Fig. 3

HIV-1 variants in Gag-DA9 and Env-EL9 HLA-B*14:02 restricted epitopes and HIV-specific CD8 + T cell responses. a Amino acid (aa) sequence variation in Gag-DA9 and Env-EL9 epitopes from proviral DNA and plasma RNA samples at different time points. Aa sequence conservation relative to the HXB2 sequence is indicated with dashes. The number of observed epitope variants vs the number of sequences analyzed at each time point is shown in parenthesis. A line separates samples collected before and after the LVC. b DA9 and Env-EL9 aa sequences representative of the different variants designed to perform the ELISpot and intracellular cytokine staining (ICS). c Quantification of HIV-1 specific-CD8 + T cell responses (y axis) against DA9 (blue), Env-EL9 WT (green) and Env-EL9 with the L592R mutation (red), determined by the ELISpot analysis, at different time points (x axis). d Gag-DA9, Env-EL9 WT, Env-EL9 with L592R and Env-EL9 592R + 588R specific-CD8 + T-cell responses before and after LVC as the proportion of peptide specific IFN-γ + production by CD8 + T-cells by multiparametric flow cytometry assay. e The pie charts show the poly-functionality of Env-EL9 (upper pies) and Env-EL9 with L592R + L588R mutations (bottom pies) specific-CD8 + T-cell responses before (Jun-06) and after (Oct-15) LVC. The pie charts are based on the proportions of cells producing combinations of IFN-γ, TNF-α, IL-2, CD107a and perforin. Single and double production of CD107a and perforin were excluded from the representations