Gag-Protease-Mediated Replication Capacity in HIV-1 Subtype C Chronic Infection: Associations with HLA Type and Clinical Parameters

Abstract

The mechanisms underlying HIV-1 control by protective HLA class I alleles are not fully understood and could involve selection of escape mutations in functionally important Gag epitopes resulting in fitness costs. This study was undertaken to investigate, at the population level, the impact of HLA-mediated immune pressure in Gag on viral fitness and its influence on HIV-1 pathogenesis. Replication capacities of 406 recombinant viruses encoding plasma-derived Gag-protease from patients chronically infected with HIV-1 subtype C were assayed in an HIV-1-inducible green fluorescent protein reporter cell line. Viral replication capacities varied significantly with respect to the specific HLA-B alleles expressed by the patient, and protective HLA-B alleles, most notably HLA-B*81, were associated with lower replication capacities. HLA-associated mutations at low-entropy sites, especially the HLA-B*81-associated 186S mutation in the TL9 epitope, were associated with lower replication capacities. Most mutations linked to alterations in replication capacity in the conserved p24 region decreased replication capacity, while most in the highly variable p17 region increased replication capacity. Replication capacity also correlated positively with baseline viral load and negatively with baseline CD4 count but did not correlate with the subsequent rate of CD4 decline. In conclusion, there is evidence that protective HLA alleles, in particular HLA-B*81, significantly influence Gag-protease function by driving sequence changes in Gag and that conserved regions of Gag should be included in a vaccine aiming to drive HIV-1 toward a less fit state. However, the long-term clinical benefit of immune-driven fitness costs is uncertain given the lack of correlation with longitudinal markers of disease progression.

CD8 + T Cell Breadth and Ex Vivo Virus Inhibition Capacity Distinguish between Viremic Controllers with and without Protective HLA Class I Alleles

“…However, in some individuals there was no reversion observed despite the loss of CD8 ϩ T cell responses. Previous studies show that some mutations within Gag have a fitness cost to the virus (32,48); however, compensatory mutations can develop and restore viral fitness, or reversion can occur, especially when the CTL pressure is lost. In our study, it is possible that the fVC ϩ individuals may have developed compensatory mutations that restored viral fitness, hence, the increasing viral load in these individuals.…”

“…Seventy HIV-1 subtype C-chronically infected participants from the Sinikithemba (SK) cohort in Durban, South Africa (3,4,32), were included in the current study. Participants were ART naive at all the time points analyzed.…”

“…Population sequencing of the gag gene was performed as previously described (32). In brief, viral RNA was isolated from plasma samples followed by reverse transcription to generate cDNA.…”

HIV-1 Conserved-Element Vaccines: Relationship between Sequence Conservation and Replicative Capacity

“…While the growth in any particular cell culture does not fully recapitulate the environment for virus survival in vivo, the replicative capacity of viruses from controllers was lower than that of viruses with inserts from chronically infected individuals. This effect was more flagrant with inserts from acutely compared to chronically infected subjects and has been attributed in part to the presence of HLA-associated polymorphisms in controllers and the development of compensatory mutations that restore fitness over time (15,20). These studies were performed using a subject-derived gene integrated in a common HIV-1 backbone (9,(15)(16)(17)(18)(19)(20)(21)(22)(23)(24), and thus the results are contingent on mutations that are private to each subject's viruses and the replicative capacity of these viruses reflect a combination of mutations that differs from one subject to the next.…”

“…Understanding of how well these cases translate at the population level has been sought with comparisons of the relative fitness, measured by replicative capacity or competitive growth assays in cell culture (10)(11)(12)(13)(14) of HIV-1 strains with gag-pro or pol inserts from both elite controllers and viremic subjects (15)(16)(17)(18)(19)(20). While the growth in any particular cell culture does not fully recapitulate the environment for virus survival in vivo, the replicative capacity of viruses from controllers was lower than that of viruses with inserts from chronically infected individuals.…”