Extensive sequence evolution in SIVΔnef.

(A) Plasma viral loads (RNA copies/ml) of 12 SIVΔnef-infected animals. The dashed black line marks the 30 copies/ml threshold. (B) Frequency of nonsynonymous mutations (>10% variant frequency) increased significantly (p = 0.001) between weeks 4 and 20 for the 5 animals whose virus was sequenced at both time points. Squares are colored according to variant frequency: blue: 10–15%, green: 16–30%, orange: 31–50%, red: 51–80%, and dark red: 81–100%. (C) The sequence evolution in animal 225–97 at weeks 2, 4 and 20 is displayed for every amino acid in the SIVΔnef proteome. The top left corner is the first amino acid of Gag and the bottom right corner is the last expressed amino acid of the truncated Nef. (D) Extensive SIVΔnef sequence evolution in animals 290–07 and 292–07 at week 20, despite undetectable plasma viral load. Lymph node cell-associated viral RNA was isolated for sequencing. (E) Significant increase (p = 0.031) in the number of nonsynonymous mutations between weeks 4 and 20 for 5 animals whose virus was sequenced at both time points.