Fig. 1: Mutational antigenic profiling workflow for CVB3.

a Overview of the experimental workflow. CVB3 populations harboring high diversity in the capsid region are neutralized or mock treated and surviving viruses amplified by infection of cells. Mutation frequencies across the capsid are then obtained via high-fidelity deep sequencing. Mutations showing positive differential selection, i.e. those whose frequency relative to that of the WT has increased following neutralization versus mock-neutralized controls, define mutations conferring escape from antibody neutralization. b Mutational antigenic profile of a neutralizing mAb. Triangles indicate sites that were experimentally validated in d and the dashed red line represents the mean+2 SD of all mutations showing positive differential selection. c Logo plot representation of sites selected for validation in d. The height of the letter is proportional to the positive differential selection value. d The IC50 fold change for the mutant versus WT virus. The dashed line indicates the upper limit of detection (LOD) of the assay, calculated as indicated in the text. e CVB3 capsid pentamer structure (PDB ID: 4GB3) with residues colored by distance to the center of the capsid. The four main antibody binding regions are indicated. f The CVB3 capsid pentamer structure colored by the positive differential selection values of the mAb antigenic profile, with a zoomed view in the right panel. Source data are provided as a Source Data file. See Figure S1 for individual replicates and the correlation between replicates, Table S1 for the surviving fraction of the viral populations after neutralization, and Table S2 for structural location of the main escape sites. See capsid_roadmaps for capsid roadmaps labeled by residue and dms_view for interactive visualization on GitHub²³.