Dominant non-synonymous mutations in proviral <i>vif</i> and <i>nef</i> in SIV controllers.

<p>In the upper panel, amino acid substitutions around SIV Vif_114–124 epitope and in other Vif regions approximately 2 years after SIVmac239 challenge are shown. In the lower panel, amino acid substitutions around SIV Nef_9–19, Nef_89–97, and Nef_193–203 epitopes and in other Nef regions approximately 2 years after SIVmac239 challenge are shown. Sequences of <i>vif</i> in macaques R03-018 and R07-008 and <i>nef</i> in macaques R07-008 were not determined because these cDNA fragments could not be amplified. Macaques R07-001 and R07-003 had multiple G-to-A mutations in <i>nef</i> (See <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005247#ppat.1005247.s001" target="_blank">S1 Fig</a>). Mutant sequences shown were completely dominant except for <i>vif</i> P138L (the ratio of wild type/mutant: 1/2) in R05-005, <i>vif</i> Q162R (1/1) in R07-006, <i>nef</i> P012T (1/10) in R06-037, and <i>nef</i> S013P (3/10), I090T (1/5), D096N (1/5), and E191K (1/5) in R07-002. In addition, subdominant <i>nef</i> mutations resulting in P012S (5/2) and G044E (5/2) were detected in macaque R07-002, while the wild-type sequences were dominant at these positions.