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

COVID-19 Genomics UK (COG-UK) Consortium; ISARIC4C Investigators

doi:10.1016/j.isci.2021.103353

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

COVID-19 Genomics UK (COG-UK) Consortium
, ISARIC4C Investigators

https://www.cogconsortium.uk
https://isaric4c.net
University of Sheffield
London School of Hygiene & Tropical Medicine
University of Oxford
University of Oxford Medical Sciences Division
Capital Medical University
Xinjiang Medical University
University of Liverpool
Nuffield Department of Medicine
University of Oxford
Liverpool University Hospitals NHS Foundation Trust
Mahidol-Oxford Tropical Medicine Research Unit
University College London

Producción científica: Contribución a una revista › Artículo › revisión exhaustiva

76 Citas (Scopus)

Resumen

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_207-215; due to P13L, P13S, and P13T in the B∗27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF_9-17; and due to T362I and P365S in the A∗03:01/A∗11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK_361-369. 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.

Idioma original	Inglés
Número de artículo	103353
Publicación	iScience
Volumen	24
N.º	11
DOI	https://doi.org/10.1016/j.isci.2021.103353
Estado	Publicada - 19 nov. 2021
Publicado de forma externa	Sí

Acceder al documento

10.1016/j.isci.2021.103353

Otros archivos y enlaces

Enlace a la publicación en Scopus

Citar esto

@article{30f2e508d77740c9ab22a13c5dae12e5,

title = "The impact of viral mutations on recognition by SARS-CoV-2 specific T cells",

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 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.",

keywords = "Immune response, Immunology, Molecular biology, Phylogenetics, Virology",

author = "\{COVID-19 Genomics UK (COG-UK) Consortium\} and \{ISARIC4C Investigators\} and \{de Silva\}, \{Thushan I.\} and Guihai Liu and Lindsey, \{Benjamin B.\} and Danning Dong and Moore, \{Shona C.\} and Hsu, \{Nienyun Sharon\} and Dhruv Shah and Dannielle Wellington and Mentzer, \{Alexander J.\} and Adrienn Angyal and Rebecca Brown and Parker, \{Matthew D.\} and Zixi Ying and Xuan Yao and Lance Turtle and Susanna Dunachie and Aanensen, \{David M.\} and Khalil Abudahab and Helen Adams and Alexander Adams and Safiah Afifi and Dinesh Aggarwal and Ahmad, \{Shazaad S.Y.\} and Louise Aigrain and Adela Alcolea-Medina and Alikhan, \{Nabil Fareed\} and Elias Allara and Roberto Amato and Tara Annett and Stephen Aplin and Ariani, \{Cristina V.\} and Hibo Asad and Amy Ash and Paula Ashfield and Fiona Ashford and Laura Atkinson and Attwood, \{Stephen W.\} and Cressida Auckland and Alp Aydin and Baker, \{David J.\} and Paul Baker and Balcazar, \{Carlos E.\} and Jonathan Ball and Barrett, \{Jeffrey C.\} and Magdalena Barrow and Edward Barton and Matthew Bashton and Bassett, \{Andrew R.\} and Rahul Batra and Chris Baxter",

note = "Publisher Copyright: {\textcopyright} 2021 The Author(s)",

year = "2021",

month = nov,

day = "19",

doi = "10.1016/j.isci.2021.103353",

language = "Ingl{\'e}s",

volume = "24",

journal = "iScience",

issn = "2589-0042",

publisher = "Elsevier Inc.",

number = "11",

}

TY - JOUR

T1 - The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

AU - COVID-19 Genomics UK (COG-UK) Consortium

AU - ISARIC4C Investigators

AU - de Silva, Thushan I.

AU - Liu, Guihai

AU - Lindsey, Benjamin B.

AU - Dong, Danning

AU - Moore, Shona C.

AU - Hsu, Nienyun Sharon

AU - Shah, Dhruv

AU - Wellington, Dannielle

AU - Mentzer, Alexander J.

AU - Angyal, Adrienn

AU - Brown, Rebecca

AU - Parker, Matthew D.

AU - Ying, Zixi

AU - Yao, Xuan

AU - Turtle, Lance

AU - Dunachie, Susanna

AU - Aanensen, David M.

AU - Abudahab, Khalil

AU - Adams, Helen

AU - Adams, Alexander

AU - Afifi, Safiah

AU - Aggarwal, Dinesh

AU - Ahmad, Shazaad S.Y.

AU - Aigrain, Louise

AU - Alcolea-Medina, Adela

AU - Alikhan, Nabil Fareed

AU - Allara, Elias

AU - Amato, Roberto

AU - Annett, Tara

AU - Aplin, Stephen

AU - Ariani, Cristina V.

AU - Asad, Hibo

AU - Ash, Amy

AU - Ashfield, Paula

AU - Ashford, Fiona

AU - Atkinson, Laura

AU - Attwood, Stephen W.

AU - Auckland, Cressida

AU - Aydin, Alp

AU - Baker, David J.

AU - Baker, Paul

AU - Balcazar, Carlos E.

AU - Ball, Jonathan

AU - Barrett, Jeffrey C.

AU - Barrow, Magdalena

AU - Barton, Edward

AU - Bashton, Matthew

AU - Bassett, Andrew R.

AU - Batra, Rahul

AU - Baxter, Chris

PY - 2021/11/19

Y1 - 2021/11/19

N2 - 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.

AB - 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.

KW - Immune response

KW - Immunology

KW - Molecular biology

KW - Phylogenetics

KW - Virology

UR - https://www.scopus.com/pages/publications/85118773166

U2 - 10.1016/j.isci.2021.103353

DO - 10.1016/j.isci.2021.103353

M3 - Artículo

AN - SCOPUS:85118773166

SN - 2589-0042

VL - 24

JO - iScience

JF - iScience

IS - 11

M1 - 103353

ER -

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

Resumen

Acceder al documento

Otros archivos y enlaces

Huella

Citar esto