The in vivo phenotypic profile of T cells reactive to severe acute respiratory syndrome (SARS)-CoV-2 antigens remains poorly understood. Conventional methods to detect antigen-reactive T cells require in vitro antigenic re-stimulation or highly individualized peptide-human leukocyte antigen (pHLA) multimers. Here, we use single-cell RNA sequencing to identify and profile SARS-CoV-2-reactive T cells from Coronavirus Disease 2019 (COVID-19) patients. To do so, we induce transcriptional shifts by antigenic stimulation in vitro and take advantage of natural T cell receptor (TCR) sequences of clonally expanded T cells as barcodes for 'reverse phenotyping'. This allows identification of SARS-CoV-2-reactive TCRs and reveals phenotypic effects introduced by antigen-specific stimulation. We characterize transcriptional signatures of currently and previously activated SARS-CoV-2-reactive T cells, and show correspondence with phenotypes of T cells from the respiratory tract of patients with severe disease in the presence or absence of virus in independent cohorts. Reverse phenotyping is a powerful tool to provide an integrated insight into cellular states of SARS-CoV-2-reactive T cells across tissues and activation states.
- Fischer, D. S.
- Ansari, M.
- Wagner, K. I.
- Jarosch, S.
- Huang, Y.
- Mayr, C. H.
- Strunz, M.
- Lang, N. J.
- D'Ippolito, E.
- Hammel, M.
- Mateyka, L.
- Weber, S.
- Wolff, L. S.
- Witter, K.
- Fernandez, I. E.
- Leuschner, G.
- Milger, K.
- Frankenberger, M.
- Nowak, L.
- Heinig-Menhard, K.
- Koch, I.
- Stoleriu, M. G.
- Hilgendorff, A.
- Behr, J.
- Pichlmair, A.
- Schubert, B.
- Theis, F. J.
- Busch, D. H.
- Schiller, H. B.
- Schober, K.
