Fig. 4

Prediction of SARS-CoV-2 T cell epitopes. (Top) Summary of predicted and IEDB-defined HLA-I (left) and HLA-II (right) SARS-CoV-2 HLA ligands, showing proportions of each derivative protein. (Middle) Funnel plot representing counts of HLA-I (left) and HLA-II (right) ligands along with proportions of HLA-I (top bar) and HLA-II (bottom bar) alleles at each filtering step. (Bottom) Summary of CD8⁺ (red, top), CD4⁺ (blue, bottom), and nested T cell epitopes (middle) after filtering criteria in S, M, and N proteins. Y-axis and size represent the U.S. population frequency of each CD8⁺ and CD4⁺ epitopes by circles. Middle track of diamonds represents overlaps between CD8⁺ and CD4⁺ epitopes, showing the overlap with greatest population frequency (size) for each region of overlap. Color of diamonds represents the proportion of overlap between CD4⁺ and CD8⁺ epitope sequences