Genomic reconstruction of the SARS-CoV-2 epidemic in England

Authors: Harald Vöhringer, Theo Sanderson, Matthew Sinnott, Nicola De Maio, Thuy Nguyen, Richard Goater, Frank Schwach, Ian Harrison, Joel Hellewell, Cristina V. Ariani, Sónia Gonçalves, David K. Jackson, Ian Johnston, Alexander W. Jung, Callum Saint, John Sillitoe, Maria Suciu, Nick Goldman, Jasmina Panovska‐Griffiths, Irina Abnizova, Louise Aigrain, Alex Alderton, Mozam Ali, Laura Allen, Roberto Amato, Ralph Anderson, Cristina V. Ariani, Siobhan Austin-Guest, Sendu Bala, Jeffrey C. Barrett, Andrew R. Bassett, Kristina Battleday, James R. Beal, Mathew A. Beale, Charlotte Beaver, Sam Bellany, Tristram Bellerby, Katie Bellis, Duncan Berger, Matthew Berriman, Emma Betteridge, Paul Bevan, Simon Binley, Jason Bishop, Kirsty Blackburn, James Bonfield, Nick Boughton, Sam Bowker, Timothy Brendler-Spaeth, Iraad F. Bronner, Tanya Brooklyn, Sarah K. Buddenborg, R.L. Bush, Catarina Caetano, Alex Cagan, Nicola Carter, Joanna Cartwright, Tiago Monteiro, Liz Chapman, Tracey-Jane Chillingworth, Peter Clapham, Richard Clark, Adrian Clarke, Catriona Clarke, Daryl Cole, Elizabeth Cook, Maria Coppola, Linda Cornell, Clare Cornwell, Craig Corton, Abby Crackett, Alison Cranage, Harriet Craven, Sarah Craw, Mark Crawford, Tim Cutts, Monika Dabrowska, Matt Davies, Robert M. Davies, Joseph Dawson, Callum Day, Aiden Densem, Thomas Dibling, Cat Dockree, D. C. Dodd, Sunil Kumar Dogga, Matthew J. Dorman, Gordon Dougan, Martin Dougherty, Alexander Dove, Lucy Drummond, Eleanor Drury, Monika Dudek, Jillian Durham, Laura Durrant, Elizabeth Easthope, Sabine Eckert, Peter Ellis, Ben W. Farr, Michael Fenton, Marcella Ferrero, Neil Flack, Howerd Fordham, Grace Forsythe, Luke Foulser, Matt Francis, Audrey Fraser, Adam Freeman, Anastasia Galvin, Maria Garcia-Casado, Alex Gedny, Sophia T. Girgis, James Glover, Sónia Gonçalves, Scott Goodwin, Oliver Gould, Marina Gourtovaia, Andy Gray, Emma Gray, Chris Griffiths, Yong Gu, Florence Guerin, Will Hamilton, Hannah Hanks, Ewan M. Harrison, Alexandria Harrott, Edward Harry, Julia Harvison, Paul T. Heath, Anastasia Hernández-Koutoucheva, Rhiannon Hobbs, Dave Holland, Sarah Holmes, Gary Hornett, Nicholas Hough, Liz Huckle, Lena Hughes-Hallet, Adam Hunter, Stephen Inglis, Sameena Iqbal, Adam Jackson, David K. Jackson, Keith James, Dorota Jamrozy, Carlos Jimenez Verdejo, Matthew Jones, Kalyan Kallepally, Leanne Kane, Keely Kay, Sally Kay, Jon Keatley, Alan Keith, Alison King, Lucy Kitchin, Matt Kleanthous, Martina Klimekova, Petra Korlević, Ksenia Krasheninnkova, Greg Lane, Cordelia Langford, Adam Laverack, Katharine Law, Mara Lawniczak, Stefanie V. Lensing, Steven Leonard, Laura Letchford, Kevin Lewis, Amanah Lewis-Wade, Jennifer Liddle, Quan Lin, Sarah Lindsay, Sally Linsdell, Rich Livett, Stephanie W. Lo, Rhona Long, Jamie Lovell, Jon Lovell, Catherine Ludden, James Mack, Mark Maddison, Aleksei Makunin, Irfan Mamun, Jenny Mansfield, Neil Marriott, Matt Martin, Matthew Mayho, Shane McCarthy, Jo McClintock, Samantha McGuigan, Sandra McHugh, Liz McMinn, Carl Meadows, Emily Mobley, Robin J. Moll, Maria Morra, Leanne Morrow, Kathryn Murie, Sian Nash, Claire Nathwani, Plamena Naydenova, Alexandra Neaverson, Rachel Nelson, Ed Nerou, Jon Nicholson, Tabea Nimz, Guillaume Noell, Sarah O’Meara, Valeriu Ohan, Karen Oliver, Charles Olney, Doug Ormond, Ágnes Oszlánczi, Steve Palmer, Yoke Fei Pang, Barbora Pardubska, Naomi Park, Aaron Parmar, Gaurang Patel, Minal Patel, Maggie Payne, Sharon J. Peacock, Arabella Petersen, Deborah Plowman, Tom Preston, Liam Prestwood, Christoph Puethe, Michael A. Quail, Diana Rajan, Shavanthi Rajatileka, Richard Rance, Suzannah Rawlings, Nicholas Redshaw, Joe Reynolds, Mark Reynolds, Simon Rice, Matt Richardson, Connor Roberts, Katrina Robinson, Melanie Robinson, David M. Robinson, Hazel Rogers, Eduardo Martin Rojo, Daljit Roopra, Mark E. Rose, Luke Rudd, Ramin Sadri, Nicholas Salmon, David Saul, Frank Schwach, Carol Scott, Phil Seekings, Lesley Shirley, Alison Simms, Matthew Sinnott, Shanthi Sivadasan, Bart Siwek, Dale Sizer, Kenneth Skeldon, Jason Skelton, Joanna Slater-Tunstill, Lisa Sloper, Nathalie Smerdon, Chris Smith, Christen Smith, James Smith, Katie Smith, Michelle Smith, Sean B. Smith, Tina Smith, Leighton Sneade, C. Soria, Catarina Sousa, Emily Souster, Andrew Sparkes, Michael Spencer-Chapman, Janet Squares, Robert Stanley, Claire Steed, Tim Stickland, Ian Still, Michael R. Stratton, Michelle Strickland, Allen Swann, Agnieszka Świątkowska, Neil Sycamore, Emma Swift, Edward Symons, Suzanne Szluha, Emma Taluy, Nunu Tao, Katy Taylor, Sam Taylor, Stacey Thompson, Mark A. Thompson, M. Thomson, Nicholas M. Thomson, Scott Thurston, Gerry Tonkin‐Hill, Dee Toombs, Benjamin Topping, Jaime M. Tovar-Corona, Daniel Ungureanu, James Uphill, Jana Urbanová, Philip Jansen Van Vuuren, Valerie E. Vancollie, Paul Voak, Danielle Walker, Matthew Walker, Matt Waller, Gary H. Ward, Charlie Weatherhogg, Niki Webb, Danni Weldon, Alan Wells, Eloise Wells, Luke Westwood, Theo Whipp, Thomas Whiteley, Georgia Whitton, Andrew Whitwham, Sara Widaa, Mia Williams, Mark Wilson, Sean Wright, Funding acquisition, leadership and supervision, metadata curation, project administration, samples and logistics, sequencing and analysis, software and analysis tools, and visualization, Samuel C. Robson, Funding acquisition, leadership and supervision, metadata curation, project administration, samples and logistics, sequencing and analysis, and software and analysis tools, Thomas R. Connor, Nicholas J. Loman, Leadership and supervision, metadata curation, project administration, samples and logistics, sequencing and analysis, software and analysis tools, and visualization, Tanya Golubchik, Funding acquisition, leadership and supervision, metadata curation, samples and logistics, sequencing and analysis, and visualization, Rocio T. Martinez Nunez, Funding acquisition, leadership and supervision, project administration, samples and logistics, sequencing and analysis, and software and analysis tools, David Bonsall, Funding acquisition, leadership and supervision, project administration, sequencing and analysis, software and analysis tools, and visualization, Andrew Rambaut, Funding acquisition, metadata curation, project administration, samples and logistics, sequencing and analysis, and software and analysis tools, Luke B. Snell, 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, Catherine Ludden, Funding acquisition, leadership and supervision, metadata curation, samples and logistics, and sequencing and analysis, Sally Corden, Eleni Nastouli, Funding acquisition, leadership and supervision, metadata curation, sequencing and analysis, and software and analysis tools, Gaia Nebbia, 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, Katrina Lythgoe, M. Estée Török, Ian Goodfellow, Leadership and supervision, metadata curation, project administration, samples and logistics, and visualization, Jacqui Prieto, Kordo Saeed, 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, Catherine Houlihan, Leadership and supervision, metadata curation, sequencing and analysis, software and analysis tools, and visualization, Dan Frampton, Metadata curation, project administration, samples and logistics, sequencing and analysis, and software and analysis tools, William L. Hamilton, Adam A. Witney, Funding acquisition, samples and logistics, sequencing and analysis, and visualization, Giselda Bucca, Funding acquisition, leadership and supervision, metadata curation and project administration, Cassie F. Pope, Funding acquisition, leadership and supervision, metadata curation, and samples and logistics, Catherine Moore, Funding acquisition, leadership and supervision, metadata curation, and sequencing and analysis, Emma C. Thomson, Funding acquisition, leadership and supervision, project administration, and samples and logistics, Ewan M. Harrison, Funding acquisition, leadership and supervision, sequencing and analysis, and visualization, Colin P. Smith, Leadership and supervision, metadata curation, project administration, and sequencing and analysis, Fiona Rogan, Leadership and supervision, metadata curation, project administration, and samples and logistics, Shaun M. Beckwith, Abigail Murray, Dawn Singleton, Kirstine Eastick, Liz A. Sheridan, Paul Randell, Leigh Jackson, Sónia Gonçalves, Leadership and supervision, metadata curation, samples and logistics, and sequencing and analysis, Derek Fairley, Matthew Loose, Joanne Watkins, Leadership and supervision, metadata curation, samples and logistics, and visualization, Samuel Moses, Leadership and supervision, metadata curation, sequencing and analysis, and software and analysis tools, Sam Nicholls, Matthew Bull, Leadership and supervision, project administration, samples and logistics, and sequencing and analysis, Darren Smith, Leadership and supervision, sequencing and analysis, software and analysis tools, and visualization, David M. Aanensen, Metadata curation, project administration, samples and logistics, and sequencing and analysis, Dinesh Aggarwal, James G. Shepherd, Martin D. Curran, Surendra Parmar, Metadata curation, project administration, sequencing and analysis, and software and analysis tools, Matthew D. Parker, Metadata curation, samples and logistics, sequencing and analysis, and software and analysis tools, Catryn Williams, Metadata curation, samples and logistics, sequencing and analysis, and visualization, Sharon Glaysher, Metadata curation, sequencing and analysis, software and analysis tools, and visualization, Anthony Underwood, Matthew Bashton, Nicole Pacchiarini, Katie F. Loveson, Matthew Byott, Project administration, sequencing and analysis, software and analysis tools, and visualization, Alessandro M. Carabelli, Funding acquisition, leadership and supervision, and metadata curation, Kate Templeton, Funding acquisition, leadership and supervision, and project administration, Thushan I. de Silva, Dennis Wang, Cordelia F. Langford, Funding acquisition, leadership and supervision, and samples and logistics, Rory Gunson, Funding acquisition, leadership and supervision, and sequencing and analysis, Simon Cottrell, Justin O’Grady, Dominic Kwiatkowski, Leadership and supervision, metadata curation and project administration, Patrick Lillie, Leadership and supervision, metadata curation, and samples and logistics, Nicholas Cortes, Nathan Moore, Claire Thomas, Phillipa Burns, Tabitha Mahungu, Steven Liggett, Leadership and supervision, metadata curation, and sequencing and analysis, Angela H. Beckett, Matthew T. G. Holden, Leadership and supervision, project administration, and samples and logistics, Lisa J. Levett, Husam Osman, Mohammed O. Hassan-Ibrahim, Leadership and supervision, project administration, and sequencing and analysis, David Simpson, Leadership and supervision, samples and logistics, and sequencing and analysis, Meera Chand, Ravi Gupta, Alistair C. Darby, Steve Paterson, Leadership and supervision, sequencing and analysis, and software and analysis tools, Oliver G. Pybus, Erik Volz, Daniela De Angelis, David L. Robertson, Andrew J. Page, Leadership and supervision, sequencing and analysis, and visualization, Andrew R. Bassett, Metadata curation, project administration, and samples and logistics, Nick Wong, Yusri Taha, Michelle J. Erkiert, Michael H. Spencer Chapman, Metadata curation, project administration, and sequencing and analysis, Rebecca Dewar, M. McHugh, Metadata curation, project administration, and software and analysis tools, Siddharth Mookerjee, Metadata curation, project administration and visualization, Stephen Aplin, Matthew Harvey, Thea Sass, Helen Umpleby, Helen Wheeler, Metadata curation, samples and logistics, and sequencing and analysis, James McKenna, Ben Warne, Joshua F. Taylor, Yasmin Chaudhry, Rhys Izuagbe, Aminu S. Jahun, Gregory R. Young, Claire McMurray, Clare M. McCann, Andrew Nelson, Scott Elliott, Metadata curation, samples and logistics, and visualization, Hannah Lowe, Metadata curation, sequencing and analysis, and software and analysis tools, Anna Price, Matthew Crown, Sara Rey, Sunando Roy, Ben Temperton, Metadata curation, sequencing and analysis, and visualization, Sharif Shaaban, Andrew R. Hesketh, Project administration, samples and logistics, and sequencing and analysis, Kenneth G. Laing, Irene M. Monahan, Judith Heaney, Project administration, samples and logistics, and visualization, Emanuela Pelosi, Siona Silviera, Eleri Wilson-Davies, Samples and logistics, software and analysis tools, and visualization, Helen Fryer, Sequencing and analysis, software and analysis tools, and visualization, Helen Adams, Louis du Plessis, Rob Johnson, William T. Harvey, Joseph Hughes, Richard Orton, Lewis G. Spurgin, Yann Bourgeois, Chris Ruis, Áine O’Toole, Theo Sanderson, Funding acquisition, and leadership and supervision, Christophe Fraser, Jonathan Edgeworth, Judith Breuer, Stephen L. Michell, John A. Todd, Funding acquisition and project administration, John P.T. Mo, David Buck, Leadership and supervision, and metadata curation, Kavitha Gajee, Gemma L. Kay, Leadership and supervision, and project administration, Sharon J. Peacock, David Heyburn, Leadership and supervision, and samples and logistics, Katie Kitchman, Alan McNally, David T. Pritchard, Samir Dervisevic, Peter Muir, Esther Robinson, Barry Vipond, Newara Ramadan, Christopher Jeanes, Jana Catalan, Neil Jones, Leadership and supervision, and sequencing and analysis, Ana da Silva Filipe, Chris Williams, Marc Fuchs, Julia Miskelly, Aaron R. Jeffries, Naomi R. Park, Metadata curation, and samples and logistics, Amy Ash, Cherian Koshy, Magdalena Barrow, Sarah L. Buchan, Anna Mantzouratou, Gemma Clark, Christopher W. Holmes, Sharon Campbell, Thomas Davis, Ngee Keong Tan, Julianne R. Brown, Kathryn Harris, Stephen P. Kidd, Paul R. Grant, Li Xu-McCrae, Alison D. Cox, Pinglawathee Madona, Marcus Pond, Paul Randell, Karen T. Withell, Cheryl Williams, Clive Graham, Rebecca Denton-Smith, Emma Swindells, Robyn Turnbull, Tim J. Sloan, Andrew Bosworth, Stephanie Hutchings, Hannah M. Pymont, Anna Casey, Liz Ratcliffe, Christopher R. Jones, Bridget Knight, Tanzina Haque, Jennifer Hart, Dianne Irish-Tavares, Eric Witele, Craig Mower, Louisa K. Watson, Jennifer Collins, Gary Eltringham, Dorian Crudgington, Ben Macklin, Miren Iturriza‐Gómara, Anita O. Lucaci, C. Patrick McClure, Metadata curation, and sequencing and analysis, Matthew Carlile, Nadine Holmes, Christopher Moore, Nathaniel Storey, Stefan Rooke, Gonzalo Yebra, Noel Craine, Malorie Perry, Nabil-Fareed Alikhan, Stephen Bridgett, Kate F. Cook, Christopher Fearn, Salman Goudarzi, Ronan A Lyons, Thomas Williams, Sam Haldenby, Metadata curation, and software and analysis tools, Robert M. Davies, Project administration, and samples and logistics, Rahul Batra, Beth Blane, Moira Spyer, Perminder Smith, Mehmet Yavus, Rachel Williams, Adhyana I. K. Mahanama, Buddhini Samaraweera, Sophia T. Girgis, Samantha E. Hansford, Angie Green, Katherine L. Bellis, Matthew J. Dorman, Project administration, and sequencing and analysis, Joshua Quick, Project administration, and software and analysis tools, Radoslaw Poplawski, Samples and logistics, and sequencing and analysis, Nicola Reynolds, Andrew Mack, Arthur Morriss, Thomas Whalley, Bindi Patel, Iliana Georgana, Myra Hosmillo, Malte L. Pinckert, Joanne Stockton, John Henderson, Amy Hollis, William T. Stanley, Wen C. Yew, Richard Myers, Alicia Thornton, Alexander Adams, Tara Annett, Hibo Asad, Alec Birchley, Jason Coombes, Johnathan M. Evans, Laia Fina, Bree Gatica-Wilcox, Lauren Gilbert, Lee Graham, Jessica Hey, Ember Hilvers, Sophie Jones, Hannah Jones, Sara Kumziene-Summerhayes, Caoimhe McKerr, Jessica Powell, Georgia Pugh, Sarah Taylor, Alexander J. Trotter, Charlotte A. Williams, Leanne M. Kermack, Benjamin H. Foulkes, Marta Gallis, Hailey Hornsby, Stavroula F. Louka, Manoj Pohare, Paige Wolverson, Peijun Zhang, George MacIntyre-Cockett, Amy Trebes, Robin J. Moll, Lynne Ferguson, Emily J. Goldstein, Alasdair Maclean, Rachael Tomb, Samples and logistics, and software and analysis tools, Igor Starinskij, Sequencing and analysis, and software and analysis tools, Laura Thomson, Joel Southgate, Moritz U. G. Kraemer, Jayna Raghwani, Alex E. Zarebski, Olivia Boyd, Lily Geidelberg, Chris J. Illingworth, Chris Jackson, David J. Pascall, Vattipally B. Sreenu, Timothy M. Freeman, Sharon N. Hsu, Benjamin B. Lindsey, Jaime M. Tovar-Corona, Sequencing and analysis, and visualization, MacGregor Cox, Software and analysis tools, and visualization, Khalil Abudahab, Mirko Menegazzo, Ben Taylor, Corin Yeats, Afrida Mukaddas, Derek Wright, Leonardo de Oliveira Martins, Rachel Colquhoun, Verity Hill, Ben Jackson, J. T. McCrone, Nathan Medd, Emily Scher, Jon-Paul Keatley, Leadership and supervision, Tanya Curran, Sian Morgan, Patrick H. Maxwell, Kenneth G. C. Smith, Sahar Eldirdiri, Anita Kenyon, Alison Holmes, James Price, Tim Wyatt, Alison E. Mather, Timofey Skvortsov, John A. Hartley, Metadata curation, Martyn F. Guest, Christine Kitchen, Ian Merrick, Robert J. Munn, Beatrice Bertolusso, Jessica Lynch, Gabrielle Vernet, Stuart A. Kirk, Elizabeth Wastnedge, Rachael Stanley, Giles Idle, Declan Bradley, Jennifer Poyner, Matilde Mori, Project administration, Owen R. Jones, Victoria Wright, Ellena Brooks, Carol Churcher, Mireille Fragakis, Katerina Galai, Andrew Jermy, Sarah Judges, Georgina M. McManus, Kim S. Smith, Elaine Westwick, Stephen W. Attwood, Frances Bolt, Alisha Davies, Elen De Lacy, Fatima Downing, Sue Edwards, Lizzie Meadows, Sarah Jeremiah, Darren Smith, Samples and logistics, Themoula Charalampous, Amita Patel, Louise Berry, Tim Boswell, Vicki M. Fleming, Hannah C. Howson‐Wells, Amelia Joseph, Manjinder Khakh, Michelle M. Lister, Paul Bird, Karlie Fallon, Thomas Helmer, Claire McMurray, Mina Odedra, Jessica R. Shaw, Julian W. Tang, Nicholas J. Willford, Victoria Blakey, Veena Raviprakash, Nicola Sheriff, Lesley-Anne Williams, Theresa Feltwell, Luke Bedford, James S. Cargill, Warwick Hughes, Jonathan P. Moore, Susanne Stonehouse, Laura Atkinson, Jack C. D. Lee, Divya Shah, Adela Alcolea, Natasha Ohemeng-Kumi, John Ramble, Jasveen Sehmi, Rebecca Williams, Wendy Chatterton, Monika Pusok, William V. Everson, Anibolina Castigador, Emily MacNaughton, Kate El Bouzidi, Temi Lampejo, Malur Sudhanva, Cassie Breen, Graciela Sluga, Shazaad Ahmad, Ryan P. George, Nicholas W. Machin, Debbie Binns, Victoria James, Rachel Blacow, Lindsay Coupland, Louise Smith, Edward Barton, Debra Padgett, Garren Scott, Aidan Cross, Mariyam Mirfenderesky, Jane Greenaway, Kevin Cole, Phillip Clarke, Nichola Duckworth, Sarah Walsh, Kelly Bicknell, Robert Impey, Sarah Wyllie, Richard Hopes, Chloe Bishop, Vicki Chalker, Laura Gifford, Zoltán Molnár, Cressida Auckland, Cariad Evans, KATE JOHNSON, David G. Partridge, Mohammad Raza, Paul Baker, Stephen Bonner, Sarah Essex, Leanne J. Murray, Andrew I. Lawton, Shirelle Burton-Fanning, Brendan Payne, Sheila Waugh, Andrea N. Gomes, Maimuna Kimuli, Darren R. Murray, Paula Ashfield, Donald Dobie, Fiona Ashford, Angus Best, Liam Crawford, Nicola Cumley, Megan Mayhew, Oliver Megram, Jeremy Mirza, Emma Moles-Garcia, Benita Percival, Leah Ensell, Helen L. Lowe, Laurentiu Maftei, Matteo Mondani, Nicola J. Chaloner, Benjamin J. Cogger, Lisa J. Easton, Hannah Huckson, J. R. Lewis, Sarah Lowdon, Cassandra S. Malone, Florence Munemo, Manasa Mutingwende, Roberto Nicodemi, Olga Podplomyk, Thomas Somassa, Andrew D. Beggs, Alex Richter, Claire Cormie, Joana Angélica Andrade Dias, Sally Forrest, Ellen E. Higginson, Mailis Maes, Jamie Young, Rose K. Davidson, Kathryn Jackson, Lance Turtle, Alexander J. Keeley, Jonathan K. Ball, Timothy Byaruhanga, Joseph Chappell, Jayasree Dey, Jack D. Hill, Emily J. Park, Arezou Fanaie, Rachel A. Hilson, Geraldine Yaze, Sequencing and analysis, Safiah Afifi, Robert Beer, Joshua Maksimovic, Kathryn McCluggage Masters, Karla Spellman, Catherine Bresner, William Fuller, Angela Marchbank, Trudy Workman, Ekaterina Shelest, Johnny Debebe, Fei Sang, Marina Escalera Zamudio, Sarah François, Bernardo Gutiérrez, Tetyana I. Vasylyeva, Flavia Flaviani, Manon Ragonnet‐Cronin, Katherine Smollett, Alice Broos, Daniel Mair, Jenna Nichols, Kyriaki Nomikou, L. Tong, Ioulia Tsatsani, S. O’Brien, Steven Rushton, Roy Sanderson, Jon Perkins, Seb Cotton, Abbie Gallagher, Elias Allara, Clare Pearson, David Bibby, Gavin Dabrera, Nicholas Ellaby, Eileen Gallagher, Jonathan Hubb, Angie Lackenby, David Lee, Nikos Manesis, Tamyo Mbisa, Steven G. Platt, Katherine A. Twohig, Mari Morgan, Alp Aydin, David Baker, Ebenezer Foster-Nyarko, Sophie J. Prosolek, Steven Rudder, Chris Baxter, Silvia Carvalho, Deborah Lavin, Arun Mariappan, Clara Radulescu, Aditi Singh, Miao Tang, Helen Morcrette, Nadua Bayzid, Marius Cotic, Carlos E. Balcazar, Michael D. Gallagher, Daniel Maloney, Thomas D. Stanton, Kathleen A. Williamson, Robin Manley, Michelle L. Michelsen, Christine Sambles, David J. Studholme, Joanna Warwick-Dugdale, Richard Eccles, Matthew Gemmell, Richard D. Gregory, Margaret Hughes, Charlotte Nelson, Lucille Rainbow, Edith E. Vamos, Hermione J. Webster, Mark Whitehead, Claudia Wierzbicki, Adrienn Angyal, Luke R. Green, Max Whiteley, Iraad F. Bronner, Ben W. Farr, Stefanie V. Lensing, Shane McCarthy, Michael A. Quail, Nicholas Redshaw, Scott A. J. Thurston, Software and analysis tools, Will Rowe, Amy Gaskin, Thanh Le-Viet, Jennifier Liddle, Ewan Birney, Erik Volz, Sebastian Funk, Dominic Kwiatkowski, Meera Chand, Iñigo Martincorena, Jeffrey C. Barrett, Moritz Gerstung - Nature 2021 cited by 119

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.