Figure 4. Percentages of unrecognized CTL epitopes in Gag, Pol, and Nef from HIV-1 proviruses do not change dramatically over long periods of time on suppressive ART.

Percentages of wild-type, unrecognized (deleted, escaped, frameshifted, or preceding stop codon), and uncharacterized epitope sequences at each dominant epitope in 5 chronic progressors on suppressive ART at 2 widely spaced time points. Provirus epitope sequences that lay in an area with unavailable sequence information were discarded from the analysis. The average number of total available epitope sequences per participant time point is shown at right. Predicted dominant epitopes in Gag, Pol, and Nef given each participant’s HLA type are shown and labeled. Epitope information can be found in Supplemental Table 2. Del, epitope lay within a mapped deletion; FS, a frameshift mutation precedes the epitope; SC, a stop codon precedes the epitope.