Comparison of <i>d_N</i> and <i>d_S</i> for the novel Mamu-B*08-restricted CD8⁺ T cell epitopes in <i>Mamu-B*08</i>-positive and <i>Mamu-B*08</i>-negative SIVmac239-infected macaques.

a)<p>We sequenced the entire open reading frames (ORFs) of <i>vif</i>, <i>rev</i>, and <i>nef</i> from chronic infection or at time of necropsy in 6 <i>Mamu-B*08</i>-positive and 34 <i>Mamu-B*08</i>-negative macaques infected with SIVmac239. We compared epitope-encoding regions to the remainder of the three ORFs using the following tests.</p>b)<p>Paired t-test (2-tailed) performed to determine whether <i>d_N</i> was equal to <i>d_S</i> in Mamu-B*08-restricted CD8⁺ T cell epitope sequences and in non-Mamu-B*08-restricted epitope regions. (n.s. = not significant)</p>c)<p>We included one amino acid N-terminal to the Nef epitopes RL10 (pos. 137–146) and RL9 (pos. 246–254) because it appeared that variation was associated with <i>Mamu-B*08</i> expression. See text and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001152#pone-0001152-g005" target="_blank">Figs. 5</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001152#pone-0001152-g006" target="_blank">6</a> for details.</p>d)<p>Two-sample t-tests (2-tailed) were performed to determine whether <i>d_N</i> and <i>d_S</i> values were significantly higher in <i>Mamu-B*08</i>-positive animals than in <i>Mamu-B*08</i>-negative animals. (n.s. = not significant)