Fig. 5. Transgenic CD8⁺ T cell-origin TCRs from 5 public clusters are activated in the context of HLA-A*03:01 and the KCY epitope.

(a) TRA- and TRB-gene usage and CDR3 sequences of transgenic TCRs from five public sequence-similarity clusters expressed in Jurkat reporter cells (Methods). (b) Frequency in PBMC of selected clonotypes in the bulk TCRβ-seq datasets from E00 to E03. (c) Heatmap showing the percent of maximal response for each TCR expressed in the Jurkat reporter cells cultured with HLA-A*03:01-expressing APC exposed to peptides of varying lengths in the region of residues 378–386 of S protein [1μg/mL] within a single experiment. (d) Heatmap showing the percent of maximal response for each TCR expressed in Jurkat reporter cells stimulated with HLA class I-expressing artificial APC with or without co-transfection of full-length S from SARS-CoV-2 strain Wuhan-1 (Wu-1) within a single experiment. Controls include APC treated with media or S alone. The last four rows of the heatmap represent a separate experiment, whereby each TCR was tested with HLA-A*03:01 and Wu-1 S or Omicron variants BA.1, BA.2, and BA.4. (e) Peptide titration (10⁻⁵ to 1 μg/mL) with SARS-CoV-2 S 10-mer (KCYGVSPTKL) and internal 9-mers (KCYGVSPTK and CYGVSPTKL) tested with TCR-transduced Jurkat reporter cells cultured with lymphoblastoid cell lines known to express HLA-A*03:01. Y-axis shows percent of reporter cells with mNeonGreen fluorescence.