It has been estimated that an average adult has approximately 10^8-10^10 unique T cell receptor (TCR) clonotypes. This incredible repertoire diversity makes it challenging to detect virus-specific TCRs that confer protection against disease and latent infection. Epstein-Barr virus (EBV), cytomegalovirus (CMV) and human papillomavirus (HPV) infections have widespread global prevalence and may cause persistent infection in individuals with compromised immunity, who lack protective virus-specific TCRs. Most of the available TCR repertoire data generated from donor samples, which are seropositive for CMV, EBV and HPV contain only the sequences of TCRβ chains and not the paired TCRα and TCRβ data, limiting the quantitative resolution needed to accurately determine TCR–antigen specificity.
Here, we demonstrate a novel high-throughput single-cell paired TCRα/β sequencing method in which we generated over 1 million TCR clonotypes from infected donor samples and from T cells expanded with viral-specific epitopes. In addition to detecting previously published CMV, EBV, HPV clonotypes, we identified several new TCR clonotypes that had expanded in response to the viral-specific epitope stimulation. We envision that this method will unlock the true potential for high-throughput TCR discovery and help advance the development of TCR-based immunotherapy strategies to prevent and treat infectious diseases.
