Fig 7.

Rapid accumulation of nucleotide substitutions in the ARF1_30-40QL11 epitope at 3 weeks after infection in M3 homozygous MCMs infected with m3KOΔnef. Virus populations were isolated and subjected to genome-wide deep sequencing. Samples came from M3 homozygous MCMs 3 weeks after infection with m3KOΔnef (A), M3 homozygous MCMs 4 weeks after infection with SIVmac239 (B), and M3 homozygous MCMs 12 weeks after infection with SIVmac239 (C). Amino acid variants in ARF1_30-40QL11 were investigated as described in Materials and Methods. The wild-type sequence and animal identification numbers are shown at the top of each panel. Masked identical bases are represented by dots, and amino acid replacements are represented by capital letters. The frequency of a given epitope variant sequence is shown. A variant sequence had to be present in at least one animal at a frequency of 1% or greater to be included in the graphic. The legend indicates the color associated with a given variant frequency. A zero indicates that no reads were detected with that sequence.