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

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Author
Lim, Wei Shen
Keyword
SARS-CoV-2
COVID-19
Viral mutations
Date
2021

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Publisher's URL
https://doi.org/10.1016/j.isci.2021.103353
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-gamma and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A*01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B*27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A*03:01/A*11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T cell lines unable to recognize variant epitopes have diverse T cell receptor repertoires. 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. Copyright © 2021 The Author(s).
Citation
de Silva, T.I., Liu, G., Lindsey, B.B., Dong, D., Moore, S.C., Hsu, N.S., Shah, D., Wellington, D., Mentzer, A.J., Angyal, A., Brown, R., Parker, M.D., Ying, Z., Yao, X., Turtle, L., Dunachie, S., Maini, M.K., Ogg, G., Knight, J.C., Peng, Y., ISARIC4C Investigators, Rowland-Jones, S.L. and Dong, T. (2021) 'The impact of viral mutations on recognition by SARS-CoV-2 specific T cells', iScience, 24(11), pp. 103353. doi: 10.1016/j.isci.2021.103353 https://doi.org/10.1016/j.isci.2021.103353.
Type
Article
URI
http://hdl.handle.net/20.500.12904/19341
Note
Wei Shen Lim is an ISARIC4C Investigator.
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