HLA class I-driven evolution of human immunodeficiency virus type 1 subtype c proteome: immune escape and viral load

Abstract

Human immunodeficiency virus type 1 (HIV-1) mutations that confer escape from cytotoxic T-lymphocyte (CTL) recognition can sometimes result in lower viral fitness. These mutations can then revert upon transmission to a new host in the absence of CTL-mediated immune selection pressure restricted by the HLA alleles of the prior host. To identify these potentially critical recognition points on the virus, we assessed HLA-driven viral evolution using three phylogenetic correction methods across full HIV-1 subtype C proteomes from a cohort of 261 South Africans and identified amino acids conferring either susceptibility or resistance to CTLs. A total of 558 CTL-susceptible and -resistant HLA-amino acid associations were identified and organized into 310 immunological sets (groups of individual associations related to a single HLA/epitope combination). Mutations away from seven susceptible residues, including four in Gag, were associated with lower plasma viral-RNA loads (q < 0.2 [where q is the expected false-discovery rate]) in individuals with the corresponding HLA alleles. The ratio of susceptible to resistant residues among those without the corresponding HLA alleles varied in the order Vpr > Gag > Rev > Pol > Nef > Vif > Tat > Env > Vpu (Fisher's exact test; P < or = 0.0009 for each comparison), suggesting the same ranking of fitness costs by genes associated with CTL escape. Significantly more HLA-B (chi(2); P = 3.59 x 10(-5)) and HLA-C (chi(2); P = 4.71 x 10(-6)) alleles were associated with amino acid changes than HLA-A, highlighting their importance in driving viral evolution. In conclusion, specific HIV-1 residues (enriched in Vpr, Gag, and Rev) and HLA alleles (particularly B and C) confer susceptibility to the CTL response and are likely to be important in the development of vaccines targeted to decrease the viral load.

FIG. 1.

Epitope map of p17 and p24 of Gag showing individual associations and immunological sets. The reference sequence was the consensus of the full-length HIV-1 sequences from South Africa. All significant individual associations identified are shown below the consensus sequence. Blue amino acids reflect the susceptible form and red the resistant form. Shaded boxes indicate immunological sets. The size of the immunological set was determined by both the individual associations and validation data. These sets were chosen to minimize the number of epitopes that explained the observed data, taking linkage disequilibrium and 9-mer overlap into account. Only significant 9-mer regions with two or more associations are shown. For example, if a susceptible and a resistant residue were at a single site, both are shown, or if more than one site was involved in the variation that makes the 9-mer association distinctive, it is shown. If there were conserved amino acids between the HLA-associated variant sites within the 9-mer, they are indicated by small gray letters. When linked HLAs were associated with the same site, the HLA with the lowest P value is shown. An HLA in green indicates that there was a gamma interferon ELISPOT reactivity pattern associated with that HLA that overlapped the associated amino acid change. In the validation area (above the consensus sequence), fuchsia shading over the HLA label indicates motifs, orange indicates B list epitopes, red indicates A list epitopes, and blue indicates predicted epitopes. Similar to the individual associations, epitopes and motifs that were inferred to be susceptible or resistant are also labeled with blue or red letters, respectively. In the association area (below the consensus sequence), a gray background indicates that the association came from linkage disequilibrium. Associations in sites with >90% gaps are not shown. See http://www.hiv.lanl.gov/content/immunology/hlatem/index.html for maps of remaining HIV-1 proteins and the extended data set.

FIG. 2.

Immunological map comparing HLA-amino acid associations from subtypes B and C that were within the same epitopes. The light-yellow boxes are the subtype B sequences from a Canadian study (12), and the light-green boxes are the subtype C sequences from this study. The underlined residues represent a site with opposing selective pressures. In this case, it is mediated by the same HLA allele but is in the context of different amino acids three sites upstream.

FIG. 3.

A comparison of the types of validation support for the individual associations found in the original data set (light-gray bars) and in the extended data set (black bars) that included additional sequences from Gag, Pol, Env, and Nef.