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 historic exposures in acute infectious diseases. Here, T cell receptor (TCR) RNA sequencing was performed on HLADR+/CD38+ CD8+ T cell subsets of hospitalized COVID-19 patients (n = 30) and healthy controls (n = 30; ten of whom had previously been exposed to SARS-CoV-2). CDR3α and CDR3β TCR regions were clustered separately before epitope specificity annotation using a database of SARS-CoV-2 associated CDR3α and CDR3β sequences corresponding to >1000 SARS-CoV-2 epitopes. The depth of the SARS-CoV-2 associated CDR3α/β sequences differentiated COVID-19 patients from the healthy controls with a receiver operating characteristic curve (ROC) area under the curve (AUC) 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 historic exposure. In essence, this work presents a new paradigm of applying the T cell repertoire to accomplish TCR-based diagnostics.