Relationship between CTL targeting and viremia.

<p>Protein-specific protective ratios were plotted as a function of the mean entropy of each HIV-1 protein. Protective ratios were calculated as the Log₁₀ of the viral load of all the individuals who did not mount a CTL response against a protein over the viral load of all the individuals who had one or more CTL response(s) directed against that protein.</p

Variation in C-clade Nef sequences, and relationship between amino acid variability and presence of HLA-class I selection pressure.

<div><p>[A] Nef consensus sequence (derived from 739 C-clade sequences from Southern African patients) plotted against Shannon entropy score. Residues at which there is an association with HLA-Class I expression are shown in grey. As previously observed, the sequence is most highly conserved in the central portion of the protein (residues 66-148) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073117#B8" target="_blank">8</a>]..</p> <p>[B] Entropy scores of residues associated with HLA-class I expression vs. those with no HLA association, showing significantly higher variability at sites at which HLA selection operates, particularly in the central conserved region. P-value by Mann Whitney U test.</p></div

Fitness competition assays between viruses mutated at residues in the sub-network associated with the HLA-B*81 epitope TPQDLNTML.

<p>The relative fitness of viruses presenting a mutation at site 177, 186 or at both sites is compared to that of the wt COT virus. Fitness competition assays were performed against a wt COT virus; the proportion of viral RNA from the mutant and wt viruses was measured at day zero, three and five (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012463#s4" target="_blank">methods</a>).</p

Relationship between number of HLA associations with Nef sequence polymorphisms and median viral load for subjects expressing that allele, for HLA-A, -B and -C alleles.

<p>Data from lineage-corrected analysis of 739 C-clade Nef sequences. P-values by Mann–Whitney U test.</p

Hubness across HIV-1 Subtype C Gag.

<p>The number of co-varying partners and the Shannon Entropy are represented for each site along the Gag protein. The blue (lower) part of the bars represent the number of AA-to-AA associations and the red (upper) part of the bars represent the number of HLA-to-AA associations at each site. The secondary axis refers to the Shannon Entropy at each site in Gag (continuous black line).</p

Relationship between HBV status and markers of HIV disease in HIV-positive women from South Africa and Botswana.

<p>Panels (A) and (B): South Africa (Durban + Kimberley cohorts pooled); Panels (C) and (D): Botswana (Gaborone). Left-hand column (panels (A) and (C)) shows CD4+ T cell counts; right-hand column (panels (B) and (D)) shows HIV-1 RNA viral load. In each case, box represents median and 25/75^th centiles, whiskers 5-95^th centiles. P values by Mann Whitney U test.</p

Map of central region of Nef showing sites of key epitopes and residues at which CD8+ selection pressure operates.

<p>Central conserved region of HIV-1 Nef is shown previously defined as HXB2 residues 81-160 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073117#B8" target="_blank">8</a>]. Corresponding B-clade and C-clade consensus sequences are shown along with SIVmac239 consensus. Positions of epitopes restricted by alleles HLA-B*27 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073117#B37" target="_blank">37</a>], HLA-B*57 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073117#B28" target="_blank">28</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073117#B64" target="_blank">64</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073117#B65" target="_blank">65</a>] and HLA-B*44 are highlighted in green, orange and blue respectively. Regions homologous to Mamu-B*08 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073117#B36" target="_blank">36</a>] and Mamu-B*17 epitopes [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073117#B66" target="_blank">66</a>] are also marked (yellow and purple respectively). SIV 115-129 also highlighted as a region recently associated with SIV control in macaques [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073117#B41" target="_blank">41</a>]. Responses to overlapping peptides 79 and 85 are associated with viraemic control, q<0.2 (black boxes). Sites of mutations selected by HLA-B*57, HLA-B*27, HLA-B*44, Mamu-B*08 and Mamu-B*17 are marked with arrows [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073117#B29" target="_blank">29</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073117#B36" target="_blank">36</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073117#B67" target="_blank">67</a>]. This highlights the substantial overlap between HIV and SIV epitopes restricted by alleles that are associated with favourable immune control.</p

Amino Acid associations in HIV-1 subtype C Gag.

<p>Associations are depicted with a circular map: AA interactions among residues are represented with arcs, which are color-coded with a white to purple gradient – white corresponding to the strongest associations (i.e., lower q-values). HLA-restricted sites are identified by the HLA allele designations around the circle.</p

Relationship between viral loads and co-varying associations linking conserved sites.

<p>Shown are associations that involved an HLA-associated site (in bold) or at which a mutation had a significant impact on viral loads.</p>a<p>Number of individuals.</p>b<p>Consensus AA at both co-varying sites.</p>c<p>Rare residues at both co-varying sites.</p>d<p>Consensus AA at one site and a rare AA at the other co-varying site.</p

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

a<p>IQR = interquartile range.</p