Recognition frequency of DR mutations.

<p>ELISpot responses to a panel of 140 DR-WT peptide pairs were assessed in 49 individuals. The number of peptide pairs for which, both WT and DR, only DR, or only WT peptides were recognized was assessed per individual. The scatter plot shows the result of three Wilcoxon tests comparing the paired data between groups, significant p values are indicated. Error bars show the median with interquartile range.</p

Peptide design for the evaluation of the “cornering hypothesis”.

<p><b>A.</b> Pro and RT CTL epitope map used for peptide design. Peptides were designed based on previously-described optimal CTL epitopes (blue lines) and overlapping statistically-predicted HLA-associated positions (red lines) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0147571#pone.0147571.ref013" target="_blank">13</a>]. Specific changes in the WT sequence known to mediate ART resistance are indicated as blue residues. <b>B.</b> 128 peptides were designed using experimentally confirmed CTL epitopes that overlap positions associated with DR. Both the WT peptide and the DR variants were synthesized. In the example shown, two DR mutations are reflected in an HLA-A*68:01-restricted epitope and four peptides were design reflecting the different combinations of mutations. <b>C.</b> Ninety additional peptides were designed based on 5 regions containing HLA footprints and DR mutation sites reported in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0147571#pone.0147571.ref013" target="_blank">13</a>]. A representative example is shown for the set of peptides designed to test the effect of DR mutation D67N, which is also associated with an HLA-B*15 footprint. Both WT and DR peptides were synthesized and tested individually.</p

Wide spectrum of differential magnitudes of response to WT and DR peptide pairs.

<p><b>A.</b> Differential magnitudes of response to each DR-WT peptide pair (Δ) are shown for each responder. Δ were calculated as the magnitude of response (SFC/million PBMC) to the DR sequence minus the magnitude of response to the WT sequence in each subject individually. A median differential magnitude of response was then calculated across all individuals responding to either the WT, the DR or both sequences. Boxes represent 50% of differential magnitude to each DR-WT peptide pair, whiskers maximum and minimum of the differential magnitude. <b>B.</b> Only median Δ responses are shown. Peptide pairs with significantly higher differential response to DR are shown in red; peptide pairs with significantly higher differential response to WT are shown in blue (p<0.05).</p