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

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

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

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