period of the disease course (e.g., elite or viremic controllers) [31]. For example, Migueles et al [19] found that the HLA-B*5701 allele is dramatically overrepresented in long-term nonprogressors. When studied within the context of a natural HIV history cohort, we find that 6.6% of EAs possess a B*5701 allele and of these 64% have progressive disease. Thus, the very high frequency of the HLA-B*5701 allele among those selected because of nonprogres- sive disease or a low viral load may represent an estimate specific to this selected subset of HIV-positive subjects, because HIV- positive individuals who have progressive disease are unlikely to be well represented in such a study group. Hence, association studies in such selected patients are more likely to identify genetic factors that are skewed towards having a significant impact on restriction of viral replication or nonprogressive disease, and may not necessarily identify the full realm of host factors that influence pathogenesis in the context of the natural clinical course of HIV disease, especially because a proportion of AIDS pathogenesis is independent of the viral load [39,44,45]. Finally, the results of the present study support our previous thesis that the host determinants of HIV pathogenesis are likely to be highly population-specific [34,36]. Similar inferences were also reported by Winkler and colleagues [35]. In this study, we found that the impact of the A10/ZNRD1, HLA-C and HCP5 alleles on disease course were evident mainly in subjects of European descent. Some of these race- specific effects are not related to the differential distribution in the frequency of these polymorphisms in European and African Americans. The exact basis for these race/ethnicity-specific effects on HIV disease is unclear. Given the differing evolutionary histories of the populations examined, one possibility is that the race/ethnicity- specific effects observed might relate to the interplay between polymorphisms in different gene systems that played an ancestral role in the contrasting host-microbe interplay found in subjects of European and African descent. For example, we found recently that the disease-accelerating effects of the CCL5 -471A/A genotype in African Americans is evident only in those who do not bear the African-specific -46C/C genotype of Duffy Antigen Receptor for Chemokines (DARC), a genotype which is thought to have arisen due to the selective pressure of specific malaria-causing species [43]. Regardless of the precise reasons for the observed race-specific effects, they add a tier of underappreciated complexity as they point to population-specific correlates of protection. Consequently, the development and evaluation of an effective HIV vaccine might need to factor in not just HIV diversity, but also host genetic diversity. Methods Study subjects HIV-positive subjects were from the Department of Defense (DoD) HIV Natural History Study (NHS) cohort followed at Wilford Hall Medical Center (WHMC) and more recently at the Brooke Army Medical Center (BAMC), San Antonio, TX. The studied population is the local component of a prospective multisite observational cohort from the United States Military’s Tri-Service AIDS Clinical Consortium (TACC) HIV Natural History Study. Unidentified cast-off blood from subjects participating in training at Lackland AFB, TX was used for the HIV-negative control population. The demographic and clinical characteristics of the References HLA, HCP5 and ZNRD1 in HIV HIV-positive WHMC cohort have been described extensively [34,36,37,38,39,59,60,61]. The voluntary, fully written informed consent of the subjects studied in this research was obtained as required by Air Force Regulation 169-9 and additional approval from the Institutional Review Board (IRB) of the University of Texas Health Science Center, San Antonio, TX. Genotyping Genotyping for HLA-B*57 and HLA-B*5701 subtypes was undertaken in 1,143 HIV+ subjects. Polymorphisms in the HCP5 (rs2395029), HLA-C59 (rs9264942) and seven SNPs in and around ZNRD1-RNF39 genes (Figure 1A) were genotyped in 1,230 HIV+ subjects and 1,129 HIV-negative subjects. Haplotypes based on HLA-A10 status and the seven ZNRD1 SNPs as well those based on HLA-B*57, HCP5 and HLA-C59 alleles were generated using unphased data. For this purpose, we used the PHASE software. Detailed materials, methods and description of the study cohort are available as supporting online material (Materials S1). Supporting Information Materials S1 Found at: doi:10.1371/journal.pone.0003636.s001 (0.20 DOC) MB Figure S1 Disease-influencing effects associated with HLA-A10 status in HIV-positive EA subjects from the WHMC cohort who had not received HAART. Found at: doi:10.1371/journal.pone.0003636.s002 (0.26 MB TIF) Figure S2 Association between HLA-A10-ZNRD1 haplotypes and rates of HIV disease progression in the EA component of the WHMC cohort. Found at: doi:10.1371/journal.pone.0003636.s003 (0.58 MB TIF) Figure S3 Association between HLA-C59-HLA-B-HCP5 haplo- types and rates of HIV disease progression in the WHMC cohort. Found at: doi:10.1371/journal.pone.0003636.s004 (1.06 MB TIF) Figure S4 Disease-influencing effects associated with HLA- B*57-NPD and HLA-B*57-PD genotypes in subjects who had not received HAART. Found at: doi:10.1371/journal.pone.0003636.s005 (0.33 MB TIF) Acknowledgments We thank S. Wegner and other members of the Infectious Disease Clinical Research Program (IDCRP) for critical support of this work. We thank D. Hepp and C. Crosby for technical assistance, and A. S. Ahuja for forbearance. The opinions or assertions contained herein are the private views of the authors, and are not to be construed as official, or as reflecting the views of the Departments of the Army, Navy, Air Force, or the Department of Defense. Author Contributions Conceived and designed the experiments: GC HK WH MJD SKA. Performed the experiments: GC WH VT SL. Analyzed the data: GC HK WH SL JC RAC MJD SKA. Contributed reagents/materials/analysis tools: VM BA ML SAA JD JC MJD SKA. Wrote the paper: GC HK WH ML JC RAC MJD SKA. 1. Johnston MI, Fauci AS (2007) An HIV vaccine–evolving concepts. N Engl J Med 356: 2073–2081. 2. Desrosiers RC (2004) Prospects for an AIDS vaccine. Nat Med 10: 221–223. 3. Walker BD, Burton DR (2008) Toward an AIDS vaccine. Science 320: 760–764. 4. Moore JP, Klasse PJ, Dolan MJ, Ahuja SK (2008) AIDS/HIV. A STEP into darkness or light? Science 320: 753–755. 5. Sekaly RP (2008) The failed HIV Merck vaccine study: a step back or a launching point for future vaccine development? J Exp Med 205: 7–12. 6. Cohen J (2007) AIDS research. Promising AIDS vaccine’s failure leaves field reeling. Science 318: 28–29. 7. AIDS Vaccine Trials:Considerations for Phase III Trial Design and Endpoints N, NIH, Nov. 16, 2001, http://www.niaid.nih.gov/vrc/pdf/p3trialsend.pdf. PLoS ONE | www.plosone.org 15 November 2008 | Volume 3 | Issue 11 | e3636