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

Marc-Emmanuel Dumas; Thushan de Silva; Guihai Liu; Benjamin Lindsey; Danning Dong; Shona Moore; Nienyun Sharon Hsu; Dhruv Shah; Dannielle Wellington; Alexander Mentzer; Adrienn Angyal; Rebecca Brown; Matthew Parker; Zixi ying; Xuan yao; Lance Turtle; Susanna Dunachie; Mala Maini; Graham Ogg; Julian Knight; yanchun Peng; Sarah Rowland-Jones; Tao Dong; David Aanensen; Khalil Abudahab; Helen Adams; Alexander Adams; Safiah Afifi; Dinesh Aggarwal; Shazaad S.y. Ahmad; Louise Aigrain; Adela Alcolea-Medina; Nabil-Fareed Alikhan; Elias Allara; Roberto Amato; Tara Annett; Stephen Aplin; Cristina Ariani; Hibo Asad; Amy Ash; Paula Ashfield; Fiona Ashford; Laura Atkinson; Stephen Attwood; Cressida Auckland; Alp Aydin; David Baker; Paul Baker; Carlos Balcazar; Jonathan Ball; Jeffrey Barrett; Magdalena Barrow; Edward Barton; Matthew Bashton; Andrew Bassett; Rahul Batra; Chris Baxter; Nadua Bayzid; Charlotte Beaver; Angela Beckett; Shaun Beckwith; Luke Bedford; Robert Beer; Andrew Beggs; Katherine Bellis; Louise Berry; Beatrice Bertolusso; Angus Best; Emma Betteridge; David Bibby; Kelly Bicknell; Debbie Binns; Alec Birchley; Paul Bird; Chloe Bishop; Rachel Blacow; Victoria Blakey; Beth Blane; Frances Bolt; James Bonfield; Stephen Bonner; David Bonsall; Tim Boswell; Andrew Bosworth; yann Bourgeois; Olivia Boyd; Declan Bradley; Cassie Breen; Catherine Bresner; Judith Breuer; Stephen Bridgett; Iraad Bronner; Ellena Brooks; Alice Broos; Julianne Brown; Giselda Bucca; Sarah Buchan; David Buck; Matthew Bull; Phillipa Burns; Shirelle Burton-Fanning; Timothy Byaruhanga; Matthew Byott; Sharon Campbell; Alessandro Carabelli; James Cargill; Matthew Carlile; Silvia Carvalho; Anna Casey; Anibolina Castigador; Jana Catalan; Vicki Chalker; Nicola Chaloner; Meera Chand; Joseph Chappell; Themoula Charalampous; Wendy Chatterton; yasmin Chaudhry; Carol Churcher; Gemma Clark; Phillip Clarke; Benjamin Cogger; Kevin Cole; Jennifer Collins; Rachel Colquhoun; Thomas Connor; Kate Cook; Jason Coombes; Sally Corden; Claire Cormie; Nicholas Cortes; Marius Cotic; Seb Cotton; Simon Cottrell; Lindsay Coupland; Macgregor Cox; Alison Cox; Noel Craine; Liam Crawford; Aidan Cross; Matthew Crown; Dorian Crudgington; Nicola Cumley; Tanya Curran; Martin Curran; Ana da Silva Filipe; Gavin Dabrera; Alistair Darby; Rose Davidson; Alisha Davies; Robert Davies; Thomas Davis; Daniela de Angelis; Elen de Lacy; Leonardo de Oliveira Martins; Johnny Debebe; Rebecca Denton-Smith; Samir Dervisevic; Rebecca Dewar; Jayasree Dey; Joana Dias; Donald Dobie; Matthew Dorman; Fatima Downing; Megan Driscoll; Louis Du Plessis; Nichola Duckworth; Jillian Durham; Kirstine Eastick; Lisa Easton; Richard Eccles; Jonathan Edgeworth; Sue Edwards; Kate El Bouzidi; Sahar Eldirdiri; Nicholas Ellaby; Scott Elliott; Gary Eltringham; Leah Ensell; Michelle Erkiert; Marina Escalera Zamudio; Sarah Essex; Johnathan Evans; Cariad Evans; William Everson; Derek Fairley; Karlie Fallon; Arezou Fanaie; Ben Farr; Christopher Fearn; Theresa Feltwell; Lynne Ferguson; Laia Fina; Flavia Flaviani; Vicki Fleming; Sally Forrest; Ebenezer Foster-Nyarko; Benjamin Foulkes; Luke Foulser; Mireille Fragakis; Dan Frampton; Sarah Francois; Christophe Fraser; Timothy Freeman; Helen Fryer; Marc Fuchs; William Fuller; Kavitha Gajee; Katerina Galai; Abbie Gallagher; Eileen Gallagher; Michael Gallagher; Marta Gallis; Amy Gaskin; Bree Gatica-Wilcox; Lily Geidelberg; Matthew Gemmell; Iliana Georgana; Ryan George; Laura Gifford; Lauren Gilbert; Sophia Girgis; Sharon Glaysher; Emily Goldstein; Tanya Golubchik; Andrea Gomes; Sónia Gonçalves; Ian Goodfellow; Scott Goodwin; Salman Goudarzi; Marina Gourtovaia; Clive Graham; Lee Graham; Paul Grant; Luke Green; Angie Green; Jane Greenaway; Richard Gregory; Martyn Guest; Rory Gunson; Ravi Gupta; Bernardo Gutierrez; Sam Haldenby; William Hamilton; Samantha Hansford; Tanzina Haque; Kathryn Harris; Ian Harrison; Ewan Harrison; Jennifer Hart; John Hartley; William Harvey; Matthew Harvey; Mohammed Hassan-Ibrahim; Judith Heaney; Thomas Helmer; John Henderson; Andrew Hesketh; Jessica Hey; David Heyburn; Ellen Higginson; Verity Hill; Jack Hill; Rachel Hilson; Ember Hilvers; Matthew T.G. Holden; Amy Hollis; Christopher Holmes; Nadine Holmes; Alison Holmes; Richard Hopes; Hailey Hornsby; Myra Hosmillo; Catherine Houlihan; Hannah Howson-Wells; Jonathan Hubb; Hannah Huckson; Warwick Hughes; Joseph Hughes; Margaret Hughes; Stephanie Hutchings; Giles Idle; Chris Illingworth; Robert Impey; Dianne Irish-Tavares; Miren Iturriza-Gomara; Rhys Izuagbe; Chris Jackson; Ben Jackson; Leigh Jackson; Kathryn Jackson; David Jackson; Aminu Jahun; Victoria James; Keith James; Christopher Jeanes; Aaron Jeffries; Sarah Jeremiah; Andrew Jermy; Michaela John; Rob Johnson; Kate Johnson; Ian Johnston; Owen Jones; Sophie Jones; Hannah Jones; Christopher Jones; Neil Jones; Amelia Joseph; Sarah Judges; Gemma Kay; Sally Kay; Jon-Paul Keatley; Alexander Keeley; Anita Kenyon; Leanne Kermack; Manjinder Khakh; Stephen Kidd; Maimuna Kimuli; Stuart Kirk; Christine Kitchen; Katie Kitchman; Bridget Knight; Cherian Koshy; Moritz U.G. Kraemer; Sara Kumziene-Summerhayes; Dominic Kwiatkowski; Angie Lackenby; Kenneth Laing; Temi Lampejo; Cordelia Langford; Deborah Lavin; Andrew Lawton; Jack Lee; David Lee; Stefanie Lensing; Steven Leonard; Lisa Levett; Thanh Le-Viet; Jonathan Lewis; Kevin Lewis; Jennifier Liddle; Steven Liggett; Patrick Lillie; Michelle Lister; Rich Livett; Stephanie Lo; Nicholas Loman; Matthew Loose; Stavroula Louka; Katie Loveson; Sarah Lowdon; Hannah Lowe; Helen Lowe; Anita Lucaci; Catherine Ludden; Jessica Lynch; Ronan Lyons; Katrina Lythgoe; Nicholas Machin; George Macintyre-Cockett; Andrew Mack; Ben Macklin; Alasdair Maclean; Emily Macnaughton; Pinglawathee Madona; Mailis Maes; Laurentiu Maftei; Adhyana I.K. Mahanama; Tabitha Mahungu; Daniel Mair; Joshua Maksimovic; Cassandra Malone; Daniel Maloney; Nikos Manesis; Robin Manley; Anna Mantzouratou; Angela Marchbank; Arun Mariappan; Inigo Martincorena; Rocio Martinez Nunez; Alison Mather; Patrick Maxwell; Megan Mayhew; Tamyo Mbisa; Clare Mccann; Shane Mccarthy; Kathryn Mccluggage; Patrick Mcclure; J.T. Mccrone; Martin Mchugh; James Mckenna; Caoimhe Mckerr; Georgina Mcmanus; Claire Mcmurray; Alan Mcnally; Lizzie Meadows; Nathan Medd; Oliver Megram; Mirko Menegazzo; Ian Merrick; Stephen Michell; Michelle Michelsen; Mariyam Mirfenderesky; Jeremy Mirza; Julia Miskelly; Emma Moles-Garcia; Robin Moll; Zoltan Molnar; Irene Monahan; Matteo Mondani; Siddharth Mookerjee; Christopher Moore; Jonathan Moore; Nathan Moore; Catherine Moore; Helen Morcrette; Sian Morgan; Mari Morgan; Matilde Mori; Arthur Morriss; Samuel Moses; Craig Mower; Peter Muir; Afrida Mukaddas; Florence Munemo; Robert Munn; Abigail Murray; Leanne Murray; Darren Murray; Manasa Mutingwende; Richard Myers; Eleni Nastouli; Gaia Nebbia; Andrew Nelson; Charlotte Nelson; Sam Nicholls; Jenna Nichols; Roberto Nicodemi; Kyriaki Nomikou; Justin O’grady; Sarah O'Brien; Mina Odedra; Natasha Ohemeng-Kumi; Karen Oliver; Richard Orton; Husam Osman; Nicole Pacchiarini; Debra Padgett; Andrew Page; Emily Park; Naomi Park; Surendra Parmar; David Partridge; David Pascall; Amita Patel; Bindi Patel; Steve Paterson; Brendan A.I. Payne; Sharon Peacock; Clare Pearson; Emanuela Pelosi; Benita Percival; Jon Perkins; Malorie Perry; Malte Pinckert; Steven Platt; Olga Podplomyk; Manoj Pohare; Marcus Pond; Cassie Pope; Radoslaw Poplawski; Jessica Powell; Jennifer Poyner; Liam Prestwood; Anna Price; James Price; Jacqui Prieto; David Pritchard; Sophie Prosolek; Georgia Pugh; Monika Pusok; Oliver Pybus; Hannah Pymont; Michael Quail; Joshua Quick; Clara Radulescu; Jayna Raghwani; Manon Ragonnet-Cronin; Lucille Rainbow; Diana Rajan; Shavanthi Rajatileka; Newara Ramadan; Andrew Rambaut; John Ramble; Paul Randell; Liz Ratcliffe; Veena Raviprakash; Mohammad Raza; Nicholas Redshaw; Sara Rey; Nicola Reynolds; Alex Richter; David Robertson; Esther Robinson; Samuel Robson; Fiona Rogan; Stefan Rooke; Will Rowe; Sunando Roy; Steven Rudder; Chris Ruis; Steven Rushton; Felicity Ryan; Kordo Saeed; Buddhini Samaraweera; Christine Sambles; Roy Sanderson; Theo Sanderson; Fei Sang; Thea Sass; Emily Scher; Garren Scott; Carol Scott; Jasveen Sehmi; Sharif Shaaban; Divya Shah; Jessica Shaw; Ekaterina Shelest; James Shepherd; Liz Sheridan; Nicola Sheriff; Lesley Shirley; John Sillitoe; Siona Silviera; David Simpson; Aditi Singh; Dawn Singleton; Timofey Skvortsov; Tim Sloan; Graciela Sluga; Ken Smith; Kim Smith; Perminder Smith; Darren Smith; Louise Smith; Colin Smith; Nikki Smith; Katherine Smollett; Luke Snell; Thomas Somassa; Joel Southgate; Karla Spellman; Michael Spencer Chapman; Lewis Spurgin; Moira Spyer; Rachael Stanley; William Stanley; Thomas Stanton; Igor Starinskij; Joanne Stockton; Susanne Stonehouse; Nathaniel Storey; David Studholme; Malur Sudhanva; Emma Swindells; yusri Taha; Ngee Keong Tan; Julian Tang; Miao Tang; Ben E.W. Taylor; Joshua Taylor; Sarah Taylor; Ben Temperton; Kate Templeton; Claire Thomas; Laura Thomson; Emma Thomson; Alicia Thornton; Scott A.J. Thurston; John Todd; Rachael Tomb; Lily Tong; Gerry Tonkin-Hill; M. Estee Torok; Jaime Tovar-Corona; Amy Trebes; Alexander Trotter; Ioulia Tsatsani; Robyn Turnbull; Katherine Twohig; Helen Umpleby; Anthony Underwood; Edith Vamos; Tetyana Vasylyeva; Sreenu Vattipally; Gabrielle Vernet; Barry Vipond; Erik Volz; Sarah Walsh; Dennis Wang; Ben Warne; Joanna Warwick-Dugdale; Elizabeth Wastnedge; Joanne Watkins; Louisa Watson; Sheila Waugh; Hermione Webster; Danni Weldon; Elaine Westwick; Thomas Whalley; Helen Wheeler; Mark Whitehead; Max Whiteley; Andrew Whitwham; Claudia Wierzbicki; Nicholas Willford; Lesley-Anne Williams; Rebecca Williams; Cheryl Williams; Chris Williams; Charlotte Williams; Rachel Williams; Thomas Williams; Catryn Williams; Kathleen Williamson; Eleri Wilson-Davies; Eric Witele; Karen Withell; Adam Witney; Paige Wolverson; Nick Wong; Trudy Workman; Victoria Wright; Derek Wright; Tim Wyatt; Sarah Wyllie; Li Xu-Mccrae; Mehmet yavus; Geraldine yaze; Corin yeats; Gonzalo yebra; Wen yew; Gregory young; Jamie young; Alex Zarebski; Peijun Zhang; J. Kenneth Baillie; Malcolm Semple; Peter J.M. Openshaw; Gail Carson; Beatrice Alex; Petros Andrikopoulos; Benjamin Bach; Wendy Barclay; Debby Bogaert; Kanta Chechi; Graham Cooke; Annemarie Docherty; Gonçalo dos Santos Correia; Jake Dunning; Tom Fletcher; Christopher Green; William Greenhalf; Julian Griffin; Rishi Gupta; Ewen Harrison; Julian Hiscox; Antonia ying Wai Ho; Peter Horby; Samreen Ijaz; Saye Khoo; Paul Klenerman; Andrew Law; Matthew Lewis; Sonia Liggi; Wei Shen Lim; Lynn Maslen; Laura Merson; Alison Meynert; Mahdad Noursadeghi; Michael Olanipekun; Anthonia Osagie; Massimo Palmarini; Carlo Palmieri; William Paxton; Georgios Pollakis; Nicholas Price; Clark Russell; Vanessa Sancho-Shimizu; Caroline Sands; Janet Scott; Louise Sigfrid; Tom Solomon; Shiranee Sriskandan; David Stuart; Charlotte Summers; Olivia Swann; Zoltan Takats; Panteleimon Takis; Richard Tedder; A.A. Roger Thompson; Ryan Thwaites; Maria Zambon; Hayley Hardwick; Chloe Donohue; Fiona Griffiths; Wilna Oosthuyzen; Cara Donegan; Rebecca Spencer; Jo Dalton; Michelle Girvan; Egle Saviciute; Stephanie Roberts; Janet Harrison; Laura Marsh; Marie Connor; Sophie Halpin; Clare Jackson; Carrol Gamble; Daniel Plotkin; James Lee; Gary Leeming; Murray Wham; Sara Clohisey; Ross Hendry; James Scott-Brown; Victoria Shaw; Sarah Mcdonald; Seán Keating; Katie Ahmed; Jane Armstrong; Milton Ashworth; Innocent Asiimwe; Siddharth Bakshi; Samantha Barlow; Laura Booth; Benjamin Brennan; Katie Bullock; Benjamin W.A. Catterall; Jordan Clark; Emily Clarke; Sarah Cole; Louise Cooper; Helen Cox; Christopher Davis; Oslem Dincarslan; Chris Dunn; Philip Dyer; Angela Elliott; Anthony Evans; Lorna Finch; Lewis W.S. Fisher; Terry Foster; Isabel Garcia-Dorival; Philip Gunning; Catherine Hartley; Rebecca Jensen; Trevor Jones; Shadia Khandaker; Katharine King; Robyn Kiy; Chrysa Koukorava; Annette Lake; Suzannah Lant; Diane Latawiec; Lara Lavelle-Langham; Daniella Lefteri; Lauren Lett; Lucia Livoti; Maria Mancini; Laurence Mcevoy; John Mclauchlan; Soeren Metelmann; Nahida Miah; Joanna Middleton; Joyce Mitchell; Ellen Murphy; Rebekah Penrice-Randal; Jack Pilgrim; Tessa Prince; Will Reynolds; P. Matthew Ridley; Debby Sales; Rebecca Shears; Benjamin Small; Krishanthi Subramaniam; Agnieska Szemiel; Aislynn Taggart; Jolanta Tanianis-Hughes; Jordan Thomas; Erwan Trochu; Libby van Tonder; Eve Wilcock; J. Eunice Zhang; Lisa Flaherty; Nicole Maziere; Emily Cass; Alejandra Doce Carracedo; Nicola Carlucci; Anthony Holmes; Hannah Massey; Lee Murphy; Nicola Wrobel; Sarah Mccafferty; Kirstie Morrice; Alan Maclean; Kayode Adeniji; Daniel Agranoff; Ken Agwuh; Dhiraj Ail; Erin Aldera; Ana Alegria; Sam Allen; Brian Angus; Abdul Ashish; Dougal Atkinson; Shahedal Bari; Gavin Barlow; Stella Barnass; Nicholas Barrett; Christopher Bassford; Sneha Basude; David Baxter; Michael Beadsworth; Jolanta Bernatoniene; John Berridge; Colin Berry; Nicola Best; Pieter Bothma; David Chadwick; Robin Brittain-Long; Naomi Bulteel; Tom Burden; Andrew Burtenshaw; Vikki Caruth; Duncan Chambler; Nigel Chee; Jenny Child; Srikanth Chukkambotla; Tom Clark; Paul Collini; Catherine Cosgrove; Jason Cupitt; Maria-Teresa Cutino-Moguel; Paul Dark; Chris Dawson; Phil Donnison; Sam Douthwaite; Andrew Drummond; Ingrid Durand; Ahilanadan Dushianthan; Tristan Dyer; Chi Eziefula; Chrisopher Fegan; Adam Finn; Duncan Fullerton; Sanjeev Garg; Atul Garg; Effrossyni Gkrania-Klotsas; Jo Godden; Arthur Goldsmith; Elaine Hardy; Stuart Hartshorn; Daniel Harvey; Peter Havalda; Daniel Hawcutt; Maria Hobrok; Luke Hodgson; Anil Hormis; Michael Jacobs; Susan Jain; Paul Jennings; Agilan Kaliappan; Vidya Kasipandian; Stephen Kegg; Michael Kelsey; Jason Kendall; Caroline Kerrison; Ian Kerslake; Oliver Koch; Gouri Koduri; George Koshy; Shondipon Laha; Steven Laird; Susan Larkin; Tamas Leiner; James Limb; Vanessa Linnett; Jeff Little; Mark Lyttle; Michael Macmahon; Ravish Mankregod; Huw Masson; Elijah Matovu; Katherine Mccullough; Ruth Mcewen; Manjula Meda; Gary Mills; Jane Minton; Kavya Mohandas; Quen Mok; James Moon; Elinoor Moore; Patrick Morgan; Craig Morris; Katherine Mortimore; Mbiye Mpenge; Rohinton Mulla; Michael Murphy; Megan Nagel; Thapas Nagarajan; Mark Nelson; Lillian Norris; Matthew O'Shea; Igor Otahal; Marlies Ostermann; Mark Pais; Selva Panchatsharam; Danai Papakonstantinou; Hassan Paraiso; Brij Patel; Natalie Pattison; Justin Pepperell; Mark Peters; Mandeep Phull; Stefania Pintus; Jagtur Singh Pooni; Tim Planche; Frank Post; David Price; Rachel Prout; Nikolas Rae; Henrik Reschreiter; Tim Reynolds; Neil Richardson; Mark Roberts; Devender Roberts; Alistair Rose; Guy Rousseau; Bobby Ruge; Brendan Ryan; Taranprit Saluja; Matthias Schmid; Aarti Shah; Prad Shanmuga; Anil Sharma; Anna Shawcross; Jeremy Sizer; Manu Shankar-Hari; Richard Smith; Catherine Snelson; Nick Spittle; Nikki Staines; Tom Stambach; Richard Stewart; Pradeep Subudhi; Tamas Szakmany; Kate Tatham; Jo Thomas; Chris Thompson; Robert Thompson; Ascanio Tridente; Darell Tupper-Carey; Mary Twagira; Nick Vallotton; Rama Vancheeswaran; Lisa Vincent-Smith; Shico Visuvanathan; Alan Vuylsteke; Sam Waddy; Rachel Wake; Andrew Walden; Ingeborg Welters; Tony Whitehouse; Paul Whittaker; Ashley Whittington; Padmasayee Papineni; Meme Wijesinghe; Martin Williams; Lawrence Wilson; Stephen Winchester; Martin Wiselka; Adam Wolverson; Daniel Wootton; Andrew Workman; Bryan yates; Peter young

doi:10.1016/j.isci.2021.103353

Journal articles

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

Marc-Emmanuel Dumas ^{1, 2, 3} Thushan de Silva Guihai Liu Benjamin Lindsey Danning Dong Shona Moore Nienyun Sharon Hsu Dhruv Shah Dannielle Wellington Alexander Mentzer Adrienn Angyal Rebecca Brown Matthew Parker Zixi ying Xuan yao Lance Turtle Susanna Dunachie Mala Maini Graham Ogg Julian Knight yanchun Peng Sarah Rowland-Jones Tao Dong David Aanensen Khalil Abudahab Helen Adams Alexander Adams Safiah Afifi Dinesh Aggarwal Shazaad S.y. Ahmad Louise Aigrain Adela Alcolea-Medina Nabil-Fareed Alikhan Elias Allara Roberto Amato Tara Annett Stephen Aplin Cristina Ariani Hibo Asad Amy Ash Paula Ashfield Fiona Ashford Laura Atkinson Stephen Attwood Cressida Auckland Alp Aydin David Baker Paul Baker Carlos Balcazar Jonathan Ball Jeffrey Barrett Magdalena Barrow Edward Barton Matthew Bashton Andrew Bassett Rahul Batra Chris Baxter Nadua Bayzid Charlotte Beaver Angela Beckett Shaun Beckwith Luke Bedford Robert Beer Andrew Beggs Katherine Bellis Louise Berry Beatrice Bertolusso Angus Best Emma Betteridge David Bibby Kelly Bicknell Debbie Binns Alec Birchley Paul Bird Chloe Bishop Rachel Blacow Victoria Blakey Beth Blane Frances Bolt James Bonfield Stephen Bonner David Bonsall Tim Boswell Andrew Bosworth yann Bourgeois Olivia Boyd Declan Bradley Cassie Breen Catherine Bresner Judith Breuer Stephen Bridgett Iraad Bronner Ellena Brooks Alice Broos Julianne Brown Giselda Bucca Sarah Buchan David Buck Matthew Bull Phillipa Burns Shirelle Burton-Fanning Timothy Byaruhanga Matthew Byott Sharon Campbell Alessandro Carabelli James Cargill Matthew Carlile Silvia Carvalho Anna Casey Anibolina Castigador Jana Catalan Vicki Chalker Nicola Chaloner Meera Chand Joseph Chappell Themoula Charalampous Wendy Chatterton yasmin Chaudhry Carol Churcher Gemma Clark Phillip Clarke Benjamin Cogger Kevin Cole Jennifer Collins Rachel Colquhoun Thomas Connor Kate Cook Jason Coombes Sally Corden Claire Cormie Nicholas Cortes Marius Cotic Seb Cotton Simon Cottrell Lindsay Coupland Macgregor Cox Alison Cox Noel Craine Liam Crawford Aidan Cross Matthew Crown Dorian Crudgington Nicola Cumley Tanya Curran Martin Curran Ana da Silva Filipe Gavin Dabrera Alistair Darby Rose Davidson Alisha Davies Robert Davies Thomas Davis Daniela de Angelis Elen de Lacy Leonardo de Oliveira Martins Johnny Debebe Rebecca Denton-Smith Samir Dervisevic Rebecca Dewar Jayasree Dey Joana Dias Donald Dobie Matthew Dorman Fatima Downing Megan Driscoll Louis Du Plessis Nichola Duckworth Jillian Durham Kirstine Eastick Lisa Easton Richard Eccles Jonathan Edgeworth Sue Edwards Kate El Bouzidi Sahar Eldirdiri Nicholas Ellaby Scott Elliott Gary Eltringham Leah Ensell Michelle Erkiert Marina Escalera Zamudio Sarah Essex Johnathan Evans Cariad Evans William Everson Derek Fairley Karlie Fallon Arezou Fanaie Ben Farr Christopher Fearn Theresa Feltwell Lynne Ferguson Laia Fina Flavia Flaviani Vicki Fleming Sally Forrest Ebenezer Foster-Nyarko Benjamin Foulkes Luke Foulser Mireille Fragakis Dan Frampton Sarah Francois Christophe Fraser Timothy Freeman Helen Fryer Marc Fuchs William Fuller Kavitha Gajee Katerina Galai Abbie Gallagher Eileen Gallagher Michael Gallagher Marta Gallis Amy Gaskin Bree Gatica-Wilcox Lily Geidelberg Matthew Gemmell Iliana Georgana Ryan George Laura Gifford Lauren Gilbert Sophia Girgis Sharon Glaysher Emily Goldstein Tanya Golubchik Andrea Gomes Sónia Gonçalves Ian Goodfellow Scott Goodwin Salman Goudarzi Marina Gourtovaia Clive Graham Lee Graham Paul Grant Luke Green Angie Green Jane Greenaway Richard Gregory Martyn Guest Rory Gunson Ravi Gupta Bernardo Gutierrez Sam Haldenby William Hamilton Samantha Hansford Tanzina Haque Kathryn Harris Ian Harrison Ewan Harrison Jennifer Hart John Hartley William Harvey Matthew Harvey Mohammed Hassan-Ibrahim Judith Heaney Thomas Helmer John Henderson Andrew Hesketh Jessica Hey David Heyburn Ellen Higginson Verity Hill Jack Hill Rachel Hilson Ember Hilvers Matthew T.G. Holden Amy Hollis Christopher Holmes Nadine Holmes Alison Holmes Richard Hopes Hailey Hornsby Myra Hosmillo Catherine Houlihan Hannah Howson-Wells Jonathan Hubb Hannah Huckson Warwick Hughes Joseph Hughes Margaret Hughes Stephanie Hutchings Giles Idle Chris Illingworth Robert Impey Dianne Irish-Tavares Miren Iturriza-Gomara Rhys Izuagbe Chris Jackson Ben Jackson Leigh Jackson Kathryn Jackson David Jackson Aminu Jahun Victoria James Keith James Christopher Jeanes Aaron Jeffries Sarah Jeremiah Andrew Jermy Michaela John Rob Johnson Kate Johnson Ian Johnston Owen Jones Sophie Jones Hannah Jones Christopher Jones Neil Jones Amelia Joseph Sarah Judges Gemma Kay Sally Kay Jon-Paul Keatley Alexander Keeley Anita Kenyon Leanne Kermack Manjinder Khakh Stephen Kidd Maimuna Kimuli Stuart Kirk Christine Kitchen Katie Kitchman Bridget Knight Cherian Koshy Moritz U.G. Kraemer Sara Kumziene-Summerhayes Dominic Kwiatkowski Angie Lackenby Kenneth Laing Temi Lampejo Cordelia Langford Deborah Lavin Andrew Lawton Jack Lee David Lee Stefanie Lensing Steven Leonard Lisa Levett Thanh Le-Viet Jonathan Lewis Kevin Lewis Jennifier Liddle Steven Liggett Patrick Lillie Michelle Lister Rich Livett Stephanie Lo Nicholas Loman Matthew Loose Stavroula Louka Katie Loveson Sarah Lowdon Hannah Lowe Helen Lowe Anita Lucaci Catherine Ludden Jessica Lynch Ronan Lyons Katrina Lythgoe Nicholas Machin George Macintyre-Cockett Andrew Mack Ben Macklin Alasdair Maclean Emily Macnaughton Pinglawathee Madona Mailis Maes Laurentiu Maftei Adhyana I.K. Mahanama Tabitha Mahungu Daniel Mair Joshua Maksimovic Cassandra Malone Daniel Maloney Nikos Manesis Robin Manley Anna Mantzouratou Angela Marchbank Arun Mariappan Inigo Martincorena Rocio Martinez Nunez Alison Mather Patrick Maxwell Megan Mayhew Tamyo Mbisa Clare Mccann Shane Mccarthy Kathryn Mccluggage Patrick Mcclure J.T. Mccrone Martin Mchugh James Mckenna Caoimhe Mckerr Georgina Mcmanus Claire Mcmurray Alan Mcnally Lizzie Meadows Nathan Medd Oliver Megram Mirko Menegazzo Ian Merrick Stephen Michell Michelle Michelsen Mariyam Mirfenderesky Jeremy Mirza Julia Miskelly Emma Moles-Garcia Robin Moll Zoltan Molnar Irene Monahan Matteo Mondani Siddharth Mookerjee Christopher Moore Jonathan Moore Nathan Moore Catherine Moore Helen Morcrette Sian Morgan Mari Morgan Matilde Mori Arthur Morriss Samuel Moses Craig Mower Peter Muir Afrida Mukaddas Florence Munemo Robert Munn Abigail Murray Leanne Murray Darren Murray Manasa Mutingwende Richard Myers Eleni Nastouli Gaia Nebbia Andrew Nelson Charlotte Nelson Sam Nicholls Jenna Nichols Roberto Nicodemi Kyriaki Nomikou Justin O’grady Sarah O'Brien Mina Odedra Natasha Ohemeng-Kumi Karen Oliver Richard Orton Husam Osman Nicole Pacchiarini Debra Padgett Andrew Page Emily Park Naomi Park Surendra Parmar David Partridge David Pascall Amita Patel Bindi Patel Steve Paterson Brendan A.I. Payne Sharon Peacock Clare Pearson Emanuela Pelosi Benita Percival Jon Perkins Malorie Perry Malte Pinckert Steven Platt Olga Podplomyk Manoj Pohare Marcus Pond Cassie Pope Radoslaw Poplawski Jessica Powell Jennifer Poyner Liam Prestwood Anna Price James Price Jacqui Prieto David Pritchard Sophie Prosolek Georgia Pugh Monika Pusok Oliver Pybus Hannah Pymont Michael Quail Joshua Quick Clara Radulescu Jayna Raghwani Manon Ragonnet-Cronin Lucille Rainbow Diana Rajan Shavanthi Rajatileka Newara Ramadan Andrew Rambaut John Ramble Paul Randell Liz Ratcliffe Veena Raviprakash Mohammad Raza Nicholas Redshaw Sara Rey Nicola Reynolds Alex Richter David Robertson Esther Robinson Samuel Robson Fiona Rogan Stefan Rooke Will Rowe Sunando Roy Steven Rudder Chris Ruis Steven Rushton Felicity Ryan Kordo Saeed Buddhini Samaraweera Christine Sambles Roy Sanderson Theo Sanderson Fei Sang Thea Sass Emily Scher Garren Scott Carol Scott Jasveen Sehmi Sharif Shaaban Divya Shah Jessica Shaw Ekaterina Shelest James Shepherd Liz Sheridan Nicola Sheriff Lesley Shirley John Sillitoe Siona Silviera David Simpson Aditi Singh Dawn Singleton Timofey Skvortsov Tim Sloan Graciela Sluga Ken Smith Kim Smith Perminder Smith Darren Smith Louise Smith Colin Smith Nikki Smith Katherine Smollett Luke Snell Thomas Somassa Joel Southgate Karla Spellman Michael Spencer Chapman Lewis Spurgin Moira Spyer Rachael Stanley William Stanley Thomas Stanton Igor Starinskij Joanne Stockton Susanne Stonehouse Nathaniel Storey David Studholme Malur Sudhanva Emma Swindells yusri Taha Ngee Keong Tan Julian Tang Miao Tang Ben E.W. Taylor Joshua Taylor Sarah Taylor Ben Temperton Kate Templeton Claire Thomas Laura Thomson Emma Thomson Alicia Thornton Scott A.J. Thurston John Todd Rachael Tomb Lily Tong Gerry Tonkin-Hill M. Estee Torok Jaime Tovar-Corona Amy Trebes Alexander Trotter Ioulia Tsatsani Robyn Turnbull Katherine Twohig Helen Umpleby Anthony Underwood Edith Vamos Tetyana Vasylyeva Sreenu Vattipally Gabrielle Vernet Barry Vipond Erik Volz Sarah Walsh Dennis Wang Ben Warne Joanna Warwick-Dugdale Elizabeth Wastnedge Joanne Watkins Louisa Watson Sheila Waugh Hermione Webster Danni Weldon Elaine Westwick Thomas Whalley Helen Wheeler Mark Whitehead Max Whiteley Andrew Whitwham Claudia Wierzbicki Nicholas Willford Lesley-Anne Williams Rebecca Williams Cheryl Williams Chris Williams Charlotte Williams Rachel Williams Thomas Williams Catryn Williams Kathleen Williamson Eleri Wilson-Davies Eric Witele Karen Withell Adam Witney Paige Wolverson Nick Wong Trudy Workman Victoria Wright Derek Wright Tim Wyatt Sarah Wyllie Li Xu-Mccrae Mehmet yavus Geraldine yaze Corin yeats Gonzalo yebra Wen yew Gregory young Jamie young Alex Zarebski Peijun Zhang J. Kenneth Baillie Malcolm Semple Peter J.M. Openshaw Gail Carson Beatrice Alex Petros Andrikopoulos Benjamin Bach Wendy Barclay Debby Bogaert Kanta Chechi Graham Cooke Annemarie Docherty Gonçalo dos Santos Correia Jake Dunning Tom Fletcher Christopher Green William Greenhalf Julian Griffin Rishi Gupta Ewen Harrison Julian Hiscox Antonia ying Wai Ho Peter Horby Samreen Ijaz Saye Khoo Paul Klenerman Andrew Law Matthew Lewis Sonia Liggi Wei Shen Lim Lynn Maslen Laura Merson Alison Meynert Mahdad Noursadeghi Michael Olanipekun Anthonia Osagie Massimo Palmarini Carlo Palmieri William Paxton Georgios Pollakis Nicholas Price Clark Russell Vanessa Sancho-Shimizu Caroline Sands Janet Scott Louise Sigfrid Tom Solomon Shiranee Sriskandan David Stuart Charlotte Summers Olivia Swann Zoltan Takats Panteleimon Takis Richard Tedder A.A. Roger Thompson Ryan Thwaites Maria Zambon Hayley Hardwick Chloe Donohue Fiona Griffiths Wilna Oosthuyzen Cara Donegan Rebecca Spencer Jo Dalton Michelle Girvan Egle Saviciute Stephanie Roberts Janet Harrison Laura Marsh Marie Connor Sophie Halpin Clare Jackson Carrol Gamble Daniel Plotkin James Lee Gary Leeming Murray Wham Sara Clohisey Ross Hendry James Scott-Brown Victoria Shaw Sarah Mcdonald Seán Keating Katie Ahmed Jane Armstrong Milton Ashworth Innocent Asiimwe Siddharth Bakshi Samantha Barlow Laura Booth Benjamin Brennan Katie Bullock Benjamin W.A. Catterall Jordan Clark Emily Clarke Sarah Cole Louise Cooper Helen Cox Christopher Davis Oslem Dincarslan Chris Dunn Philip Dyer Angela Elliott Anthony Evans Lorna Finch Lewis W.S. Fisher Terry Foster Isabel Garcia-Dorival Philip Gunning Catherine Hartley Rebecca Jensen Trevor Jones Shadia Khandaker Katharine King Robyn Kiy Chrysa Koukorava Annette Lake Suzannah Lant Diane Latawiec Lara Lavelle-Langham Daniella Lefteri Lauren Lett Lucia Livoti Maria Mancini Laurence Mcevoy John Mclauchlan Soeren Metelmann Nahida Miah Joanna Middleton Joyce Mitchell Ellen Murphy Rebekah Penrice-Randal Jack Pilgrim Tessa Prince Will Reynolds P. Matthew Ridley Debby Sales Rebecca Shears Benjamin Small Krishanthi Subramaniam Agnieska Szemiel Aislynn Taggart Jolanta Tanianis-Hughes Jordan Thomas Erwan Trochu Libby van Tonder Eve Wilcock J. 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1 Division of Computational and Systems Medicine, Imperial College London, London, SW7 2AZ, UK

2 Imperial College London - National Heart and Lung Institute

3 CNRS - Centre National de la Recherche Scientifique

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

Document type :

Journal articles

Domain :

Life Sciences [q-bio] / Biochemistry, Molecular Biology / Biochemistry [q-bio.BM]

Life Sciences [q-bio] / Immunology

Complete list of metadata

https://hal-cnrs.archives-ouvertes.fr/hal-03451248
Contributor : Marc-Emmanuel Dumas Connect in order to contact the contributor
Submitted on : Friday, November 26, 2021 - 1:08:49 PM
Last modification on : Friday, April 1, 2022 - 3:56:52 AM

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

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

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