Fig. 2: Subsets of progenitors of exhausted T cells during the acute-phase of infection.

Representative flow cytometry gating plots of dextramer-positive CD8⁺ T cell populations analysed longitudinally targeting autologous epitopes identified from circulating viral populations, in clearers (CL) (a) and chronic progressors (CH) (b). Each plot shows dextramer positive cells (coloured) and the frequency of phenotypic subsets based: T_EX (PD-1^highCD127^low), T_PINT (PD-1^intCD127^low), T_ML (PD-1^highCD127^high), T_MEM (PD-1^lowCD127^high), and T_EFF (CD127^lowPD-1^low). DPI: days post-infection. Shown are cells gated from a lymphocyte/singlet/live population that were CD19 negative, CD3, and CD8 positive. c Group comparison of phenotypic subsets of HCV-specific populations segregated by disease outcome. Individual points represent unique individual, timepoint and epitope specificity. Data are presented as median and 75% quantile. N = 116 biologically independent blood samples and 10 epitope specificities. d Comparisons of the proportion of cells with positive expression of protein markers measured by flow cytometry between dextramer positive and total CD8⁺ T cells in both disease outcomes, split into early (≤120 DPI) and late (>120 DPI) time points. Individual points represent populations from each individual’s sample time points, and from each epitope specificity, N = 44 biologically independent samples were used. Data are presented as median and 75% quantile. Pairwise group comparisons were performed utilising a two-sided Wilcoxon signed-rank test. e Plots showing the proportion of dextramer-positive CD8⁺ T cell populations with positive expression of phenotypic markers (measured by flow cytometry) over the course of the infections (DPI values). Lines represent linear regression, and adjusted coefficients and p values are shown in the legend of each plot. Continuous lines (dashed) represent significant (not significant) linear fits (p-value <0.05). f Similar to e, plots of the proportion of dextramer positive CD8⁺ T cell populations with positive expression of phenotypic markers (measured by flow cytometry) and IFN-γ ELISpot values (number of SFU per million PBMC) on a log₁₀-scale.