Diagnosing Viral Infections Through T-Cell Receptor Sequencing of Activated CD8+ T Cells

T-cell-based diagnostic tools identify pathogen exposure but lack differentiation between recent and historical exposures in acute infectious diseases. Here, T-cell receptor (TCR) RNA sequencing was performed on HLA-DR+/CD38(+)CD8(+) T-cell subsets of hospitalized coronavirus disease 2019 (COVID-19) patients (n = 30) and healthy controls (n = 30; 10 of whom had previously been exposed to severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]). CDR3 alpha and CDR3 beta TCR regions were clustered separately before epitope specificity annotation using a database of SARS-CoV-2-associated CDR3 alpha and CDR3 beta sequences corresponding to >1000 SARS-CoV-2 epitopes. The depth of the SARS-CoV-2-associated CDR3 alpha/beta sequences differentiated COVID-19 patients from the healthy controls with a receiver operating characteristic area under the curve of 0.84 +/- 0.10. Hence, annotating TCR sequences of activated CD8+ T cells can be used to diagnose an acute viral infection and discriminate it from historical exposure. In essence, this work presents a new paradigm for applying the T-cell repertoire to accomplish TCR-based diagnostics.