HLA, HCP5 and ZNRD1 in HIV Figure 4. Disease-influencing effects associated with HLA-B*57/HCP5/HLA-C-containing genotypes. (A) Six genotypic groups (enumerated, color-coded) were derived by accounting first for the presence or absence of HLA-B*57 alleles and the wild-type (T/T), heterozygous (T/C) or homozygous (C/C) state for the SNP in HLA-C. This group of subjects was stratified further based on presence or absence of the HCP5-G allele. Number of subjects in each genotypic group is shown within the color-coded boxes. ‘‘+’’ and ‘‘-’’ denotes ‘‘presence’’ and ‘‘absence’’, respectively. (B) The disease-influencing effects associated with the six genotypic groups shown in panel A. (C) Kaplan-Meier plots depicting the influence of the HCP5 SNP on disease progression in subjects in genotypic group 2 stratified according to presence (group 2A) or absence (group 2B) of the HCP5-G allele. P values in panels B and C are by the logrank test. (D) HLA-B*57/HCP5/HLA-C genotypes that associate with nonprogressive disease (B*57-NPD, i.e., groups 1, 2B and 3 depicted in panels A–C) or progressive disease (B*57-PD; group 2A depicted in panel A and C) compared with genotypes that lack HLA-B*57. RH, relative hazards; CI, confidence interval; P, significance value obtained by Cox proportional hazards modeling; n, number of subjects. The RH was computed before (values above complete horizontal line) and after (below) adjustment for ethnic background, cohort membership across different therapy eras, CCL3L1-CCR5 genetic risk group status and whether date of seroconversion was known. All plots are Kaplan-Meier curves for time to AIDS development (1987 criteria). (E) Association of the genotypes shown in panel D with virologic and immunologic markers of HIV disease. {M-W P refers to significance values obtained by Mann-Whitney test for comparison between HLA-B*57-NPD genotype and the remaining cohort subjects. bCD4, nCD4, cCD4, VL and DTH are as described in Figure 2E. (F) The distribution of HLA-B*57-NPD or HLA-B*57-PD genotypes was examined according to time to AIDS or duration of AIDS-free status (left panel) as well as according to steady-state viral load (right panel). Data are from all subjects in the cohort. Time to AIDS or duration of AIDS-free status is shown on the bottom of the left panel and indicates time to AIDS in ,2, 2 to ,5, and $5 years, and no development of AIDS during the first 10 years or after 10 or more years of follow-up. Steady-state viral load shown on the right was categorized as ,10,000, 10,000 to ,20,000, 20,000 to ,55,000 and $55,000 copies/ml. P value at the top of left panel is significance value for a linear trend obtained using chi-square test for linear trend. doi:10.1371/journal.pone.0003636.g004 allele in the univariate analysis (Coeff = 20.25; P = 0.03, Table 1, model 3) was not evident when this allele was examined in a multivariate context with B*57 alone (Coeff = 0.46; P = 0.005, Table 1, model 5), or with the B*57 allele and HLA-C59 genotypes together (Coeff = 0.56; P = 0.001, Table 1, model 6). Thus, the opposing direction of the viral load-influencing effects of the HCP5- G allele observed in the univariate (negative value for the regression coefficients in Table 1, model 3; Coeff = 20.25) and multivariate (positive value for the regression coefficients in Table 1, models 5 (Coeff = 0.46) and 6 (Coeff = 0.56)) analyses closely mirrored the opposing direction of the disease-influencing effects of the HCP5-G allele observed in univariate and multivariate analyses. Thus, once the protective effects associated with HLA-B*57 or HLA-C59-C are partitioned out, the HCP5-G allele associated with not only a faster rate of disease progression (RH = 2.19; 95% CI = 1.07–4.46; P = 0.032), but also a higher viral load (Coeff = 0.56; 95% CI = 0.23–0.88; P = 0.001; Table 1, model 6). Analyses of the final multivariate regression model also revealed that the HLA-B*57, HLA-C59 and HCP5 alleles together explained 4.66% of the variability in the steady-state viral load in the WHMC HIV+ cohort (R2 estimate for model 6 in Table 2). Additionally, the final model indicates that HLA-B*57 alleles might confer a greater protective effect on early viral replication than HLA-C59 alleles (Coefficient values in model 6 in Table 2 for B*57 was 20.82, whereas it was HLA-C59 20.08 and 20.26 for heterozygosity and homozygosity for the HLA-C59-C allele). Table 2. Analysis of the disease-modulating effects of HLA-B*57, the HLA-C59 and HCP5 alleles/genotypes in HIV+ subjects from the WHMC cohort. Model Covariates Time to AIDS Steady-state viral load 1 2 3 4 5 6 HLA-B*57 HLA-C59 HCP5 HLA-B*57 HLA-C59 HLA-B*57 HCP5 HLA-B*57 HLA-C59 Heterozygosity Homozygosity Heterozygosity Homozygosity Heterozygosity Homozygosity HCP5 RH 0.38 0.81 0.66 0.67 0.39 0.81 0.72 0.25 2.06 0.26 0.81 0.69 2.19 95% CI 0.23–0.63 0.65–0.99 0.46–0.95 0.39–1.14 0.24–0.65 0.66–1.00 0.50–1.02 0.13–0.51 0.98–4.33 0.13–0.51 0.66–0.99 0.48–0.99 1.07–4.46 P 0.0002 0.041 0.025 0.135 0.0003 0.051 0.067 0.0001 0.056 0.043 0.044 0.032 8.561025 Coeff 20.53 20.07 20.26 20.25 20.51 20.06 20.21 20.79 0.46 -0.82 20.08 20.26 0.56 95% CI 20.71 to 20.35 20.18 to 0.03 20.42 to 20.09 20.48 to 20.02 20.69 to 20.33 20.16 to 0.04 20.38 to 20.05 21.05 to 20.54 0.14 to 0.78 21.07 to 20.56 20.18 to 0.02 20.43 to 20.09 0.23 to 0.88 R2 0.0324 0.0072 0.0038 0.0368 0.0392 P 7.161029 0.172 0.003 0.030 2.961028 0.270 0.012 1.361029 0.005 0.124 0.002 0.001 3.7610210 0.0466 Results are from univariate and multivariate Cox proportional hazards regression (for the outcome of time to AIDS (1987 criteria)) and linear regression models (for the outcome of log10 steady-state viral load) in all subjects from the WHMC cohort. RH, relative hazards; CI, confidence interval, Coeff, regression coefficient obtained from linear regression model. R2, the explained variability in steady-state viral loads was measured using the R2 estimated by analysis of variance (ANOVA). doi:10.1371/journal.pone.0003636.t002 PLoS ONE | www.plosone.org 10 November 2008 | Volume 3 | Issue 11 | e3636