Central role of reverting mutations in HLA associations with human immunodeficiency virus set point

Abstract

Much uncertainty still exists over what T-cell responses need to be induced by an effective human immunodeficiency virus (HIV) vaccine. Previous studies have hypothesized that the effective CD8(+) T-cell responses are those driving the selection of escape mutations that reduce viral fitness and therefore revert post-transmission. In this study, we adopted a novel approach to define better the role of reverting escape mutations in immune control of HIV infection. This analysis of sequences from 710 study subjects with chronic C-clade HIV type 1 infection demonstrates the importance of mutations that impose a fitness cost in the control of viremia. Consistent with previous studies, the viral set points associated with each HLA-B allele are strongly correlated with the number of Gag-specific polymorphisms associated with the relevant HLA-B allele (r = -0.56, P = 0.0034). The viral set points associated with each HLA-C allele were also strongly correlated with the number of Pol-specific polymorphisms associated with the relevant HLA-C allele (r = -0.67, P = 0.0047). However, critically, both these correlations were dependent solely on the polymorphisms identified as reverting. Therefore, despite the inevitable evolution of viral escape, viremia can be controlled through the selection of mutations that are detrimental to viral fitness. The significance of these results is in highlighting the rationale for an HIV vaccine that can induce these broad responses.

FIG. 1.

Number of HIV polymorphisms associated with host HLA, derived from analysis of C-clade sequences from 710 individuals. The number of HLA-associated HIV mutations in Gag, Pol, and Nef and the percentage of reverting sites are shown for q < 0.05 (A) and q < 0.2 (C). The total numbers of HLA-associated mutations according to HLA class I restriction are shown for associations with q < 0.05 (B) and q < 0.2 (D).

FIG. 2.

Relationship between the number of HLA-B-associated polymorphisms in C-clade Gag (n = 673) and Pol (n = 461) sequences and the median viral load. The number of HIV sequence polymorphisms associated with alleles expressed at a ≥0.5% phenotypic frequency is plotted against the median viral load for patients expressing that allele. Shown are HLA-B-selected mutations in Gag for q < 0.05 (A) and q < 0.2 (B) and HLA-C-selected mutations in Pol for q < 0.05 (C) and q < 0.2 (D). We excluded associations where a four-digit type was unknown and associations pertaining to more than one allele at a given position (due to linkage), unless the allele responsible for the association could be determined on the basis of a previously defined epitope with the correct restriction.

FIG. 3.

Relationship between the number of HLA-B-associated polymorphisms in C-clade Gag sequences (n = 673) and the median viral load, according to the presence or absence of reversion. The number of sites of HIV polymorphism associated with HLA-B alleles expressed at a ≥0.5% phenotypic frequency is plotted against the median viral load for patients with that allele, at sites where reversion was identified (A, B) and where no reversion was identified (C, D), for associations with q < 0.05 (A, C) and q < 0.2 (B, D).

FIG. 4.

Relationship between CD8⁺ T-cell responses determined by IFN-γ ELISPOT assay and the median viral load for 681 HIV-infected individuals. The numbers of statistically significant (P < 0.00075) HLA-B-associated responses to peptides in Gag (A), Pol (B), and Nef (C) and HLA-A-associated responses to Pol (D) are plotted against the median viral load for patients expressing that allele.