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

Authors :: de Silva TI
Liu G
Lindsey BB
Dong D
Moore SC
Hsu NS
Shah D
Wellington D
Mentzer AJ
Angyal A
Brown R
Parker MD
Ying Z
Yao X
Turtle L
Dunachie S
Maini MK
Ogg G
Knight JC
Peng Y
Rowland-Jones SL
Dong T
Source :: IScience [iScience] 2021 Nov 19; Vol. 24 (11), pp. 103353. Date of Electronic Publication: 2021 Oct 28.
Publication Year :: 2021
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. Complete loss of T cell responsiveness was seen due to Q213K in the A∗01:01-restricted CD8+ ORF3a epitope FTSDYYQLY <subscript>207-215</subscript> ; due to P13L, P13S, and P13T in the B∗27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF <subscript>9-17</subscript> ; and due to T362I and P365S in the A∗03:01/A∗11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK <subscript>361-369</subscript> . 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.<br />Competing Interests: The authors have no competing interests to declare.<br /> (© 2021 The Author(s).)