Characteristics of 2031 Southern African adult subjects with C-Clade HIV-1 infection enrolled in four cohorts.

a<p>IQR = interquartile range.</p

Multivariate analysis of pairs of HLA Class I alleles, showing pairs associated with favourable impact on HIV-1 disease control, with respect to maintenance of CD4+ T cell count and/or viral load suppression (q<0.2).

a<p>Pairs in bold and underlined are those that remain significant with a more stringent q<0.05.</p>b<p>Linkage is reported if relevant; otherwise designated as N/S = not significant (corrected for multiple comparisons; only values p<1.9E-05 are reported), or N/A = not applicable (two alleles at same locus).</p

Univariate analysis of the impact of HLA Class I alleles on HIV-1 viral load in 2031 HIV-1 C-clade infected Southern African subjects (q<0.2).

a<p>Alleles in bold and underlined are those that remain significant with a more stringent FDR of q<0.05.</p>b<p>Alleles with a positive weight (above double line) are associated with statistically significant disease control; alleles with a negative weight (below double line) are associated with hazardous (detrimental) outcome.</p

Univariate analysis of the impact of HLA Class I alleles on CD4+ T cell count in 2031 HIV-1 C-clade infected Southern African subjects (q<0.2).

a<p>Alleles in bold and underlined are those that remain significant with a more stringent FDR of q<0.05.</p>b<p>Alleles with a positive weight (above double line) are associated with statistically significant disease control; alleles with a negative weight (below double line) are associated with hazardous (detrimental) outcome.</p

Changes in associations between HLA Class I alleles and HIV amino acid polymorphisms for patients with CD4 cell counts <100 cells/µl compared with patients with CD4 cell counts >500 cells/µl.

<p>The change in the strength of associations between HLA Class I alleles and specific HIV amino acid polymorphisms in patients with high and low CD4 cell counts is shown for HIV-1 (a.) Gag, (b.) Pol and (c.) Nef. Change in strength of the association is reported on the Y-axis as a log(2)-adjusted value. Associations are recorded on the X-axis according to the restricting HLA Class I allele and the specific viral polymorphism – e.g. B45-H28R in Gag means that in the presence of HLA B*45, Gag amino acid 28 mutates from a Histidine (H) to an Arginine (R). In this case there is at least a 40-fold change in the log(2)-adjusted odds ratio for this association in patients with CD4 counts <100 cells/µl compared with less progressed patients with CD4 cell counts >500 cells/µl. (All fold changes are capped at a value of 40).</p

Prevalence of compensatory mutations with the T242N mutation in the HLA-B57 and B*5801 restricted epitope, Gag TW10.

<p>In the 100% stacked column, the y-axis shows the number of mutations accumulated at the three Gag protein amino acid sites (H219Q, I223V and M228I) that compensate for the T242N mutation <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019018#pone.0019018-Brockman1" target="_blank">[27]</a>. The x-axis depicts the categorical CD4 T cell count strata and the number of patients within each strata (the “High CD4” group refers to patients with CD4 T cell counts >500 cells/µl, the “Intermediate CD4” group refers to patients with CD4 T cell counts between 200 and 400 cells/µl, and the “Low CD4” group refers to patients with CD4 T cell counts <100 cells/µl).</p

Gamma interferon ELISPOT responses in patients with CD4 counts above and below 100 cells/µl.

<p>Recognition of overlapping peptides covering the full HIV genome is shown in patients with CD4 cell counts above and below 100 cells/µl. ELISPOT responses are displayed as (a.) the absolute breadth of responses, reflecting the mean number of overlapping peptides recognised by each patient for each HIV protein and, (b.) the relative breadth, reflecting the proportion of ELISPOT responses targeted against different HIV proteins in patients within different CD4 count strata.</p

Viral replication capacity according to HLA Class I and CD4 cell count.

<p>(a) Viral replication capacity (VRC) of chimeric NL4-3 viruses containing patient autologous gag-protease stratified by HLA Class I. The VRC is expressed as percentage growth rate compared to control strains. The p-value is calculated using Mann-Whitney test. Panel (b.) shows further stratification according to CD4 cell count. The y-axis depicts VRC, expressed as percentage growth and the x-axis depicts HLA class I, with each HLA class I category divided further into “low” CD4 T cell count strata (<100 cells/mm3) and “high” CD4 T cell count (>500 cells/mm3). The p-value is calculated using Mann-Whitney test.</p

HLA-related associated polymorphisms in the HIV Nef protein in different CD4 count strata.

<p>The table shows the results of the association analysis between HLA Class I alleles and HIV viral polymorphisms in HIV Nef. The columns of the table detail the HIV protein, the associated HLA Class I allele and viral polymorphism, whether the association lies in, or within, the flanking region of a known restricted epitope and whether this association is expected to revert in HLA-mismatched hosts. The q values for the statistically significant associations for the whole cohort, the ‘high’ CD4 count subgroup (>500 cells/µl) and ‘low’ CD4 count subgroup (<100 cells/µl) are shown, followed by the log₂-adjusted odds ratios for the ‘high’ and ‘low’ groups. In the final column, the p value is reported, where there is a significant difference between the two odds ratios.</p

Viral replication capacity (VRC) in viruses with mutants in (a) Gag TL9 and (b) Gag TW10 according to HLA Class I and CD4 cell count.

<p>In panel (a), the y-axis depicts viral replication fitness (VRC) of chimeric NL4-3 viruses containing patient autologous <i>gag-protease</i>, expressed as percentage growth rate compared to a control recombinant NL4-3 strain. The x-axis depicts the stratification of patients according to (i) HLA-B*8101, (ii) polymorphic status within the <i>gag</i> TL9 epitope in all patients, (iii) polymorphic status of <i>gag</i> TL9 in patients with HLA B*8101, (iv) presence of T186S in <i>gag</i> in Gag TL9, and (v) T186S further stratified according to the CD4 T cell count (<100 cells/µl or >500 cells/µl). The p-value is calculated using Mann-Whitney test. In (b), patients are stratified according to (i) HLA-B*57 or B*5801 alleles, (ii) polymorphic status within the <i>gag</i> TW10 epitope, (iii) polymorphic status of TW10 in patients with HLA-B*57 or B*5801 alleles, (iv) polymorphic status of amino acid position 242 (within TW10 epitope – T242N) in all patients and (v) by T242N in patients with HLA-B*57 or B*5801 according to CD4 count. The viral isolates possessing other known costly escape mutations (A163G and T186S) are excluded from this analysis. The p-value is calculated using Mann Whitney test.</p