

“…Since CTL escape mutations in key Gag epitopes have been linked to lower viral replication capacity (7,8,18,(28)(29)(30)(31)(32)40), the numbers of these mutations in paired mother-infant sequences were compared. It was observed that Gag epitope escape mutations were frequently transmitted, as has been reported in studies of viruses from early HIV-1 infection in adults (8,19,37), but overall, infant-derived viruses had fewer Gag epitope escape mutations than did viruses from the mothers, and therefore, the frequency of these mutations did not explain the difference in replication capacities between mothers and their infants. We also investigated the hypothesis that early escape in the infant-derived viruses was driving the lower replication capacity by analyzing sequences for HLA-associated footprints in Gag, but we found no evidence that this was the case.…”

“…The pNL4-3Δgag-protease plasmid was generated (52) and prepared (18) as described previously. Ten micrograms of BstEII-digested pNL4-3Δgag-protease and ϳ80 l of the gag-protease PCR product were cotransfected into 2.5 million CEM-GXR25 cells (GXR cells) (60) in 800 l R10 medium via electroporation at 300 V and 500 F (18,37). The electroporated cells were allowed to recover for 1 h before the contents of each cuvette were transferred to 25-cm 2 flasks containing 4 ml medium.…”

Non-synonymous Substitutions in HIV-1 GAG Are Frequent in Epitopes Outside the Functionally Conserved Regions and Associated With Subtype Differences

“…However, the high rate of non-synonymous substitutions outside the HIV_gagconsv epitopes implies that escape mutants outside the HIV_gagconsv are more likely to be integrated into the HIV-1 latent cellular reservoir landscape. This is because latent reservoir strains are established during the early stages of infection and are known to compose majorly of CTL immune escape strains ( Deng et al, 2014 ; Gounder et al, 2015 ; Roberts et al, 2015 ; Leitman et al, 2017 ). Therefore, these latent reservoirs may require a broad CTL response for clearance, as previously alluded to Deng et al (2014) .…”

Lower Viral Loads and Slower CD4+T-Cell Count Decline in MRKAd5 HIV-1 Vaccinees Expressing Disease-Susceptible HLA-B*58:02

“…To determine the viral set point more accurately, we also defined the long-term chronic set point as the median of all pre-ART viral loads available as (1) including the diagnostic (acute) measurement, (2) excluding the diagnostic measurement, (3) including all measurements from >2 weeks after diagnosis, (4) including all measurements from >1 month after diagnosis, or (5) including all measurements from >3 months after diagnosis. Chronic set points were very similar irrespective of the definition, and results using definition 4 are reported here because this may most accurately reflect the beginning of the chronic phase [ 21 , 22 ]. Set-point differences between vaccinees and placebo recipients were analyzed using the Mann–Whitney U test (Prism v5.0c).…”