Unique features of HLA-mediated HIV evolution in a Mexican cohort: a comparative study

Abstract

Background: Mounting evidence indicates that HLA-mediated HIV evolution follows highly stereotypic pathways that result in HLA-associated footprints in HIV at the population level. However, it is not known whether characteristic HLA frequency distributions in different populations have resulted in additional unique footprints.

Methods: The phylogenetic dependency network model was applied to assess HLA-mediated evolution in datasets of HIV pol sequences from free plasma viruses and peripheral blood mononuclear cell (PBMC)-integrated proviruses in an immunogenetically unique cohort of Mexican individuals. Our data were compared with data from the IHAC cohort, a large multi-center cohort of individuals from Canada, Australia and the USA.

Results: Forty three different HLA-HIV codon associations representing 30 HLA-HIV codon pairs were observed in the Mexican cohort (q < 0.2). Strikingly, 23 (53%) of these associations differed from those observed in the well-powered IHAC cohort, strongly suggesting the existence of unique characteristics in HLA-mediated HIV evolution in the Mexican cohort. Furthermore, 17 of the 23 novel associations involved HLA alleles whose frequencies were not significantly different from those in IHAC, suggesting that their detection was not due to increased statistical power but to differences in patterns of epitope targeting. Interestingly, the consensus differed in four positions between the two cohorts and three of these positions could be explained by HLA-associated selection. Additionally, different HLA-HIV codon associations were seen when comparing HLA-mediated selection in plasma viruses and PBMC archived proviruses at the population level, with a significantly lower number of associations in the proviral dataset.

Conclusion: Our data support universal HLA-mediated HIV evolution at the population level, resulting in detectable HLA-associated footprints in the circulating virus. However, it also strongly suggests that unique genetic backgrounds in different HIV-infected populations may influence HIV evolution in a particular direction as particular HLA-HIV codon associations are determined by specific HLA frequency distributions. Our analysis also suggests a dynamic HLA-associated evolution in HIV with fewer HLA-HIV codon associations observed in the proviral compartment, which is likely enriched in early archived HIV sequences, compared to the plasma virus compartment. These results highlight the importance of comparative HIV evolutionary studies in immunologically different populations worldwide.

Figure 1

Geographical residence of the individuals included in the study. The map shows data for 302 antiretroviral treatment-naïve HIV-infected individuals. States in red account for 98.3% of the individuals included in the study. States in white account for 1.7% of the individuals of the cohort.

Figure 2

Most frequent three-gene class I HLA haplotypes in a Mexican cohort of HIV-positive individuals. Genetic frequencies were calculated for 292 HIV-positive individuals from Central/Southern Mexico. Gametic phase for each individual was estimated using the pseudo-Bayesian algorithm ELB, using the program Arlequin v3.11. HLA-A, B and C genes were typed at low/medium resolution by SSP-PCR as described in Methods. Haplotypes with frequencies over 1% in the cohort are shown.

Figure 3

Differences in HLA frequencies between HIV-positive and HIV-negative Mexicans. Allelic frequencies were calculated for HLA-A and B genes, in the cohort of 292 HIV-positive individuals from this study (dark grey) and compared to those previously reported for a cohort of 381 individuals of 191 Mexican families by Barquera et al [38] (light grey). HLA typing in both cases was carried out by SSP-PCR as described in the Methods. For comparability, HLA nomenclature for histocompatibility used by Barquera et al. was substituted with its genetic equivalent, i.e. B65 and B64 were included as B*14 alleles; B62, B63, B70, B71, B72, and B75 were included as B*15 alleles; and B61, and B60 were included as B*40 alleles, according to the equivalents accepted by the WHO Nomenclature Committee for Factors of the HLA System .

Figure 4

Marked differences in HLA allele frequencies in three clade B-infected cohorts. Population frequencies for class I HLA genes A, B and C were compared between the Mexican cohort described in this study (n = 292) (dark grey). The combined IHAC cohort including individuals from British Columbia, Canada; Western Australia and the USA (n = 1845) (light grey) [37] (Brumme ZL, John M, et al, PLoS ONE 2009, in press), and the British Columbia HOMER cohort (n = 1045) (white) described in detail previously [34]. **Significant differences (q < 0.05) between the Mexican cohorts and both the IHAC and the HOMER cohorts, *significant differences (q < 0.05) between the Mexican cohort and the IHAC cohort only.

Figure 5

Protease and RT phylogenetic dependency network for the Mexican cohort. A phylogenetic dependency network map was generated with the PhyloDv software . Pol positions are drawn counter clockwise, with the N-terminus of the protease at the 3 o'clock position, and the first RT codon corresponding to position 100. Lines indicate associations between codons (inside the circle) or between HLA alleles and codons (outside the circle). Colors indicate q-values of the most significant associations between two attributes. Associations with q < 0.2 for 280 individuals from Central/Southern Mexico were included.

Figure 6

Epitope map supporting HLA-HIV polymorphism associations obtained by the Phylogenetic Dependency Network model in the Mexican cohort. HLA-HIV polymorphism associations were searched in pol sequences derived from 280 individuals from Central/Southern Mexico using the previously described PDN model [14] that corrects for the confounding effects of HIV phylogeny, HIV codon covariation, and linkage disequilibrium of HLA alleles. Significant HLA-HIV polymorphism associations (q < 0.2) were located in an epitope map. Strongly significant associations (q < 0.05) are marked with yellow stars. Experimentally defined CTL epitopes are shown in black http://www.hiv.lanl.gov/content/immunology/index.html, epitopes predicted by HLA peptide binding motifs are shown in blue (Motif Scan, Los Alamos HIV Database, http://www.hiv.lanl.gov/content/immunology/tools-links.html ). Target HIV positions are shown in bold, including the predictor HLA allele and the associated amino acid residue in different colors depending on the type of leaf distribution of the association obtained with the PDN model, i.e. escape (purple; having the predictor HLA makes it less likely to have the target amino acid), attraction (red; having the predictor HLA makes it more likely to have the target amino acid), reversion (green, not having the predictor HLA makes it more likely to have the target amino acid), repulsion (light blue; not having the predictor HLA makes it less likely to have the target amino acid). Amino acids in lower case indicate associations obtained without considering codon covariation. HLA-HIV polymorphism associations in the Mexican cohort were compared to the ones observed in the multicenter IHAC cohort including 1845 individuals from British Columbia, Canada, the USA and Western Australia [37] (Brumme ZL, John M, et al, PLoS ONE 2009, in press). Shared associations between the Mexican and IHAC cohorts are shown in blue rectangles; shared target HIV positions with shared target amino acids that were associated with different predictor HLA alleles in each cohort are shown in yellow rectangles; shared target positions with different HLA predictors and different associated target amino acids are shown in pink rectangles. HLA-associated HIV positions observed exclusively in the Mexican cohort are marked with red circles.

Figure 7

HLA-HIV codon and HIV codon-HIV codon associations for the free plasma virus and PBMC proviral Pol sequences. Phylogenetic dependency network maps were generated with the PhyloDv software . Each map shows HLA associations as tags pointing to their corresponding sites, and HIV codon-HIV codon associations as inner arcs connecting the associated sites. Plasma: all associations in free plasma virus from 250 patients that had a corresponding PBMC proviral sequence. Proviral: all associations for 250 PBMC proviral sequences. Conserved (shared): shared HLA-site or site-site associations between proviral and plasma sequences. If one amino acid at one site was associated with two different amino acids at another site (e.g. one for escape, one for reversion), only one association was counted. Unique plasma: associations only found to be significant in free plasma virus samples. Unique proviral: Associations only found to be significant in PBMC proviral samples. Significance was calculated with the binomial test; q-values are represented as a heat map shown in the lower inset. Associations with q < 0.2 are shown (all associations had p < 0.002). The upper inset table shows the number of significant associations in each map.