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

Harald S. Vöhringer, Theo Sanderson, Matthew Sinnott Orcid Logo, Nicola De Maio, Thuy Nguyen, Richard Goater Orcid Logo, Frank Schwach, Ian Harrison Orcid Logo, Joel Hellewell Orcid Logo, Cristina V. Ariani, Sonia Gonçalves, David K. Jackson Orcid Logo, Ian Johnston, Alexander W. Jung, Callum Saint Orcid Logo, John Sillitoe, Maria Suciu, Nick Goldman Orcid Logo, Jasmina Panovska-Griffiths Orcid Logo, Irina Abnizova, Louise Aigrain, Alex Alderton, Mozam Ali, Laura Allen, Roberto Amato, Ralph Anderson, Cristina Ariani, Siobhan Austin-Guest, Sendu Bala, Jeffrey Barrett, Andrew Bassett, Kristina Battleday, James Beal, Mathew Beale, Charlotte Beaver, Sam Bellany, Tristram Bellerby, Katie Bellis, Duncan Berger, Matt Berriman, Emma Betteridge, Paul Bevan, Simon Binley, Jason Bishop, Kirsty Blackburn, James Bonfield, Nick Boughton, Sam Bowker, Timothy Brendler-Spaeth, Iraad Bronner, Tanya Brooklyn, Sarah Kay Buddenborg, Robert Bush, Catarina Caetano, Alex Cagan, Nicola Carter, Joanna Cartwright, Tiago Carvalho 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 Davies, Joseph Dawson, Callum Day, Aiden Densem, Thomas Dibling, Cat Dockree, David Dodd, Sunil Dogga, Matthew Dorman, Gordon Dougan, Martin Dougherty, Alexander Dove, Lucy Drummond, Eleanor Drury, Monika Dudek, Jillian Durham, Laura Durrant, Elizabeth Easthope, Sabine Eckert, Pete Ellis, Ben 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 Girgis, James Glover, Sonia Goncalves, Scott Goodwin, Oliver Gould, Marina Gourtovaia, Andy Gray, Emma Gray, Coline Griffiths, Yong Gu, Florence Guerin, Will Hamilton, Hannah Hanks, Ewan Harrison, Alexandria Harrott, Edward Harry, Julia Harvison, Paul Heath, Anastasia Hernandez-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 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 Korlevic, Ksenia Krasheninnkova, Greg Lane, Cordelia Langford, Adam Laverack, Katharine Law, Mara Lawniczak, Stefanie Lensing, Steven Leonard, Laura Letchford, Kevin Lewis, Amanah Lewis-Wade, Jennifer Liddle, Quan Lin, Sarah Lindsay, Sally Linsdell, Rich Livett, Stephanie 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 Moll, Maria Morra, Leanne Morrow, Kathryn Murie, Sian Nash, Claire Nathwani, Plamena Naydenova, Alexandra Neaverson, Rachel Nelson, Ed Nerou, Jon Nicholson, Tabea Nimz, Guillaume G. Noell, Sarah O’Meara, Valeriu Ohan, Karen Oliver, Charles Olney, Doug Ormond, Agnes Oszlanczi, Steve Palmer, Yoke Fei Pang, Barbora Pardubska, Naomi Park, Aaron Parmar, Gaurang Patel, Minal Patel, Maggie Payne, Sharon Peacock, Arabella Petersen, Deborah Plowman, Tom Preston, Liam Prestwood, Christoph Puethe, Michael 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 Robinson, Hazel Rogers, Eduardo Martin Rojo, Daljit Roopra, Mark 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 Smith, Tina Smith, Leighton Sneade, Carmen Diaz 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 Swiatkowska, Neil Sycamore, Emma Swift, Edward Symons, Suzanne Szluha, Emma Taluy, Nunu Tao, Katy Taylor, Sam Taylor, Stacey Thompson, Mark Thompson, Mark Thomson, Nicholas Thomson, Scott Thurston, Gerry Tonkin-Hill, Dee Toombs, Benjamin Topping, Jaime Tovar-Corona, Daniel Ungureanu, James Uphill, Jana Urbanova, Philip Jansen Van Vuuren, Valerie Vancollie, Paul Voak, Danielle Walker, Matthew Walker, Matt Waller, Gary 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, Samuel C. Robson, Thomas R. Connor, Nicholas J. Loman, Tanya Golubchik, Rocio T. Martinez Nunez, David Bonsall, Andrew Rambaut, Luke B. Snell, Catherine Ludden, Sally Corden, Eleni Nastouli, Gaia Nebbia, Katrina Lythgoe, M. Estee Torok, Ian G. Goodfellow, Jacqui A. Prieto, Kordo Saeed, Catherine Houlihan, Dan Frampton, William L. Hamilton, Adam A. Witney, Giselda Bucca, Cassie F. Pope, Catherine Moore, Emma C. Thomson, Ewan M. Harrison, Colin P. Smith, Fiona Rogan, Shaun M. Beckwith, Abigail Murray, Dawn Singleton, Kirstine Eastick, Liz A. Sheridan, Paul Randell, Leigh M. Jackson, Sónia Gonçalves, Derek J. Fairley, Matthew W. Loose, Joanne Watkins, Samuel Moses, Sam Nicholls, Matthew Bull, Darren L. Smith, David M. Aanensen, Dinesh Aggarwal, James G. Shepherd, Martin D. Curran, Surendra Parmar, Matthew D. Parker, Catryn Williams, Sharon Glaysher, Anthony P. Underwood, Matthew Bashton, Nicole Pacchiarini, Katie F. Loveson, Matthew Byott, Alessandro M. Carabelli, Kate E. Templeton, Thushan I. de Silva, Dennis Wang, Cordelia F. Langford, Rory N. Gunson, Simon Cottrell, Justin O’Grady, Dominic Kwiatkowski, Patrick J. Lillie, Nicholas Cortes, Nathan Moore, Claire Thomas, Phillipa J. Burns, Tabitha W. Mahungu, Steven Liggett, Angela H. Beckett, Matthew T. G. Holden, Lisa J. Levett, Husam Osman, Mohammed O. Hassan-Ibrahim, David A. Simpson, Meera Chand, Ravi K. Gupta, Alistair C. Darby, Steve Paterson, Oliver G. Pybus, Erik Volz, Daniela de Angelis, David L. Robertson, Andrew J. Page, Andrew R. Bassett, Nick Wong, Yusri Taha, Michelle J. Erkiert, Michael H. Spencer Chapman, Rebecca Dewar, Martin P. McHugh, Siddharth Mookerjee, Stephen Aplin, Matthew Harvey, Thea Sass, Helen Umpleby, Helen Wheeler, James P. 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, Hannah Lowe, Anna Price, Matthew R. Crown, Sara Rey, Sunando Roy, Ben Temperton, Sharif Shaaban, Andrew R. Hesketh, Kenneth G. Laing, Irene M. Monahan, Judith Heaney, Emanuela Pelosi, Siona Silviera, Eleri Wilson-Davies, Helen Fryer, Helen Adams, Louis du Plessis, Rob Johnson, William T. Harvey, Joseph Hughes, Richard J. Orton, Lewis G. Spurgin, Yann Bourgeois, Chris Ruis, Áine O’Toole, Theo Sanderson, Christophe Fraser, Jonathan Edgeworth, Judith Breuer, Stephen L. Michell, John A. Todd, Michaela John, David Buck, Kavitha Gajee, Gemma L. Kay, Sharon J. Peacock, David Heyburn, Katie Kitchman, Alan McNally, David T. Pritchard, Samir Dervisevic, Peter Muir, Esther Robinson, Barry B. Vipond, Newara A. Ramadan, Christopher Jeanes, Jana Catalan, Neil Jones, Ana da Silva Filipe, Chris Williams, Marc Fuchs, Julia Miskelly, Aaron R. Jeffries, Naomi R. Park, 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 A. Harris, Stephen P. Kidd, Paul R. Grant, Li Xu-McCrae, Alison Cox, Pinglawathee Madona, Marcus Pond, Paul A. 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 A. 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-Gomara, Anita O. Lucaci, Patrick C. McClure, 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 T. Haldenby, Robert M. Davies, Rahul Batra, Beth Blane, Moira J. Spyer, Perminder Smith, Mehmet Yavus, Rachel J. Williams, Adhyana I. K. Mahanama, Buddhini Samaraweera, Sophia T. Girgis, Samantha E. Hansford, Angie Green, Katherine L. Bellis, Matthew J. Dorman, Joshua Quick, Radoslaw Poplawski, Nicola Reynolds, Andrew Mack, Arthur Morriss, Thomas Whalley, Bindi Patel, Iliana Georgana, Myra Hosmillo, Malte L. Pinckert, Joanne Stockton, John H. Henderson, Amy Hollis, William 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 R. 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, Igor Starinskij, Laura Thomson, Joel Southgate, Moritz U. G. Kraemer, Jayna Raghwani, Alex E. Zarebski, Olivia Boyd, Lily Geidelberg, Chris J. Illingworth, Chris Jackson, David Pascall, Sreenu Vattipally, Timothy M. Freeman, Sharon N. Hsu, Benjamin B. Lindsey, Jaime M. Tovar-Corona, MacGregor Cox, Khalil Abudahab, Mirko Menegazzo, Ben E. W. Taylor, Corin A. Yeats, Afrida Mukaddas, Derek W. Wright, Leonardo de Oliveira Martins, Rachel Colquhoun, Verity Hill, Ben Jackson, J. T. McCrone, Nathan Medd, Emily Scher, Jon-Paul Keatley, Tanya Curran, Sian Morgan, Patrick Maxwell, Ken Smith, Sahar Eldirdiri, Anita Kenyon, Alison H. Holmes, James R. Price, Tim Wyatt, Alison E. Mather, Timofey Skvortsov, John A. Hartley, Martyn Guest, Christine Kitchen, Ian Merrick, Robert Munn, Beatrice Bertolusso, Jessica Lynch, Gabrielle Vernet, Stuart Kirk, Elizabeth Wastnedge, Rachael Stanley, Giles Idle, Declan T. Bradley, Jennifer Poyner, Matilde Mori, Owen Jones, Victoria Wright, Ellena Brooks, Carol M. 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, Nikki Smith, Themoula Charalampous, Amita Patel, Louise Berry, Tim Boswell, Vicki M. Fleming, Hannah C. Howson-Wells, Amelia Joseph, Manjinder Khakh, Michelle M. Lister, Paul W. Bird, Karlie Fallon, Thomas Helmer, Claire L. McMurray, Mina Odedra, Jessica 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 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 Everson, Anibolina Castigador, Emily Macnaughton, Kate El Bouzidi, Temi Lampejo, Malur Sudhanva, Cassie Breen, Graciela Sluga, Shazaad S. Y. 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, Zoltan Molnar, 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 A. I. 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, Jonathan Lewis, Sarah Lowdon, Cassandra S. Malone, Florence Munemo, Manasa Mutingwende, Roberto Nicodemi, Olga Podplomyk, Thomas Somassa, Andrew Beggs, Alex Richter, Claire Cormie, Joana Dias, Sally Forrest, Ellen E. Higginson, Mailis Maes, Jamie Young, Rose K. Davidson, Kathryn A. Jackson, Lance Turtle, Alexander J. Keeley, Jonathan Ball, Timothy Byaruhanga, Joseph G. Chappell, Jayasree Dey, Jack D. Hill, Emily J. Park, Arezou Fanaie, Rachel A. Hilson, Geraldine Yaze, 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 Francois, Bernardo Gutierrez, Tetyana I. Vasylyeva, Flavia Flaviani, Manon Ragonnet-Cronin, Katherine L. Smollett, Alice Broos, Daniel Mair, Jenna Nichols, Kyriaki Nomikou, Lily Tong, Ioulia Tsatsani, Sarah 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 Platt, Katherine A. Twohig, Mari Morgan, Alp Aydin, David J. Baker, Ebenezer Foster-Nyarko, Sophie J. Prosolek, Steven Rudder, Chris Baxter, Sílvia F. 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 M. Sambles, David J. Studholme, Joanna Warwick-Dugdale, Richard Eccles, Matthew Gemmell, Richard 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 A. McCarthy, Michael A. Quail, Nicholas M. Redshaw, Scott A. J. Thurston, Will Rowe, Amy Gaskin, Thanh Le-Viet, Jennifier Liddle, Ewan Birney Orcid Logo, Erik Volz Orcid Logo, Sebastian Funk Orcid Logo, Dominic Kwiatkowski Orcid Logo, Meera Chand, Inigo Martincorena Orcid Logo, Jeffrey C. Barrett Orcid Logo, Moritz Gerstung Orcid Logo, (The Wellcome Sanger Institute COVID-19 Surveillance Team), (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), (Funding acquisition, leadership and supervision, metadata curation, project administration, samples and logistics, sequencing and analysis, and software and analysis tools), (Leadership and supervision, metadata curation, project administration, samples and logistics, sequencing and analysis, software and analysis tools, and visualization), (Funding acquisition, leadership and supervision, metadata curation, samples and logistics, sequencing and analysis, and visualization), (Funding acquisition, leadership and supervision, project administration, samples and logistics, sequencing and analysis, and software and analysis tools), (Funding acquisition, leadership and supervision, project administration, sequencing and analysis, software and analysis tools, and visualization), (Funding acquisition, metadata curation, project administration, samples and logistics, sequencing and analysis, and software and analysis tools), (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), (Funding acquisition, leadership and supervision, metadata curation, samples and logistics, and sequencing and analysis), (Funding acquisition, leadership and supervision, metadata curation, sequencing and analysis, and software and analysis tools), (Funding acquisition, leadership and supervision, project administration, samples and logistics, and sequencing and analysis), (Leadership and supervision, metadata curation, project administration, 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metadata curation, and sequencing and analysis), (Funding acquisition, leadership and supervision, project administration, and samples and logistics), (Funding acquisition, leadership and supervision, sequencing and analysis, and visualization), (Leadership and supervision, metadata curation, project administration, and sequencing and analysis), (Leadership and supervision, metadata curation, project administration, and samples and logistics), (Leadership and supervision, metadata curation, samples and logistics, and sequencing and analysis), (Leadership and supervision, metadata curation, samples and logistics, and visualization), (Leadership and supervision, metadata curation, sequencing and analysis, and software and analysis tools), (Leadership and supervision, project administration, samples and logistics, and sequencing and analysis), (Leadership and supervision, sequencing and analysis, software and analysis tools, and visualization), (Metadata curation, project administration, samples and logistics, and sequencing and analysis), (Metadata curation, project administration, sequencing and analysis, and software and analysis tools), (Metadata curation, samples and logistics, sequencing and analysis, and software and analysis tools), (Metadata curation, samples and logistics, sequencing and analysis, and visualization), (Metadata curation, sequencing and analysis, software and analysis tools, and visualization), (Project administration, sequencing and analysis, software and analysis tools, and visualization), (Funding acquisition, leadership and supervision, and metadata curation), (Funding acquisition, leadership and supervision, and project administration), (Funding acquisition, leadership and supervision, and samples and logistics), (Funding acquisition, leadership and supervision, and sequencing and analysis), (Leadership and supervision, metadata curation and project administration), (Leadership and supervision, metadata curation, and samples and logistics), (Leadership and supervision, metadata curation, and sequencing and analysis), (Leadership and supervision, project administration, and samples and logistics), (Leadership and supervision, project administration, and sequencing and analysis), (Leadership and supervision, samples and logistics, and sequencing and analysis), (Leadership and supervision, sequencing and analysis, and software and analysis tools), (Leadership and supervision, sequencing and analysis, and visualization), (Metadata curation, project administration, and samples and logistics), (Metadata curation, project administration, and sequencing and analysis), (Metadata curation, project administration, and software and analysis tools), (Metadata curation, project administration and visualization), (Metadata curation, samples and logistics, and sequencing and analysis), (Metadata curation, samples and logistics, and visualization), (Metadata curation, sequencing and analysis, and software and analysis tools), (Metadata curation, sequencing and analysis, and visualization), (Project administration, samples and logistics, and sequencing and analysis), (Project administration, samples and logistics, and visualization), (Samples and logistics, software and analysis tools, and visualization), (Sequencing and analysis, software and analysis tools, and visualization), (Funding acquisition, and leadership and supervision), (Funding acquisition and project administration), (Leadership and supervision, and metadata curation), (Leadership and supervision, and project administration), (Leadership and supervision, and samples and logistics), (Leadership and supervision, and sequencing and analysis), (Metadata curation, and samples and logistics), (Metadata curation, and sequencing and analysis), (Metadata curation, and software and analysis tools), (Project administration, and samples and logistics), (Project administration, and sequencing and analysis), (Project administration, and software and analysis tools), (Samples and logistics, and sequencing and analysis), (Samples and logistics, and software and analysis tools), (Sequencing and analysis, and software and analysis tools), (Sequencing and analysis, and visualization), (Software and analysis tools, and visualization), (Leadership and supervision), (Metadata curation), (Project administration), (Samples and logistics), (Sequencing and analysis), (Software and analysis tools), Ronan Lyons Orcid Logo

Nature, Volume: 600, Issue: 7889, Pages: 506 - 511

Swansea University Author: Ronan Lyons Orcid Logo

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Abstract

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 diffe...

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Published in: Nature
ISSN: 0028-0836 1476-4687
Published: Springer Science and Business Media LLC 2021
Online Access: Check full text

URI: https://cronfa.swan.ac.uk/Record/cronfa66422
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Abstract: 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.
Item Description: Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England available at https://doi.org/10.1038/s41586-022-04887-8
College: Faculty of Medicine, Health and Life Sciences
Funders: Open access funding provided by Deutsches Krebsforschungszentrum (DKFZ).
Issue: 7889
Start Page: 506
End Page: 511