The impact of viral mutations on recognition by SARS-CoV-2 specific T-cells

  1. Thushan I. de Silva
  2. Guihai Liu
  3. Benjamin B Lindsey
  4. Danning Dong
  5. Dhruv Shah
  6. Alexander J. Mentzer
  7. Adrienn Angyal
  8. Rebecca Brown
  9. Matthew D. Parker
  10. Zixi Ying
  11. Xuan Yao
  12. Lance Turtle
  13. Susanna Dunachie
  14. COVID-19 Genomics UK (COG-UK) Consortium
  15. Mala K. Maini
  16. Graham Ogg
  17. Julian C. Knight
  18. Yanchun Peng
  19. Sarah L. Rowland-Jones
  20. Tao Dong
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Abstract

We identify amino acid variants within dominant SARS-CoV-2 T-cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T-cells assessed by IFN-γ and cytotoxic killing assays. These data demonstrate the potential for T-cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T-cell as well as humoral immunity.

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