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

Genomics. 2021 Mar;113(2):456-462. doi: 10.1016/j.ygeno.2020.12.036. Epub 2020 Dec 28.

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.

Keywords: COVID-19; TCR bias; TCR repertoire; scTCR-seq.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19 / genetics*
  • COVID-19 / immunology
  • Female
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Male
  • Receptors, Antigen, T-Cell / genetics*
  • SARS-CoV-2*
  • Single-Cell Analysis*
  • T-Lymphocytes / immunology

Substances

  • Receptors, Antigen, T-Cell