iScience (Nov 2021)

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

  • Thushan I. de Silva,
  • Guihai Liu,
  • Benjamin B. Lindsey,
  • Danning Dong,
  • Shona C. Moore,
  • Nienyun Sharon Hsu,
  • Dhruv Shah,
  • Dannielle Wellington,
  • Alexander J. Mentzer,
  • Adrienn Angyal,
  • Rebecca Brown,
  • Matthew D. Parker,
  • Zixi Ying,
  • Xuan Yao,
  • Lance Turtle,
  • Susanna Dunachie,
  • Mala K. Maini,
  • Graham Ogg,
  • Julian C. Knight,
  • Yanchun Peng,
  • Sarah L. Rowland-Jones,
  • Tao Dong,
  • David M. 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 V. Ariani,
  • Hibo Asad,
  • Amy Ash,
  • Paula Ashfield,
  • Fiona Ashford,
  • Laura Atkinson,
  • Stephen W. Attwood,
  • Cressida Auckland,
  • Alp Aydin,
  • David J. Baker,
  • Paul Baker,
  • Carlos E. Balcazar,
  • Jonathan Ball,
  • Jeffrey C. Barrett,
  • Magdalena Barrow,
  • Edward Barton,
  • Matthew Bashton,
  • Andrew R. Bassett,
  • Rahul Batra,
  • Chris Baxter,
  • Nadua Bayzid,
  • Charlotte Beaver,
  • Angela H. Beckett,
  • Shaun M. Beckwith,
  • Luke Bedford,
  • Robert Beer,
  • Andrew Beggs,
  • Katherine L. Bellis,
  • Louise Berry,
  • Beatrice Bertolusso,
  • Angus Best,
  • Emma Betteridge,
  • David Bibby,
  • Kelly Bicknell,
  • Debbie Binns,
  • Alec Birchley,
  • Paul W. 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 T. Bradley,
  • Cassie Breen,
  • Catherine Bresner,
  • Judith Breuer,
  • Stephen Bridgett,
  • Iraad F. Bronner,
  • Ellena Brooks,
  • Alice Broos,
  • Julianne R. Brown,
  • Giselda Bucca,
  • Sarah L. Buchan,
  • David Buck,
  • Matthew Bull,
  • Phillipa J. Burns,
  • Shirelle Burton-Fanning,
  • Timothy Byaruhanga,
  • Matthew Byott,
  • Sharon Campbell,
  • Alessandro M. Carabelli,
  • James S. Cargill,
  • Matthew Carlile,
  • Silvia F. Carvalho,
  • Anna Casey,
  • Anibolina Castigador,
  • Jana Catalan,
  • Vicki Chalker,
  • Nicola J. Chaloner,
  • Meera Chand,
  • Joseph G. Chappell,
  • Themoula Charalampous,
  • Wendy Chatterton,
  • Yasmin Chaudhry,
  • Carol M. Churcher,
  • Gemma Clark,
  • Phillip Clarke,
  • Benjamin J. Cogger,
  • Kevin Cole,
  • Jennifer Collins,
  • Rachel Colquhoun,
  • Thomas R. Connor,
  • Kate F. 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 R. Crown,
  • Dorian Crudgington,
  • Nicola Cumley,
  • Tanya Curran,
  • Martin D. Curran,
  • Ana da Silva Filipe,
  • Gavin Dabrera,
  • Alistair C. Darby,
  • Rose K. Davidson,
  • Alisha Davies,
  • Robert M. 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 J. Dorman,
  • Fatima Downing,
  • Megan Driscoll,
  • Louis du Plessis,
  • Nichola Duckworth,
  • Jillian Durham,
  • Kirstine Eastick,
  • Lisa J. Easton,
  • Richard Eccles,
  • Jonathan Edgeworth,
  • Sue Edwards,
  • Kate El Bouzidi,
  • Sahar Eldirdiri,
  • Nicholas Ellaby,
  • Scott Elliott,
  • Gary Eltringham,
  • Leah Ensell,
  • Michelle J. Erkiert,
  • Marina Escalera Zamudio,
  • Sarah Essex,
  • Johnathan M. Evans,
  • Cariad Evans,
  • William Everson,
  • Derek J. Fairley,
  • Karlie Fallon,
  • Arezou Fanaie,
  • Ben W. Farr,
  • Christopher Fearn,
  • Theresa Feltwell,
  • Lynne Ferguson,
  • Laia Fina,
  • Flavia Flaviani,
  • Vicki M. Fleming,
  • Sally Forrest,
  • Ebenezer Foster-Nyarko,
  • Benjamin H. Foulkes,
  • Luke Foulser,
  • Mireille Fragakis,
  • Dan Frampton,
  • Sarah Francois,
  • Christophe Fraser,
  • Timothy M. Freeman,
  • Helen Fryer,
  • Marc Fuchs,
  • William Fuller,
  • Kavitha Gajee,
  • Katerina Galai,
  • Abbie Gallagher,
  • Eileen Gallagher,
  • Michael D. Gallagher,
  • Marta Gallis,
  • Amy Gaskin,
  • Bree Gatica-Wilcox,
  • Lily Geidelberg,
  • Matthew Gemmell,
  • Iliana Georgana,
  • Ryan P. George,
  • Laura Gifford,
  • Lauren Gilbert,
  • Sophia T. Girgis,
  • Sharon Glaysher,
  • Emily J. Goldstein,
  • Tanya Golubchik,
  • Andrea N. Gomes,
  • Sónia Gonçalves,
  • Ian G. Goodfellow,
  • Scott Goodwin,
  • Salman Goudarzi,
  • Marina Gourtovaia,
  • Clive Graham,
  • Lee Graham,
  • Paul R. Grant,
  • Luke R. Green,
  • Angie Green,
  • Jane Greenaway,
  • Richard Gregory,
  • Martyn Guest,
  • Rory N. Gunson,
  • Ravi K. Gupta,
  • Bernardo Gutierrez,
  • Sam T. Haldenby,
  • William L. Hamilton,
  • Samantha E. Hansford,
  • Tanzina Haque,
  • Kathryn A. Harris,
  • Ian Harrison,
  • Ewan M. Harrison,
  • Jennifer Hart,
  • John A. Hartley,
  • William T. Harvey,
  • Matthew Harvey,
  • Mohammed O. Hassan-Ibrahim,
  • Judith Heaney,
  • Thomas Helmer,
  • John H. Henderson,
  • Andrew R. Hesketh,
  • Jessica Hey,
  • David Heyburn,
  • Ellen E. Higginson,
  • Verity Hill,
  • Jack D. Hill,
  • Rachel A. Hilson,
  • Ember Hilvers,
  • Matthew T.G. Holden,
  • Amy Hollis,
  • Christopher W. Holmes,
  • Nadine Holmes,
  • Alison H. Holmes,
  • Richard Hopes,
  • Hailey R. Hornsby,
  • Myra Hosmillo,
  • Catherine Houlihan,
  • Hannah C. Howson-Wells,
  • Jonathan Hubb,
  • Hannah Huckson,
  • Warwick Hughes,
  • Joseph Hughes,
  • Margaret Hughes,
  • Stephanie Hutchings,
  • Giles Idle,
  • Chris J. Illingworth,
  • Robert Impey,
  • Dianne Irish-Tavares,
  • Miren Iturriza-Gomara,
  • Rhys Izuagbe,
  • Chris Jackson,
  • Ben Jackson,
  • Leigh M. Jackson,
  • Kathryn A. Jackson,
  • David K. Jackson,
  • Aminu S. Jahun,
  • Victoria James,
  • Keith James,
  • Christopher Jeanes,
  • Aaron R. Jeffries,
  • Sarah Jeremiah,
  • Andrew Jermy,
  • Michaela John,
  • Rob Johnson,
  • Kate Johnson,
  • Ian Johnston,
  • Owen Jones,
  • Sophie Jones,
  • Hannah Jones,
  • Christopher R. Jones,
  • Neil Jones,
  • Amelia Joseph,
  • Sarah Judges,
  • Gemma L. Kay,
  • Sally Kay,
  • Jon-Paul Keatley,
  • Alexander J. Keeley,
  • Anita Kenyon,
  • Leanne M. Kermack,
  • Manjinder Khakh,
  • Stephen P. Kidd,
  • Maimuna Kimuli,
  • Stuart Kirk,
  • Christine Kitchen,
  • Katie Kitchman,
  • Bridget A. Knight,
  • Cherian Koshy,
  • Moritz U.G. Kraemer,
  • Sara Kumziene-Summerhayes,
  • Dominic Kwiatkowski,
  • Angie Lackenby,
  • Kenneth G. Laing,
  • Temi Lampejo,
  • Cordelia F. Langford,
  • Deborah Lavin,
  • Andrew I. Lawton,
  • Jack Lee,
  • David Lee,
  • Stefanie V. Lensing,
  • Steven Leonard,
  • Lisa J. Levett,
  • Thanh Le-Viet,
  • Jonathan Lewis,
  • Kevin Lewis,
  • Jennifier Liddle,
  • Steven Liggett,
  • Patrick J. Lillie,
  • Michelle M. Lister,
  • Rich Livett,
  • Stephanie Lo,
  • Nicholas J. Loman,
  • Matthew W. Loose,
  • Stavroula F. Louka,
  • Katie F. Loveson,
  • Sarah Lowdon,
  • Hannah Lowe,
  • Helen L. Lowe,
  • Anita O. Lucaci,
  • Catherine Ludden,
  • Jessica Lynch,
  • Ronan A. Lyons,
  • Katrina Lythgoe,
  • Nicholas W. Machin,
  • George MacIntyre-Cockett,
  • Andrew Mack,
  • Ben Macklin,
  • Alasdair Maclean,
  • Emily Macnaughton,
  • Pinglawathee Madona,
  • Mailis Maes,
  • Laurentiu Maftei,
  • Adhyana I.K. Mahanama,
  • Tabitha W. Mahungu,
  • Daniel Mair,
  • Joshua Maksimovic,
  • Cassandra S. Malone,
  • Daniel Maloney,
  • Nikos Manesis,
  • Robin Manley,
  • Anna Mantzouratou,
  • Angela Marchbank,
  • Arun Mariappan,
  • Inigo Martincorena,
  • Rocio T. Martinez Nunez,
  • Alison E. Mather,
  • Patrick Maxwell,
  • Megan Mayhew,
  • Tamyo Mbisa,
  • Clare M. McCann,
  • Shane A. McCarthy,
  • Kathryn McCluggage,
  • Patrick C. McClure,
  • J.T. McCrone,
  • Martin P. McHugh,
  • James P. McKenna,
  • Caoimhe McKerr,
  • Georgina M. McManus,
  • Claire L. McMurray,
  • Claire McMurray,
  • Alan McNally,
  • Lizzie Meadows,
  • Nathan Medd,
  • Oliver Megram,
  • Mirko Menegazzo,
  • Ian Merrick,
  • Stephen L. Michell,
  • Michelle L. Michelsen,
  • Mariyam Mirfenderesky,
  • Jeremy Mirza,
  • Julia Miskelly,
  • Emma Moles-Garcia,
  • Robin J. Moll,
  • Zoltan Molnar,
  • Irene M. 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 J. Murray,
  • Darren R. 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 J. Orton,
  • Husam Osman,
  • xeine O'Toole,
  • Nicole Pacchiarini,
  • Debra Padgett,
  • Andrew J. Page,
  • Emily J. Park,
  • Naomi R. Park,
  • Surendra Parmar,
  • David G. Partridge,
  • David Pascall,
  • Amita Patel,
  • Bindi Patel,
  • Steve Paterson,
  • Brendan A.I. Payne,
  • Sharon J. Peacock,
  • Clare Pearson,
  • Emanuela Pelosi,
  • Benita Percival,
  • Jon Perkins,
  • Malorie Perry,
  • Malte L. Pinckert,
  • Steven Platt,
  • Olga Podplomyk,
  • Manoj Pohare,
  • Marcus Pond,
  • Cassie F. Pope,
  • Radoslaw Poplawski,
  • Jessica Powell,
  • Jennifer Poyner,
  • Liam Prestwood,
  • Anna Price,
  • James R. Price,
  • Jacqui A. Prieto,
  • David T. Pritchard,
  • Sophie J. Prosolek,
  • Georgia Pugh,
  • Monika Pusok,
  • Oliver G. Pybus,
  • Hannah M. Pymont,
  • Michael A. Quail,
  • Joshua Quick,
  • Clara Radulescu,
  • Jayna Raghwani,
  • Manon Ragonnet-Cronin,
  • Lucille Rainbow,
  • Diana Rajan,
  • Shavanthi Rajatileka,
  • Newara A. Ramadan,
  • Andrew Rambaut,
  • John Ramble,
  • Paul A. Randell,
  • Paul Randell,
  • Liz Ratcliffe,
  • Veena Raviprakash,
  • Mohammad Raza,
  • Nicholas M. Redshaw,
  • Sara Rey,
  • Nicola Reynolds,
  • Alex Richter,
  • David L. Robertson,
  • Esther Robinson,
  • Samuel C. Robson,
  • Fiona Rogan,
  • Stefan Rooke,
  • Will Rowe,
  • Sunando Roy,
  • Steven Rudder,
  • Chris Ruis,
  • Steven Rushton,
  • Felicity Ryan,
  • Kordo Saeed,
  • Buddhini Samaraweera,
  • Christine M. 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 G. Shepherd,
  • Liz A. Sheridan,
  • Nicola Sheriff,
  • Lesley Shirley,
  • John Sillitoe,
  • Siona Silviera,
  • David A. Simpson,
  • Aditi Singh,
  • Dawn Singleton,
  • Timofey Skvortsov,
  • Tim J. Sloan,
  • Graciela Sluga,
  • Ken Smith,
  • Kim S. Smith,
  • Perminder Smith,
  • Darren L. Smith,
  • Louise Smith,
  • Colin P. Smith,
  • Nikki Smith,
  • Katherine L. Smollett,
  • Luke B. Snell,
  • Thomas Somassa,
  • Joel Southgate,
  • Karla Spellman,
  • Michael H. Spencer Chapman,
  • Lewis G. Spurgin,
  • Moira J. Spyer,
  • Rachael Stanley,
  • William Stanley,
  • Thomas D. Stanton,
  • Igor Starinskij,
  • Joanne Stockton,
  • Susanne Stonehouse,
  • Nathaniel Storey,
  • David J. Studholme,
  • Malur Sudhanva,
  • Emma Swindells,
  • Yusri Taha,
  • Ngee Keong Tan,
  • Julian W. Tang,
  • Miao Tang,
  • Ben E.W. Taylor,
  • Joshua F. Taylor,
  • Sarah Taylor,
  • Ben Temperton,
  • Kate E. Templeton,
  • Claire Thomas,
  • Laura Thomson,
  • Emma C. Thomson,
  • Alicia Thornton,
  • Scott A.J. Thurston,
  • John A. Todd,
  • Rachael Tomb,
  • Lily Tong,
  • Gerry Tonkin-Hill,
  • M. Estee Torok,
  • Jaime M. Tovar-Corona,
  • Amy Trebes,
  • Alexander J. Trotter,
  • Ioulia Tsatsani,
  • Robyn Turnbull,
  • Katherine A. Twohig,
  • Helen Umpleby,
  • Anthony P. Underwood,
  • Edith E. Vamos,
  • Tetyana I. Vasylyeva,
  • Sreenu Vattipally,
  • Gabrielle Vernet,
  • Barry B. Vipond,
  • Erik M. Volz,
  • Sarah Walsh,
  • Dennis Wang,
  • Ben Warne,
  • Joanna Warwick-Dugdale,
  • Elizabeth Wastnedge,
  • Joanne Watkins,
  • Louisa K. Watson,
  • Sheila Waugh,
  • Hermione J. Webster,
  • Danni Weldon,
  • Elaine Westwick,
  • Thomas Whalley,
  • Helen Wheeler,
  • Mark Whitehead,
  • Max Whiteley,
  • Andrew Whitwham,
  • Claudia Wierzbicki,
  • Nicholas J. Willford,
  • Lesley-Anne Williams,
  • Rebecca Williams,
  • Cheryl Williams,
  • Chris Williams,
  • Charlotte A. Williams,
  • Rachel J. Williams,
  • Thomas Williams,
  • Catryn Williams,
  • Kathleen A. Williamson,
  • Eleri Wilson-Davies,
  • Eric Witele,
  • Karen T. Withell,
  • Adam A. Witney,
  • Paige Wolverson,
  • Nick Wong,
  • Trudy Workman,
  • Victoria Wright,
  • Derek W. Wright,
  • Tim Wyatt,
  • Sarah Wyllie,
  • Li Xu-McCrae,
  • Mehmet Yavus,
  • Geraldine Yaze,
  • Corin A. Yeats,
  • Gonzalo Yebra,
  • Wen C. Yew,
  • Gregory R. Young,
  • Jamie Young,
  • Alex E. Zarebski,
  • Peijun Zhang,
  • J. Kenneth Baillie,
  • Malcolm G. Semple,
  • Peter J.M. Openshaw,
  • Gail Carson,
  • Beatrice Alex,
  • Petros Andrikopoulos,
  • Benjamin Bach,
  • Wendy S. Barclay,
  • Debby Bogaert,
  • Meera Chand,
  • Kanta Chechi,
  • Graham S. Cooke,
  • Ana da Silva Filipe,
  • Annemarie B. Docherty,
  • Gonçalo dos Santos Correia,
  • Marc-Emmanuel Dumas,
  • Jake Dunning,
  • Tom Fletcher,
  • Christopher A. Green,
  • William Greenhalf,
  • Julian L. Griffin,
  • Rishi K. Gupta,
  • Ewen M. Harrison,
  • Julian A. Hiscox,
  • Antonia Ying Wai Ho,
  • Peter W. Horby,
  • Samreen Ijaz,
  • Saye Khoo,
  • Paul Klenerman,
  • Andrew Law,
  • Matthew R. Lewis,
  • Sonia Liggi,
  • Wei Shen Lim,
  • Lynn Maslen,
  • Alexander J. Mentzer,
  • Laura Merson,
  • Alison M. Meynert,
  • Mahdad Noursadeghi,
  • Michael Olanipekun,
  • Anthonia Osagie,
  • Massimo Palmarini,
  • Carlo Palmieri,
  • William A. Paxton,
  • Georgios Pollakis,
  • Nicholas Price,
  • Andrew Rambaut,
  • David L. Robertson,
  • Clark D. Russell,
  • Vanessa Sancho-Shimizu,
  • Caroline J. Sands,
  • Janet T. Scott,
  • Louise Sigfrid,
  • Tom Solomon,
  • Shiranee Sriskandan,
  • David Stuart,
  • Charlotte Summers,
  • Olivia V. Swann,
  • Zoltan Takats,
  • Panteleimon Takis,
  • Richard S. Tedder,
  • A.A. Roger Thompson,
  • Emma C. Thomson,
  • Ryan S. Thwaites,
  • Maria Zambon,
  • Hayley Hardwick,
  • Chloe Donohue,
  • Fiona Griffiths,
  • Wilna Oosthuyzen,
  • Cara Donegan,
  • Rebecca G. 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,
  • Andrew Law,
  • Murray Wham,
  • Sara Clohisey,
  • Ross Hendry,
  • James Scott-Brown,
  • Victoria Shaw,
  • Sarah E. McDonald,
  • Seán Keating,
  • Katie A. Ahmed,
  • Jane A. Armstrong,
  • Milton Ashworth,
  • Innocent G. Asiimwe,
  • Siddharth Bakshi,
  • Samantha L. Barlow,
  • Laura Booth,
  • Benjamin Brennan,
  • Katie Bullock,
  • Benjamin W.A. Catterall,
  • Jordan J. Clark,
  • Emily A. 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 L. Jensen,
  • Christopher B. Jones,
  • Trevor R. Jones,
  • Shadia Khandaker,
  • Katharine King,
  • Robyn T. Kiy,
  • Chrysa Koukorava,
  • Annette Lake,
  • Suzannah Lant,
  • Diane Latawiec,
  • Lara Lavelle-Langham,
  • Daniella Lefteri,
  • Lauren Lett,
  • Lucia A. Livoti,
  • Maria Mancini,
  • Sarah McDonald,
  • Laurence McEvoy,
  • John McLauchlan,
  • Soeren Metelmann,
  • Nahida S. Miah,
  • Joanna Middleton,
  • Joyce Mitchell,
  • Shona C. Moore,
  • Ellen G. Murphy,
  • Rebekah Penrice-Randal,
  • Jack Pilgrim,
  • Tessa Prince,
  • Will Reynolds,
  • P. Matthew Ridley,
  • Debby Sales,
  • Victoria E. Shaw,
  • Rebecca K. Shears,
  • Benjamin Small,
  • Krishanthi S. 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 L. 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,
  • David Chadwick,
  • Duncan Chambler,
  • Nigel Chee,
  • Jenny Child,
  • Srikanth Chukkambotla,
  • Tom Clark,
  • Paul Collini,
  • Catherine Cosgrove,
  • Jason Cupitt,
  • Maria-Teresa Cutino-Moguel,
  • Paul Dark,
  • Chris Dawson,
  • Samir Dervisevic,
  • Phil Donnison,
  • Sam Douthwaite,
  • Andrew Drummond,
  • Ingrid DuRand,
  • Ahilanadan Dushianthan,
  • Tristan Dyer,
  • Cariad Evans,
  • Chi Eziefula,
  • Chrisopher Fegan,
  • Adam Finn,
  • Duncan Fullerton,
  • Sanjeev Garg,
  • Sanjeev Garg,
  • Atul Garg,
  • Effrossyni Gkrania-Klotsas,
  • Jo Godden,
  • Arthur Goldsmith,
  • Clive Graham,
  • Elaine Hardy,
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Journal volume & issue
Vol. 24, no. 11
p. 103353

Abstract

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Summary: 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