Genomic reconstruction of the SARS-CoV-2 epidemic in England
Authors: Vöhringer Harald S. , Sanderson Theo , Sinnott Matthew , De Maio Nicola , Nguyen Thuy , Goater Richard , Schwach Frank , Harrison Ian , Hellewell Joel , Ariani Cristina V. , Gonçalves Sonia , Jackson David K. , Johnston Ian , Jung Alexander W. , Saint Callum , Sillitoe John , Suciu Maria , Goldman Nick , Panovska-Griffiths Jasmina ,   The Wellcome Sanger Institute COVID-19 Surveillance Team, Abnizova Irina , Aigrain Louise , Alderton Alex , Ali Mozam , Allen Laura , Amato Roberto , Anderson Ralph , Ariani Cristina , Austin-Guest Siobhan , Bala Sendu , Barrett Jeffrey , Bassett Andrew , Battleday Kristina , Beal James , Beale Mathew , Beaver Charlotte , Bellany Sam , Bellerby Tristram , Bellis Katie , Berger Duncan , Berriman Matt , Betteridge Emma , Bevan Paul , Binley Simon , Bishop Jason , Blackburn Kirsty , Bonfield James , Boughton Nick , Bowker Sam , Brendler-Spaeth Timothy , Bronner Iraad , Brooklyn Tanya , Buddenborg Sarah Kay , Bush Robert , Caetano Catarina , Cagan Alex , Carter Nicola , Cartwright Joanna , Monteiro Tiago Carvalho , Chapman Liz , Chillingworth Tracey-Jane , Clapham Peter , Clark Richard , Clarke Adrian , Clarke Catriona , Cole Daryl , Cook Elizabeth , Coppola Maria , Cornell Linda , Cornwell Clare , Corton Craig , Crackett Abby , Cranage Alison , Craven Harriet , Craw Sarah , Crawford Mark , Cutts Tim , Dabrowska Monika , Davies Matt , Davies Robert , Dawson Joseph , Day Callum , Densem Aiden , Dibling Thomas , Dockree Cat , Dodd David , Dogga Sunil , Dorman Matthew , Dougan Gordon , Dougherty Martin , Dove Alexander , Drummond Lucy , Drury Eleanor , Dudek Monika , Durham Jillian , Durrant Laura , Easthope Elizabeth , Eckert Sabine , Ellis Pete , Farr Ben , Fenton Michael , Ferrero Marcella , Flack Neil , Fordham Howerd , Forsythe Grace , Foulser Luke , Francis Matt , Fraser Audrey , Freeman Adam , Galvin Anastasia , Garcia-Casado Maria , Gedny Alex , Girgis Sophia , Glover James , Goncalves Sonia , Goodwin Scott , Gould Oliver , Gourtovaia Marina , Gray Andy , Gray Emma , Griffiths Coline , Gu Yong , Guerin Florence , Hamilton Will , Hanks Hannah , Harrison Ewan , Harrott Alexandria , Harry Edward , Harvison Julia , Heath Paul , Hernandez-Koutoucheva Anastasia , Hobbs Rhiannon , Holland Dave , Holmes Sarah , Hornett Gary , Hough Nicholas , Huckle Liz , Hughes-Hallet Lena , Hunter Adam , Inglis Stephen , Iqbal Sameena , Jackson Adam , Jackson David , James Keith , Jamrozy Dorota , Verdejo Carlos Jimenez , Jones Matthew , Kallepally Kalyan , Kane Leanne , Kay Keely , Kay Sally , Keatley Jon , Keith Alan , King Alison , Kitchin Lucy , Kleanthous Matt , Klimekova Martina , Korlevic Petra , Krasheninnkova Ksenia , Lane Greg , Langford Cordelia , Laverack Adam , Law Katharine , Lawniczak Mara , Lensing Stefanie , Leonard Steven , Letchford Laura , Lewis Kevin , Lewis-Wade Amanah , Liddle Jennifer , Lin Quan , Lindsay Sarah , Linsdell Sally , Livett Rich , Lo Stephanie , Long Rhona , Lovell Jamie , Lovell Jon , Ludden Catherine , Mack James , Maddison Mark , Makunin Aleksei , Mamun Irfan , Mansfield Jenny , Marriott Neil , Martin Matt , Mayho Matthew , McCarthy Shane , McClintock Jo , McGuigan Samantha , McHugh Sandra , McMinn Liz , Meadows Carl , Mobley Emily , Moll Robin , Morra Maria , Morrow Leanne , Murie Kathryn , Nash Sian , Nathwani Claire , Naydenova Plamena , Neaverson Alexandra , Nelson Rachel , Nerou Ed , Nicholson Jon , Nimz Tabea , Noell Guillaume G. , O’Meara Sarah , Ohan Valeriu , Oliver Karen , Olney Charles , Ormond Doug , Oszlanczi Agnes , Palmer Steve , Pang Yoke Fei , Pardubska Barbora , Park Naomi , Parmar Aaron , Patel Gaurang , Patel Minal , Payne Maggie , Peacock Sharon , Petersen Arabella , Plowman Deborah , Preston Tom , Prestwood Liam , Puethe Christoph , Quail Michael , Rajan Diana , Rajatileka Shavanthi , Rance Richard , Rawlings Suzannah , Redshaw Nicholas , Reynolds Joe , Reynolds Mark , Rice Simon , Richardson Matt , Roberts Connor , Robinson Katrina , Robinson Melanie , Robinson David , Rogers Hazel , Rojo Eduardo Martin , Roopra Daljit , Rose Mark , Rudd Luke , Sadri Ramin , Salmon Nicholas , Saul David , Schwach Frank , Scott Carol , Seekings Phil , Shirley Lesley , Simms Alison , Sinnott Matthew , Sivadasan Shanthi , Siwek Bart , Sizer Dale , Skeldon Kenneth , Skelton Jason , Slater-Tunstill Joanna , Sloper Lisa , Smerdon Nathalie , Smith Chris , Smith Christen , Smith James , Smith Katie , Smith Michelle , Smith Sean , Smith Tina , Sneade Leighton , Soria Carmen Diaz , Sousa Catarina , Souster Emily , Sparkes Andrew , Spencer-Chapman Michael , Squares Janet , Stanley Robert , Steed Claire , Stickland Tim , Still Ian , Stratton Michael R. , Strickland Michelle , Swann Allen , Swiatkowska Agnieszka , Sycamore Neil , Swift Emma , Symons Edward , Szluha Suzanne , Taluy Emma , Tao Nunu , Taylor Katy , Taylor Sam , Thompson Stacey , Thompson Mark , Thomson Mark , Thomson Nicholas , Thurston Scott , Tonkin-Hill Gerry , Toombs Dee , Topping Benjamin , Tovar-Corona Jaime , Ungureanu Daniel , Uphill James , Urbanova Jana , Van Vuuren Philip Jansen , Vancollie Valerie , Voak Paul , Walker Danielle , Walker Matthew , Waller Matt , Ward Gary , Weatherhogg Charlie , Webb Niki , Weldon Danni , Wells Alan , Wells Eloise , Westwood Luke , Whipp Theo , Whiteley Thomas , Whitton Georgia , Whitwham Andrew , Widaa Sara , Williams Mia , Wilson Mark , Wright Sean ,   The COVID-19 Genomics UK (COG-UK) Consortium*,   Funding acquisition, leadership and supervision, metadata curation, project administration, samples and logistics, sequencing and analysis, software and analysis tools, and visualization, Robson Samuel C. ,   Funding acquisition, leadership and supervision, metadata curation, project administration, samples and logistics, sequencing and analysis, and software and analysis tools, Connor Thomas R. , Loman Nicholas J. ,   Leadership and supervision, metadata curation, project administration, samples and logistics, sequencing and analysis, software and analysis tools, and visualization, Golubchik Tanya ,   Funding acquisition, leadership and supervision, metadata curation, samples and logistics, sequencing and analysis, and visualization, Martinez Nunez Rocio T. ,   Funding acquisition, leadership and supervision, project administration, samples and logistics, sequencing and analysis, and software and analysis tools, Bonsall David ,   Funding acquisition, leadership and supervision, project administration, sequencing and analysis, software and analysis tools, and visualization, Rambaut Andrew ,   Funding acquisition, metadata curation, project administration, samples and logistics, sequencing and analysis, and software and analysis tools, Snell Luke B. ,   Leadership and supervision, metadata curation, project administration, samples and logistics, software and analysis tools, and visualization,   Funding acquisition, leadership and supervision, metadata curation, project administration, and samples and logistics, Ludden Catherine ,   Funding acquisition, leadership and supervision, metadata curation, samples and logistics, and sequencing and analysis, Corden Sally , Nastouli Eleni ,   Funding acquisition, leadership and supervision, metadata curation, sequencing and analysis, and software and analysis tools, Nebbia Gaia ,   Funding acquisition, leadership and supervision, project administration, samples and logistics, and sequencing and analysis,   Leadership and supervision, metadata curation, project administration, samples and logistics, and sequencing and analysis, Lythgoe Katrina , Torok M. Estee , Goodfellow Ian G. ,   Leadership and supervision, metadata curation, project administration, samples and logistics, and visualization, Prieto Jacqui A. , Saeed Kordo ,   Leadership and supervision, metadata curation, project administration, sequencing and analysis, and software and analysis tools,   Leadership and supervision, metadata curation, samples and logistics, sequencing and analysis, and visualization, Houlihan Catherine ,   Leadership and supervision, metadata curation, sequencing and analysis, software and analysis tools, and visualization, Frampton Dan ,   Metadata curation, project administration, samples and logistics, sequencing and analysis, and software and analysis tools, Hamilton William L. , Witney Adam A. ,   Funding acquisition, samples and logistics, sequencing and analysis, and visualization, Bucca Giselda ,   Funding acquisition, leadership and supervision, metadata curation and project administration, Pope Cassie F. ,   Funding acquisition, leadership and supervision, metadata curation, and samples and logistics, Moore Catherine ,   Funding acquisition, leadership and supervision, metadata curation, and sequencing and analysis, Thomson Emma C. ,   Funding acquisition, leadership and supervision, project administration, and samples and logistics, Harrison Ewan M. ,   Funding acquisition, leadership and supervision, sequencing and analysis, and visualization, Smith Colin P. ,   Leadership and supervision, metadata curation, project administration, and sequencing and analysis, Rogan Fiona ,   Leadership and supervision, metadata curation, project administration, and samples and logistics, Beckwith Shaun M. , Murray Abigail , Singleton Dawn , Eastick Kirstine , Sheridan Liz A. , Randell Paul , Jackson Leigh M. , Gonçalves Sónia ,   Leadership and supervision, metadata curation, samples and logistics, and sequencing and analysis, Fairley Derek J. , Loose Matthew W. , Watkins Joanne ,   Leadership and supervision, metadata curation, samples and logistics, and visualization, Moses Samuel ,   Leadership and supervision, metadata curation, sequencing and analysis, and software and analysis tools, Nicholls Sam , Bull Matthew ,   Leadership and supervision, project administration, samples and logistics, and sequencing and analysis, Smith Darren L. ,   Leadership and supervision, sequencing and analysis, software and analysis tools, and visualization, Aanensen David M. ,   Metadata curation, project administration, samples and logistics, and sequencing and analysis, Aggarwal Dinesh , Shepherd James G. , Curran Martin D. , Parmar Surendra ,   Metadata curation, project administration, sequencing and analysis, and software and analysis tools, Parker Matthew D. ,   Metadata curation, samples and logistics, sequencing and analysis, and software and analysis tools, Williams Catryn ,   Metadata curation, samples and logistics, sequencing and analysis, and visualization, Glaysher Sharon ,   Metadata curation, sequencing and analysis, software and analysis tools, and visualization, Underwood Anthony P. , Bashton Matthew , Pacchiarini Nicole , Loveson Katie F. , Byott Matthew ,   Project administration, sequencing and analysis, software and analysis tools, and visualization, Carabelli Alessandro M. ,   Funding acquisition, leadership and supervision, and metadata curation, Templeton Kate E. ,   Funding acquisition, leadership and supervision, and project administration, de Silva Thushan I. , Wang Dennis , Langford Cordelia F. ,   Funding acquisition, leadership and supervision, and samples and logistics, Gunson Rory N. ,   Funding acquisition, leadership and supervision, and sequencing and analysis, Cottrell Simon , O’Grady Justin , Kwiatkowski Dominic ,   Leadership and supervision, metadata curation and project administration, Lillie Patrick J. ,   Leadership and supervision, metadata curation, and samples and logistics, Cortes Nicholas , Moore Nathan , Thomas Claire , Burns Phillipa J. , Mahungu Tabitha W. , Liggett Steven ,   Leadership and supervision, metadata curation, and sequencing and analysis, Beckett Angela H. , Holden Matthew T. G. ,   Leadership and supervision, project administration, and samples and logistics, Levett Lisa J. , Osman Husam , Hassan-Ibrahim Mohammed O. ,   Leadership and supervision, project administration, and sequencing and analysis, Simpson David A. ,   Leadership and supervision, samples and logistics, and sequencing and analysis, Chand Meera , Gupta Ravi K. , Darby Alistair C. , Paterson Steve ,   Leadership and supervision, sequencing and analysis, and software and analysis tools, Pybus Oliver G. , Volz Erik , de Angelis Daniela , Robertson David L. , Page Andrew J. ,   Leadership and supervision, sequencing and analysis, and visualization, Bassett Andrew R. ,   Metadata curation, project administration, and samples and logistics, Wong Nick , Taha Yusri , Erkiert Michelle J. , Spencer Chapman Michael H. ,   Metadata curation, project administration, and sequencing and analysis, Dewar Rebecca , McHugh Martin P. ,   Metadata curation, project administration, and software and analysis tools, Mookerjee Siddharth ,   Metadata curation, project administration and visualization, Aplin Stephen , Harvey Matthew , Sass Thea , Umpleby Helen , Wheeler Helen ,   Metadata curation, samples and logistics, and sequencing and analysis, McKenna James P. , Warne Ben , Taylor Joshua F. , Chaudhry Yasmin , Izuagbe Rhys , Jahun Aminu S. , Young Gregory R. , McMurray Claire , McCann Clare M. , Nelson Andrew , Elliott Scott ,   Metadata curation, samples and logistics, and visualization, Lowe Hannah ,   Metadata curation, sequencing and analysis, and software and analysis tools, Price Anna , Crown Matthew R. , Rey Sara , Roy Sunando , Temperton Ben ,   Metadata curation, sequencing and analysis, and visualization, Shaaban Sharif , Hesketh Andrew R. ,   Project administration, samples and logistics, and sequencing and analysis, Laing Kenneth G. , Monahan Irene M. , Heaney Judith ,   Project administration, samples and logistics, and visualization, Pelosi Emanuela , Silviera Siona , Wilson-Davies Eleri ,   Samples and logistics, software and analysis tools, and visualization, Fryer Helen ,   Sequencing and analysis, software and analysis tools, and visualization, Adams Helen , du Plessis Louis , Johnson Rob , Harvey William T. , Hughes Joseph , Orton Richard J. , Spurgin Lewis G. , Bourgeois Yann , Ruis Chris , O’Toole Áine , Sanderson Theo ,   Funding acquisition, and leadership and supervision, Fraser Christophe , Edgeworth Jonathan , Breuer Judith , Michell Stephen L. , Todd John A. ,   Funding acquisition and project administration, John Michaela , Buck David ,   Leadership and supervision, and metadata curation, Gajee Kavitha , Kay Gemma L. ,   Leadership and supervision, and project administration, Peacock Sharon J. , Heyburn David ,   Leadership and supervision, and samples and logistics, Kitchman Katie , McNally Alan , Pritchard David T. , Dervisevic Samir , Muir Peter , Robinson Esther , Vipond Barry B. , Ramadan Newara A. , Jeanes Christopher , Catalan Jana , Jones Neil ,   Leadership and supervision, and sequencing and analysis, da Silva Filipe Ana , Williams Chris , Fuchs Marc , Miskelly Julia , Jeffries Aaron R. , Park Naomi R. ,   Metadata curation, and samples and logistics, Ash Amy , Koshy Cherian , Barrow Magdalena , Buchan Sarah L. , Mantzouratou Anna , Clark Gemma , Holmes Christopher W. , Campbell Sharon , Davis Thomas , Tan Ngee Keong , Brown Julianne R. , Harris Kathryn A. , Kidd Stephen P. , Grant Paul R. , Xu-McCrae Li , Cox Alison , Madona Pinglawathee , Pond Marcus , Randell Paul A. , Withell Karen T. , Williams Cheryl , Graham Clive , Denton-Smith Rebecca , Swindells Emma , Turnbull Robyn , Sloan Tim J. , Bosworth Andrew , Hutchings Stephanie , Pymont Hannah M. , Casey Anna , Ratcliffe Liz , Jones Christopher R. , Knight Bridget A. , Haque Tanzina , Hart Jennifer , Irish-Tavares Dianne , Witele Eric , Mower Craig , Watson Louisa K. , Collins Jennifer , Eltringham Gary , Crudgington Dorian , Macklin Ben , Iturriza-Gomara Miren , Lucaci Anita O. , McClure Patrick C. ,   Metadata curation, and sequencing and analysis, Carlile Matthew , Holmes Nadine , Moore Christopher , Storey Nathaniel , Rooke Stefan , Yebra Gonzalo , Craine Noel , Perry Malorie , Alikhan Nabil-Fareed , Bridgett Stephen , Cook Kate F. , Fearn Christopher , Goudarzi Salman , Lyons Ronan A. , Williams Thomas , Haldenby Sam T. ,   Metadata curation, and software and analysis tools, Davies Robert M. ,   Project administration, and samples and logistics, Batra Rahul , Blane Beth , Spyer Moira J. , Smith Perminder , Yavus Mehmet , Williams Rachel J. , Mahanama Adhyana I. K. , Samaraweera Buddhini , Girgis Sophia T. , Hansford Samantha E. , Green Angie , Bellis Katherine L. , Dorman Matthew J. ,   Project administration, and sequencing and analysis, Quick Joshua ,   Project administration, and software and analysis tools, Poplawski Radoslaw ,   Samples and logistics, and sequencing and analysis, Reynolds Nicola , Mack Andrew , Morriss Arthur , Whalley Thomas , Patel Bindi , Georgana Iliana , Hosmillo Myra , Pinckert Malte L. , Stockton Joanne , Henderson John H. , Hollis Amy , Stanley William , Yew Wen C. , Myers Richard , Thornton Alicia , Adams Alexander , Annett Tara , Asad Hibo , Birchley Alec , Coombes Jason , Evans Johnathan M. , Fina Laia , Gatica-Wilcox Bree , Gilbert Lauren , Graham Lee , Hey Jessica , Hilvers Ember , Jones Sophie , Jones Hannah , Kumziene-Summerhayes Sara , McKerr Caoimhe , Powell Jessica , Pugh Georgia , Taylor Sarah , Trotter Alexander J. , Williams Charlotte A. , Kermack Leanne M. , Foulkes Benjamin H. , Gallis Marta , Hornsby Hailey R. , Louka Stavroula F. , Pohare Manoj , Wolverson Paige , Zhang Peijun , MacIntyre-Cockett George , Trebes Amy , Moll Robin J. , Ferguson Lynne , Goldstein Emily J. , Maclean Alasdair , Tomb Rachael ,   Samples and logistics, and software and analysis tools, Starinskij Igor ,   Sequencing and analysis, and software and analysis tools, Thomson Laura , Southgate Joel , Kraemer Moritz U. G. , Raghwani Jayna , Zarebski Alex E. , Boyd Olivia , Geidelberg Lily , Illingworth Chris J. , Jackson Chris , Pascall David , Vattipally Sreenu , Freeman Timothy M. , Hsu Sharon N. , Lindsey Benjamin B. , Tovar-Corona Jaime M. ,   Sequencing and analysis, and visualization, Cox MacGregor ,   Software and analysis tools, and visualization, Abudahab Khalil , Menegazzo Mirko , Taylor Ben E. W. , Yeats Corin A. , Mukaddas Afrida , Wright Derek W. , de Oliveira Martins Leonardo , Colquhoun Rachel , Hill Verity , Jackson Ben , McCrone J. T. , Medd Nathan , Scher Emily , Keatley Jon-Paul ,   Leadership and supervision, Curran Tanya , Morgan Sian , Maxwell Patrick , Smith Ken , Eldirdiri Sahar , Kenyon Anita , Holmes Alison H. , Price James R. , Wyatt Tim , Mather Alison E. , Skvortsov Timofey , Hartley John A. ,   Metadata curation, Guest Martyn , Kitchen Christine , Merrick Ian , Munn Robert , Bertolusso Beatrice , Lynch Jessica , Vernet Gabrielle , Kirk Stuart , Wastnedge Elizabeth , Stanley Rachael , Idle Giles , Bradley Declan T. , Poyner Jennifer , Mori Matilde ,   Project administration, Jones Owen , Wright Victoria , Brooks Ellena , Churcher Carol M. , Fragakis Mireille , Galai Katerina , Jermy Andrew , Judges Sarah , McManus Georgina M. , Smith Kim S. , Westwick Elaine , Attwood Stephen W. , Bolt Frances , Davies Alisha , De Lacy Elen , Downing Fatima , Edwards Sue , Meadows Lizzie , Jeremiah Sarah , Smith Nikki ,   Samples and logistics, Charalampous Themoula , Patel Amita , Berry Louise , Boswell Tim , Fleming Vicki M. , Howson-Wells Hannah C. , Joseph Amelia , Khakh Manjinder , Lister Michelle M. , Bird Paul W. , Fallon Karlie , Helmer Thomas , McMurray Claire L. , Odedra Mina , Shaw Jessica , Tang Julian W. , Willford Nicholas J. , Blakey Victoria , Raviprakash Veena , Sheriff Nicola , Williams Lesley-Anne , Feltwell Theresa , Bedford Luke , Cargill James S. , Hughes Warwick , Moore Jonathan , Stonehouse Susanne , Atkinson Laura , Lee Jack C. D. , Shah Divya , Alcolea Adela , Ohemeng-Kumi Natasha , Ramble John , Sehmi Jasveen , Williams Rebecca , Chatterton Wendy , Pusok Monika , Everson William , Castigador Anibolina , Macnaughton Emily , El Bouzidi Kate , Lampejo Temi , Sudhanva Malur , Breen Cassie , Sluga Graciela , Ahmad Shazaad S. Y. , George Ryan P. , Machin Nicholas W. , Binns Debbie , James Victoria , Blacow Rachel , Coupland Lindsay , Smith Louise , Barton Edward , Padgett Debra , Scott Garren , Cross Aidan , Mirfenderesky Mariyam , Greenaway Jane , Cole Kevin , Clarke Phillip , Duckworth Nichola , Walsh Sarah , Bicknell Kelly , Impey Robert , Wyllie Sarah , Hopes Richard , Bishop Chloe , Chalker Vicki , Gifford Laura , Molnar Zoltan , Auckland Cressida , Evans Cariad , Johnson Kate , Partridge David G. , Raza Mohammad , Baker Paul , Bonner Stephen , Essex Sarah , Murray Leanne J. , Lawton Andrew I. , Burton-Fanning Shirelle , Payne Brendan A. I. , Waugh Sheila , Gomes Andrea N. , Kimuli Maimuna , Murray Darren R. , Ashfield Paula , Dobie Donald , Ashford Fiona , Best Angus , Crawford Liam , Cumley Nicola , Mayhew Megan , Megram Oliver , Mirza Jeremy , Moles-Garcia Emma , Percival Benita , Ensell Leah , Lowe Helen L. , Maftei Laurentiu , Mondani Matteo , Chaloner Nicola J. , Cogger Benjamin J. , Easton Lisa J. , Huckson Hannah , Lewis Jonathan , Lowdon Sarah , Malone Cassandra S. , Munemo Florence , Mutingwende Manasa , Nicodemi Roberto , Podplomyk Olga , Somassa Thomas , Beggs Andrew , Richter Alex , Cormie Claire , Dias Joana , Forrest Sally , Higginson Ellen E. , Maes Mailis , Young Jamie , Davidson Rose K. , Jackson Kathryn A. , Turtle Lance , Keeley Alexander J. , Ball Jonathan , Byaruhanga Timothy , Chappell Joseph G. , Dey Jayasree , Hill Jack D. , Park Emily J. , Fanaie Arezou , Hilson Rachel A. , Yaze Geraldine ,   Sequencing and analysis, Afifi Safiah , Beer Robert , Maksimovic Joshua , Masters Kathryn McCluggage , Spellman Karla , Bresner Catherine , Fuller William , Marchbank Angela , Workman Trudy , Shelest Ekaterina , Debebe Johnny , Sang Fei , Zamudio Marina Escalera , Francois Sarah , Gutierrez Bernardo , Vasylyeva Tetyana I. , Flaviani Flavia , Ragonnet-Cronin Manon , Smollett Katherine L. , Broos Alice , Mair Daniel , Nichols Jenna , Nomikou Kyriaki , Tong Lily , Tsatsani Ioulia , O’Brien Sarah , Rushton Steven , Sanderson Roy , Perkins Jon , Cotton Seb , Gallagher Abbie , Allara Elias , Pearson Clare , Bibby David , Dabrera Gavin , Ellaby Nicholas , Gallagher Eileen , Hubb Jonathan , Lackenby Angie , Lee David , Manesis Nikos , Mbisa Tamyo , Platt Steven , Twohig Katherine A. , Morgan Mari , Aydin Alp , Baker David J. , Foster-Nyarko Ebenezer , Prosolek Sophie J. , Rudder Steven , Baxter Chris , Carvalho Sílvia F. , Lavin Deborah , Mariappan Arun , Radulescu Clara , Singh Aditi , Tang Miao , Morcrette Helen , Bayzid Nadua , Cotic Marius , Balcazar Carlos E. , Gallagher Michael D. , Maloney Daniel , Stanton Thomas D. , Williamson Kathleen A. , Manley Robin , Michelsen Michelle L. , Sambles Christine M. , Studholme David J. , Warwick-Dugdale Joanna , Eccles Richard , Gemmell Matthew , Gregory Richard , Hughes Margaret , Nelson Charlotte , Rainbow Lucille , Vamos Edith E. , Webster Hermione J. , Whitehead Mark , Wierzbicki Claudia , Angyal Adrienn , Green Luke R. , Whiteley Max , Bronner Iraad F. , Farr Ben W. , Lensing Stefanie V. , McCarthy Shane A. , Quail Michael A. , Redshaw Nicholas M. , Thurston Scott A. J. ,   Software and analysis tools, Rowe Will , Gaskin Amy , Le-Viet Thanh , Liddle Jennifier , Birney Ewan , Volz Erik , Funk Sebastian , Kwiatkowski Dominic , Chand Meera , Martincorena Inigo , Barrett Jeffrey C. , Gerstung Moritz 
Published: October 2021

The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.