Fig. 1: Schematic overview of antigen-TCR pairing and multiomic analysis of T-cells (APMAT) in COVID-19 participants. | Nature Communications

Fig. 1: Schematic overview of antigen-TCR pairing and multiomic analysis of T-cells (APMAT) in COVID-19 participants.

From: APMAT analysis reveals the association between CD8 T cell receptors, cognate antigen, and T cell phenotype and persistence

Fig. 1

Created in BioRender58. a Participants in the study, broken down by COVID-19 severity. b The experimental and computational flow of APMAT. i Construction of the large SCT-pMHC library representing HLA-A*02:01 peptide-MHC complexes covering antigens from across the full SARS-CoV-2 proteome. ii Antigen-specific T cells are captured from pooled patient PBMCs with barcoded SCT multimers for scRNAseq analysis. iii Patient i.d.’s are assigned to each single cell by matching SNP analysis from whole genome with scRNAseq data. iv-vii For each T cell, the physicochemical properties of the peptide antigen and the CDR3β domain of the TCRs are analyzed to identify statistical associations between the CDR3β-peptide antigen interface with T cell phenotype. viii T cell clonotype persistence from acute disease to convalescence is similarly associated with the physicochemical properties of the TCR:antigen.

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