Extended Data Figure 1. CTL escape variants dominate the latent reservoir of CP-treated HIV-1-positive individuals, but not AP-treated individuals.

Frequency of variants in Gag CTL epitopes in proviruses from resting CD4⁺ T cells. Results of all 25 patients tested are shown. Only optimal CTL epitopes relevant to each patient’s HLA type are listed in linear positional order on the X axis. Results from both Pacbio (left bar) and MiSeq (right bar) sequencing platforms are shown for each epitope. The absence of bars above a listed epitope indicates that only wild type sequences were detected. For each mutation in a CTL epitope, information regarding the effect of the mutation on CTL recognition from the Los Alamos National Laboratory (LANL) HIV Molecular Immunology Database or from ELISpot assays described herein was used to assign the mutation to one of the categories indicated at the bottom. See Methods for definitions of these categories.