Comprehensive analysis of TCR repertoire in COVID-19 using single cell sequencing

Highlights

• We performed single-cell V(D) J sequencing for 12 COVID-19 patients.

• Comparative analyses of TCR repertoire between COVID-19 patients and controls, as well as other virus-infected samples.

• TCR clonal diversity is significantly reduced in COVID-19 patients.

• Preferential usage of T cell receptor is significantly different in several viral infections.

Abstract

T-cell receptor (TCR) is crucial in T cell-mediated virus clearance. To date, TCR bias has been observed in various diseases. However, studies on the TCR repertoire of COVID-19 patients are lacking. Here, we used single-cell V(D)J sequencing to conduct comparative analyses of TCR repertoire between 12 COVID-19 patients and 6 healthy controls, as well as other virus-infected samples. We observed distinct T cell clonal expansion in COVID-19. Further analysis of VJ gene combination revealed 6 VJ pairs significantly increased, while 139 pairs significantly decreased in COVID-19 patients. When considering the VJ combination of α and β chains at the same time, the combination with the highest frequency on COVID-19 was TRAV12-2-J27-TRBV7-9-J2-3. Besides, preferential usage of V and J gene segments was also observed in samples infected by different viruses. Our study provides novel insights on TCR in COVID-19, which contribute to our understanding of the immune response induced by SARS-CoV-2.