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The impact of viral mutations on recognition by SARS-CoV-2 specific T cells.
de Silva, Thushan I; Liu, Guihai; Lindsey, Benjamin B; Dong, Danning; Moore, Shona C; Hsu, Nienyun Sharon; Shah, Dhruv; Wellington, Dannielle; Mentzer, Alexander J; Angyal, Adrienn; Brown, Rebecca; Parker, Matthew D; Ying, Zixi; Yao, Xuan; Turtle, Lance; Dunachie, Susanna; Maini, Mala K; Ogg, Graham; Knight, Julian C; Peng, Yanchun; Rowland-Jones, Sarah L; Dong, Tao.
  • de Silva TI; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK.
  • Liu G; Vaccines and Immunity Theme, Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia.
  • Lindsey BB; Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK.
  • Dong D; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
  • Moore SC; Beijing You'an Hospital, Capital Medical University, Beijing, China.
  • Hsu NS; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK.
  • Shah D; Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK.
  • Wellington D; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
  • Mentzer AJ; CAMS Key Laboratory of Tumor Immunology and Radiation Therapy, Xinjiang Tumor Hospital, Xinjiang Medical University, China.
  • Angyal A; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool CH64 7TE, UK.
  • Brown R; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK.
  • Parker MD; Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK.
  • Ying Z; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK.
  • Yao X; Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK.
  • Turtle L; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
  • Dunachie S; Nuffield Department of Medicine, University of Oxford, NDM Research Building, Oxford OX3 7FZ, UK.
  • Maini MK; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK.
  • Ogg G; The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK.
  • Knight JC; Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK.
  • Peng Y; Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK.
  • Rowland-Jones SL; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
  • Dong T; Chinese Academy of Medical Sciences (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK.
iScience ; 24(11): 103353, 2021 Nov 19.
Article in English | MEDLINE | ID: covidwho-1509904
Preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
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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. Complete loss of T cell responsiveness was seen due to Q213K in the A∗0101-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B∗2705-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A∗0301/A∗1101-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.
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Full text: Available Collection: International databases Database: MEDLINE Type of study: Experimental Studies Topics: Variants Language: English Journal: IScience Year: 2021 Document Type: Article Affiliation country: J.isci.2021.103353

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Experimental Studies Topics: Variants Language: English Journal: IScience Year: 2021 Document Type: Article Affiliation country: J.isci.2021.103353