Nevertheless, future studies are clearly warranted to clarify the role of ZNRD1 in AIDS pathogenesis as it was among the more than 250 candidate genes identified by a large-scale siRNA screen used to identify host factors required by HIV-1 [51]. Second, our results may provide a basis to clarify the disease- or viral load-influencing effects of the SNPs in HCP5 and HLA-C. (i) In multivariate models, after accounting for the protective effects of HLA-B*57 alleles, we find that the HCP5-G appears to have detrimental effects on both viral load and disease progression. Thus, we surmise that when examined in isolation the true phenotypic effects associated with the HCP5-G allele might be obscured because of its strong LD with protective B*57 alleles. We propose that the protective associations detected previously for the HCP5-G allele [27] are perhaps due to a specific set of B*57-containing genotypes, i.e., those that are also homozygous for the HLA-C59-C allele (Figure 4, group 3). (ii) Based on the LD between B*57 and HLA-C59-C alleles and the significant beneficial influence of HLA-B*57-containing genotypes on viral restriction and disease course observed here and in many prior studies [11,12,14,17,19,20,21,22], we suggest that the dominant protective effects attributable to HLA-C59-C alleles may be because of their presence in specific B*57-containing genotypes. (iii) We suggest that the differences in the extent to which the HLA-C59 and HCP5 alleles explained the variability in the steady-state viral load detected in a natural history cohort versus that observed in the GWAS might relate to epidemiological considerations. The com- bined analysis of subjects who achieved a steady-state viral load and those who had virologic characteristics similar to those of spontaneous HIV controllers [31,52,53] might be one reason why such a strong association for viral load was detected for HLA-C59 and HCP5 alleles, yet these alleles were not among those detected when using disease progression as a phenotypic endpoint [27]. Consistent with this possibility, the preliminary results of a separate GWAS in HIV controllers also revealed an association between HLA-C59 and HCP5 alleles and restriction of viral replication [54]. We are mindful that other epidemiologic considerations might also contribute to differing genotype-phenotype associations. This could include the criteria used to define disease progression, which was rate of CD4 decline or time to initiation of HAART in the GWAS [27] versus a clinical endpoint used herein. Thus, it is conceivable that the varying (i) characteristics (e.g., ethnicity, risk behavior) of the subjects, (ii) selection criteria used for entry into the study as well as (iii) phenotypic endpoints used may collectively account for some of the differences in the results of the genotype-phenotype association studies. Third, the LD patterns detected herein are not completely unanticipated because the MHC locus is known to have small recombination rates and a high degree of LD, hence, increasing the number of extended haplotypic blocks in this genomic area [32]. The nature of these extended haplotypes differ in their genetic composition and the prevalence of these extended haplotypes also vary significantly according to continent-of-origin [32]. Notably, several extended HLA haplotypes that have relevance to HIV-AIDS have been identified [55,56]. LD with protective HLA alleles might provide a basis for why a large proportion of the SNPs identified in the GWAS were in the MHC locus, including additional HCP5 and HLA-C SNPs [27]. Similar considerations of LD might also have applicability to the inferences of GWAS for other diseases in which HLA-B*57 and other HLA alleles play pathogenic roles. For example, a recent GWAS implicated the HCP5-G allele as a determinant of psoriasis [57]. Fourth, we provide a genetic basis for the long-standing but highly underappreciated conundrum of why some B*57-carrying individ- uals have a progressive disease course whereas others exhibit a strikingly slow clinical course [19,20,22,42]. The prevailing viewpoint is that possession of a B*57 allele confers strong protection against HLA, HCP5 and ZNRD1 in HIV early viral replication and disease progression. However, the studies especially of Migueles et al [19] and Navis et al [22] suggest that a substantial proportion of HIV+ subjects who possess a B*57 allele, including those possessing B*5701 can have a progressive disease course. A very striking example of this conundrum was reported recently by Bailey et al who studied a HIV-1 transmission pair [42]: while both transmission pairs were HLA-B*57 positive, the transmitter progressed to AIDS, whereas the recipient was an elite controller. The contrasting clinical phenotypes of nonprogressive vs progressive disease course associated with carriage of a HLA-B*57 allele has been attributed to differences in cytotoxic T lymphocyte (CTL) escape mutations and CTL activity against epitopes in Gag as well as to differential viral replication capacities [20,22]. Here, we show that specific HLA-C59/HLA-B*57/HCP5 containing genotypes may represent multiplex ‘genetic signatures’ that have differential effects on HIV disease course. These genetic findings have broad biologic and public health significance as the immunologic features linked to protective vs non-protective B*57-containing genotypes may have practical value in achieving a detailed understanding of the immunologic correlates of virologic control and nonprogressive disease. Fifth, our findings place a spotlight on that aspect of pathogenesis that is influenced by parameters whose effects are independent of the viral burden. This point is illustrated by two observations (i) HLA-A10 affects disease course without influencing the viral load, and (ii) HLA-B*57-containing genotypes that convey a nonprogres- sive disease course do so partly by restricting viral replication (as reflected by the viral load) and also by impacting on parameters that are independent of the viral load. These observations are reminiscent of our previous results where we found that CCL3L1- CCR5 genotypes also influence disease progression, in part, by impacting on parameters that are independent of the viral load [37,38]. Although the full nature of these viral load-independent parameters is as yet unknown, their importance in pathogenesis is inferred from (i) prior findings showing that the viral load does not explain the full extent of variability in AIDS progression rates [39] or rate of CD4 cell decline [44,45], and (ii) findings in non-human primates who are naturally infected with simian immunodeficiency virus, as these animals exhibit a non-progressive disease despite high viral loads [58]. Hence, consideration of both the viral load and viral load-independent parameters might help mitigate the confounding that may occur in HIV vaccine and genetic-epidemiologic studies in which the viral load is used as the primary surrogate marker for vaccine efficacy or disease outcome, respectively. Additionally, findings from animal studies [2] and mathematical modeling [23,24,25,26] support the hope that imperfect, T-cell based disease-modifying, i.e., therapeutic vaccines, by reducing plasma viral load at the population level might abate the epidemic. However, the clinical [44,45], and genotype-phenotype relation- ships observed herein and previously [39] raise the possibility that for a therapeutic vaccine to be efficacious in mitigating disease progression rates, in addition to reducing the viral load, the vaccine may also need to target pathogenic viral load-independent factors. Sixth, within the context of a natural history cohort of HIV- positive individuals we find that there is a gradual enrichment of protective HLA-B*57 genotypes in subjects who remain AIDS free for a prolonged duration. This gradual shift emphasizes that the relative contribution of a genetic factor that confers the phenotype of nonprogressive disease within the context of a natural history cohort may not be identical to the contribution of the same genetic factor in subjects who are selected for analyses based on specific clinical characteristics such as those with nonprogessive disease (e.g., long-term nonprogressors), or virologic characteristics such as untreated subjects who maintain very low viral loads during some PLoS ONE | www.plosone.org 14 November 2008 | Volume 3 | Issue 11 | e3636