Comparison of dN and dS for the novel Mamu-B*08-restricted CD8+ T cell epitopes in Mamu-B*08-positive and Mamu-B*08-negative SIVmac239-infected macaques.

a)We sequenced the entire open reading frames (ORFs) of vif, rev, and nef from chronic infection or at time of necropsy in 6 Mamu-B*08-positive and 34 Mamu-B*08-negative macaques infected with SIVmac239. We compared epitope-encoding regions to the remainder of the three ORFs using the following tests.b)Paired t-test (2-tailed) performed to determine whether dN was equal to dS in Mamu-B*08-restricted CD8+ T cell epitope sequences and in non-Mamu-B*08-restricted epitope regions. (n.s. = not significant)c)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 Mamu-B*08 expression. See text and Figs. 5 and 6 for details.d)Two-sample t-tests (2-tailed) were performed to determine whether dN and dS values were significantly higher in Mamu-B*08-positive animals than in Mamu-B*08-negative animals. (n.s. = not significant)