HLA, HCP5 and ZNRD1 in HIV 0.17 (0.07–0.41), ,0.001 0.22 (0.09–0.54), 0.001 0.24 (0.10–0.59), 0.002 0.21 (0.07–0.67), 0.008 0.20 (0.08–0.48), ,0.001 0.18 (0.07–0.43), ,0.001 0.27 (0.11–0.66), 0.004 0.25 (0.08–0.78), 0.017 0.24 (0.08–0.76), 0.015 0.25 (0.08–0.80), 0.019 1 2 3 4 5 6 7 8 9 10 None Baseline CD4 (C) Nadir CD4 (N) Steady-state VL (V) DTH (D) Moderate-High GRG (G) C, N C, N, V C, N, V, D C, N, V, D, G N 1,126 974 974 977 973 974 829 828 815 1,102 0.90 (0.49–1.64), 0.734 1.33 (0.73–2.44), 0.347 0.95 (0.52–1.73), 0.867 1.34 (0.73–2.45), 0.342 0.66 (0.36–1.22), 0.185 0.81 (0.44–1.48), 0.492 1.17 (0.64–2.14), 0.612 1.19 (0.65–2.18), 0.582 0.92 (0.50–1.73), 0.806 0.85 (0.45–1.62), 0.629 Table 4. Viral load-independent disease-influencing effects of HLA-B*57-containing genotypes. Model # Covariates B*57-PD RH (95% CI), P B*57-NPD RH (95% CI), P Results are from nested multivariate Cox proportional hazards models for the outcome of time to AIDS (1987 criteria) for subjects assigned to B*57-PD and B*57-NPD before (none, model 1) and after adjustment for covariates individually (models 2 to 6) or in unison (models 7 to 10). Data is presented as relative hazard (RH) with 95% CI and P values. The reference group for all the comparisons is those who lack a B*57 allele (relative hazard = 1). N, number of subjects. B*57-PD represents subjects who possess B*57-containing genotypes that associate with progressive disease whereas B*57-NPD represents subjects who possess B*57-containing genotypes that associate with non-progressive disease (as shown in Figure 4D). doi:10.1371/journal.pone.0003636.t004 whether HLA-B*57-NPD genotypes affected disease progression independent of the viral load. Before accounting for any of the covariates, those HIV-positive persons categorized to B*57-NPD had an ,83% lower risk of progressing to AIDS compared to individuals who lacked a HLA- B*57 allele (RH = 0.17; 95% CI = 0.07–0.41; Table 4, model 1). We next adjusted–individually and in unison–for the disease- influencing effects of several explanatory variables. These analyses revealed that even after adjustment for the disease-influencing effects of these covariates, the B*57-NPD genotypes remained strong independent predictors of a slow rate of disease progression (Table 4, models 2 to 10). By contrast, the rates of disease progression among those categorized to B*57-PD and those lacking a B*57 allele were not statistically different (Table 4, model 1), and this association remained after inclusion of the other covariates in the model (Table 4, models 2 to 10). Discussion The salient genetic-epidemiologic findings of this study conducted in a natural history cohort of HIV-1 subjects are as follows. First, because of their LD patterns, the associations for ZNRD1 alleles were evident only when these alleles were also present with alleles that categorize to the HLA-A10 serogroup. Second, heterozygosity and homozygosity for the HLA-C59 allele were associated with disease retardation, but because of LD between HLA-C and B*57 alleles, the maximal beneficial effects associated with HLA-C-bearing genotypes were evident when they were present in HLA-B*57-containing genotypes. Third, because the HCP5-G allele is in nearly 100% LD with the B*5701 allele, the genotype-phenotype relationships observed for genotypes that contain B*57 and HCP5-G alleles reflected those of B*5701-containing genotypes. We find that those HCP5-G-carrrying individuals who have one copy of HLA-C59-C (i.e., heterozygous for HLA-C59-C) had a progressive disease course whereas most of those who bear two copies of the HLA-C59-C allele (i.e., homozygous for HLA-C59-C) have a nonprogressive disease course. Fourth, after partitioning out the protective effects of B*57, the HCP5-G allele was associated with disease-acceleration and enhanced viral replication, and these associations for HCP5-G were otherwise masked because of its LD with the protective B*57 alleles. Fifth, ZNRD1 alleles influenced disease course without impacting on the viral load. Sixth, the influence of the HLA-C on the steady-state viral load was much lower than that of HLA-B*57 alleles, and the extent of variability in steady-state viral load that can be explained by HLA-C alleles independent of HLA-B*57 was significantly lower than that reported previously [27]. Seventh, because of the aforemen- tioned LD and genotype-phenotype patterns, we find that B*57- containing genotypes could be stratified into two categories, one of which associated with striking disease retardation, the other with a disease course that is similar to that observed in individuals who lack a B*57 allele. Finally, we found that B*57-containing genotypes that associate with a slower disease course influenced progression rates by impacting both the viral load as well as parameters that are independent of the viral load. Below, we discuss the seven major implications of these findings within the context of how they apply to AIDS pathogenesis, vaccine development, and genotype-phenotype association studies. First, our results provide a basis to clarify the role of ZNRD1 in HIV pathogenesis. Using several different analytical approaches we find that in the European American component of the HIV+ cohort we studied, associations of the alleles in or around ZNRD1 or RNF39 with disease progression are not attributable to an independent effect of these alleles on HIV disease course, but rather to their strong LD with HLA-A10 alleles. In the cohort studied, there was a higher proportion of subjects who had ZNRD1-containing haplotypes that lacked HLA-A10 than individuals with ZNRD1-C/A10-containing haplotypes. Despite this, ZNRD1-C/A10-lacking haplotypes were not associated with a slower rate of disease progression whereas the ZNRD1-C/A10-containing haplotypes were. Additionally, HLA-A10- containing genotypes that lacked ZNRD1 alleles were also associated with a slower disease course. Collectively, these findings suggest that HLA-A10 may be an important determinant of the rate of HIV disease progression in European Americans. Previous association studies also suggest that serogroup HLA-A10 may convey a protective effect [46]. Additionally, HLA-A*25 (a subtype of A10) is known to present gag epitopes [47,48,49], and HLA-A*26 (a subtype of A10) restricted gag responses have been also reported [50]. These prior reports in conjunction with our genetic epidemiologic findings invoke the possibility that HLA-A10 carriers elicit protective immune responses against key HIV-1-derived peptides, and consideration of this possibility might have value for understanding the host factors that influence AIDS pathogenesis and for vaccine development. PLoS ONE | www.plosone.org 13 November 2008 | Volume 3 | Issue 11 | e3636