Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection

Abstract

During acute human immunodeficiency virus type 1 (HIV-1) infection, early host cellular immune responses drive viral evolution. The rates and extent of these mutations, however, remain incompletely characterized. In a cohort of 98 individuals newly infected with HIV-1 subtype B, we longitudinally characterized the rates and extent of HLA-mediated escape and reversion in Gag, Pol, and Nef using a rational definition of HLA-attributable mutation based on the analysis of a large independent subtype B data set. We demonstrate rapid and dramatic HIV evolution in response to immune pressures that in general reflect established cytotoxic T-lymphocyte (CTL) response hierarchies in early infection. On a population level, HLA-driven evolution was observed in approximately 80% of published CTL epitopes. Five of the 10 most rapidly evolving epitopes were restricted by protective HLA alleles (HLA-B*13/B*51/B*57/B*5801; P = 0.01), supporting the importance of a strong early CTL response in HIV control. Consistent with known fitness costs of escape, B*57-associated mutations in Gag were among the most rapidly reverting positions upon transmission to non-B*57-expressing individuals, whereas many other HLA-associated polymorphisms displayed slow or negligible reversion. Overall, an estimated minimum of 30% of observed substitutions in Gag/Pol and 60% in Nef were attributable to HLA-associated escape and reversion events. Results underscore the dominant role of immune pressures in driving early within-host HIV evolution. Dramatic differences in escape and reversion rates across codons, genes, and HLA restrictions are observed, highlighting the complexity of viral adaptation to the host immune response.

FIG. 1.

Locations of HLA-associated substitutions within optimally defined CTL epitopes. Published sequences of the 71 optimally defined CTL epitopes harboring at least one HLA-associated polymorphic site, based on analysis of over 1,200 persons with chronic infection, are listed. HLA-associated polymorphic residues are indicated in red. Overlapping and/or variant epitopes restricted by the same HLA allele were removed to avoid double counting of escape mutations. A complete list of all optimally defined epitopes is available at http://www.hiv.lanl.gov/content/immunology/tables/optimal_ctl_summary.html.

FIG. 2.

First-year rates of escape among HLA-restricted, optimally defined CTL epitopes. The rates of escape in optimally defined CTL epitopes in Gag (blue diamonds), Pol (red squares), and Nef (green triangles) in the first year of infection are shown. Vertical bars indicate 95% confidence intervals. Epitopes were restricted to those containing a predefined HLA-associated polymorphism (Fig. 1). Note that this analysis incorporates an estimate of cases where the epitope may have escaped prior to baseline sampling, performed by analyzing each individual's baseline HIV sequence for known HLA-restricted escape mutations. Note that in doing so, we cannot discriminate cases of the very early selection of escape mutations from rare cases where an escaped variant may have been acquired at transmission.

FIG. 3.

Rates of CTL escape generally reflect known immunodominance hierarchies of CTL epitope recognition in primary infection. The recognition frequencies of specific HLA-restricted epitopes (assessed by IFN-γ ELISpot assays measuring CTL responses to optimally described HIV peptides in a cohort of 289 individuals in primary HIV infection) (7, 76) are indicated in the left panels. Kaplan-Meier curves representing the corresponding rates of escape are indicated in the right panels in matching colors. Note that there are two cases where Kaplan-Meier curves for a pair of epitopes are superimposed so that only one curve is visible; these are B*08 EV9 and DL9 (which do not escape) and B*07 FL9 and TM9 (which overlap and share a single escaping site; Fig. 1).

FIG. 4.

Correlation between frequencies of recognition and escape by protein. Spearman's rank correlation was used to characterize the relationship between the frequencies of recognition of CTL epitopes in Gag, Pol, and Nef with their corresponding frequencies of escape in the first year of infection. A regression line was drawn to highlight trends. All tested CTL epitopes are represented; those recognized and/or evolving at frequencies of >∼40% are labeled with the epitope name and HLA restriction.

FIG. 5.

Locations and first-year rates of commonly observed reversions within published HLA-restricted epitopes in Gag, Pol, and Nef. Conservative estimates of the rates of reversion of known HLA-associated escape mutations in the absence of the restricting HLA (expressed as percent reversions/person-month) at Gag, Pol, and Nef codons within published HLA-restricted CTL epitopes are shown, along with the total number of observations (transmitted mutations) at each codon. A minimum of five observed cases of the transmission of the escaped variant was required for display. Note that in contrast to the escape analysis, this analysis does not take into consideration reversions that may have occurred prior to the baseline sampling. Thus, estimated reversion rates represent considerable underestimates of the true rate and are not directly comparable to epitope escape rates. PR, protease.