Viral sequencing of Gag containing the GagCM9 CD8 epitope and its known compensatory mutation amino acid locations showed little viral escape.
(a–g) We performed bulk viral Sanger sequencing at weeks two, ten, and twenty post-infection of the GagCM9 epitope and surrounding amino acids. The SIVsmE660 stock contains the isoleucine to valine GagCM9 upstream compensatory mutation at position 161, which all animals maintained throughout the acute and chronic phases of infection. Dots indicate no amino acid deviation from SIVmac239. Animal r02049 had no detectable virus at week 20; therefore, its virus could not be sequenced.