FIG 8.

Frequencies of WT and mutated Nef RL10 epitope reads at week 2.4 p.i. (A and B) Similar to the description in the legend to Fig. 7, we characterized the viral quasispecies that constitute the Nef RL10 epitope in virus replicating in the group 1 (A) and group 2 (B) animals at week 2.4 p.i. All variants detected in >1% of sequenced reads are listed. Individual mutants that comprised <1% of sequenced reads were grouped in the same category (Variants <1%), and their combined frequencies are shown. The frequency of the predominant viral quasispecies in each animal is in boldface. Elite-controller macaques are marked with “EC” above their IDs. (C) Comparison of the percentages of WT epitope reads detected in plasma from the group 1 and group 2 macaques at week 2.4 p.i. using the Mann-Whitney test. The lines represent medians, and each symbol denotes one monkey. The average numbers of sequencing reads obtained from animals in groups 1 and 2 at this time point were 3,194 and 2,333, respectively.