The impact of viral mutations on recognition by SARS-CoV-2 specific T-cells
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...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Journal article |
| Language: | English |
| Published: |
Cell Press
2021
|
| _version_ | 1797069192627748864 |
|---|---|
| author | 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 |
| author_facet | 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 |
| author_sort | de Silva, TI |
| collection | OXFORD |
| description | 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 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. |
| first_indexed | 2024-03-06T22:20:50Z |
| format | Journal article |
| id | oxford-uuid:54ffc1a5-c731-4cab-aa89-b3699df2dda2 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T22:20:50Z |
| publishDate | 2021 |
| publisher | Cell Press |
| record_format | dspace |
| spelling | oxford-uuid:54ffc1a5-c731-4cab-aa89-b3699df2dda22022-03-26T16:41:19ZThe impact of viral mutations on recognition by SARS-CoV-2 specific T-cellsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:54ffc1a5-c731-4cab-aa89-b3699df2dda2EnglishSymplectic ElementsCell Press2021de Silva, TILiu, GLindsey, BBDong, DMoore, SCHsu, NSShah, DWellington, DMentzer, AJAngyal, ABrown, RParker, MDYing, ZYao, XTurtle, LDunachie, SMaini, MKOgg, GKnight, JCPeng, YRowland-Jones, SLDong, TWe 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 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. |
| spellingShingle | 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 The impact of viral mutations on recognition by SARS-CoV-2 specific T-cells |
| title | The impact of viral mutations on recognition by SARS-CoV-2 specific T-cells |
| title_full | The impact of viral mutations on recognition by SARS-CoV-2 specific T-cells |
| title_fullStr | The impact of viral mutations on recognition by SARS-CoV-2 specific T-cells |
| title_full_unstemmed | The impact of viral mutations on recognition by SARS-CoV-2 specific T-cells |
| title_short | The impact of viral mutations on recognition by SARS-CoV-2 specific T-cells |
| title_sort | impact of viral mutations on recognition by sars cov 2 specific t cells |
| work_keys_str_mv | AT desilvati theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT liug theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT lindseybb theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT dongd theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT mooresc theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT hsuns theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT shahd theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT wellingtond theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT mentzeraj theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT angyala theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT brownr theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT parkermd theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT yingz theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT yaox theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT turtlel theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT dunachies theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT mainimk theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT oggg theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT knightjc theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT pengy theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT rowlandjonessl theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT dongt theimpactofviralmutationsonrecognitionbysarscov2specifictcells AT desilvati impactofviralmutationsonrecognitionbysarscov2specifictcells AT liug impactofviralmutationsonrecognitionbysarscov2specifictcells AT lindseybb impactofviralmutationsonrecognitionbysarscov2specifictcells AT dongd impactofviralmutationsonrecognitionbysarscov2specifictcells AT mooresc impactofviralmutationsonrecognitionbysarscov2specifictcells AT hsuns impactofviralmutationsonrecognitionbysarscov2specifictcells AT shahd impactofviralmutationsonrecognitionbysarscov2specifictcells AT wellingtond impactofviralmutationsonrecognitionbysarscov2specifictcells AT mentzeraj impactofviralmutationsonrecognitionbysarscov2specifictcells AT angyala impactofviralmutationsonrecognitionbysarscov2specifictcells AT brownr impactofviralmutationsonrecognitionbysarscov2specifictcells AT parkermd impactofviralmutationsonrecognitionbysarscov2specifictcells AT yingz impactofviralmutationsonrecognitionbysarscov2specifictcells AT yaox impactofviralmutationsonrecognitionbysarscov2specifictcells AT turtlel impactofviralmutationsonrecognitionbysarscov2specifictcells AT dunachies impactofviralmutationsonrecognitionbysarscov2specifictcells AT mainimk impactofviralmutationsonrecognitionbysarscov2specifictcells AT oggg impactofviralmutationsonrecognitionbysarscov2specifictcells AT knightjc impactofviralmutationsonrecognitionbysarscov2specifictcells AT pengy impactofviralmutationsonrecognitionbysarscov2specifictcells AT rowlandjonessl impactofviralmutationsonrecognitionbysarscov2specifictcells AT dongt impactofviralmutationsonrecognitionbysarscov2specifictcells |