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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, samples and logistics, and sequencing and analysis), (Leadership and supervision, metadata curation, project administration, samples and logistics, and visualization), (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), (Leadership and supervision, metadata curation, sequencing and analysis, software and analysis tools, and visualization), (Metadata curation, project administration, samples and logistics, sequencing and analysis, and software and analysis tools), (Funding acquisition, samples and logistics, sequencing and analysis, and visualization), (Funding acquisition, leadership and supervision, metadata curation and project administration), (Funding acquisition, leadership and supervision, metadata curation, and samples and logistics), (Funding acquisition, leadership and supervision, 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
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URI: https://cronfa.swan.ac.uk/Record/cronfa66422
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fullrecord <?xml version="1.0" encoding="utf-8"?><rfc1807 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema"><bib-version>v2</bib-version><id>66422</id><entry>2024-05-15</entry><title>Genomic reconstruction of the SARS-CoV-2 epidemic in England</title><swanseaauthors><author><sid>83efcf2a9dfcf8b55586999d3d152ac6</sid><ORCID>0000-0001-5225-000X</ORCID><firstname>Ronan</firstname><surname>Lyons</surname><name>Ronan Lyons</name><active>true</active><ethesisStudent>false</ethesisStudent></author></swanseaauthors><date>2024-05-15</date><deptcode>MEDS</deptcode><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.</abstract><type>Journal Article</type><journal>Nature</journal><volume>600</volume><journalNumber>7889</journalNumber><paginationStart>506</paginationStart><paginationEnd>511</paginationEnd><publisher>Springer Science and Business Media LLC</publisher><placeOfPublication/><isbnPrint/><isbnElectronic/><issnPrint>0028-0836</issnPrint><issnElectronic>1476-4687</issnElectronic><keywords/><publishedDay>16</publishedDay><publishedMonth>12</publishedMonth><publishedYear>2021</publishedYear><publishedDate>2021-12-16</publishedDate><doi>10.1038/s41586-021-04069-y</doi><url/><notes>Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England available at https://doi.org/10.1038/s41586-022-04887-8</notes><college>COLLEGE NANME</college><department>Medical School</department><CollegeCode>COLLEGE CODE</CollegeCode><DepartmentCode>MEDS</DepartmentCode><institution>Swansea University</institution><apcterm/><funders>Open access funding provided by Deutsches Krebsforschungszentrum (DKFZ).</funders><projectreference/><lastEdited>2024-06-24T12:29:31.9625493</lastEdited><Created>2024-05-15T08:23:25.2739890</Created><path><level id="1">Faculty of Medicine, Health and Life Sciences</level><level id="2">Swansea University Medical School - Health Data Science</level></path><authors><author><firstname>Harald S.</firstname><surname>Vöhringer</surname><order>1</order></author><author><firstname>Theo</firstname><surname>Sanderson</surname><order>2</order></author><author><firstname>Matthew</firstname><surname>Sinnott</surname><orcid>0000-0002-3054-7846</orcid><order>3</order></author><author><firstname>Nicola De</firstname><surname>Maio</surname><order>4</order></author><author><firstname>Thuy</firstname><surname>Nguyen</surname><order>5</order></author><author><firstname>Richard</firstname><surname>Goater</surname><orcid>0000-0001-9954-841x</orcid><order>6</order></author><author><firstname>Frank</firstname><surname>Schwach</surname><order>7</order></author><author><firstname>Ian</firstname><surname>Harrison</surname><orcid>0000-0003-4117-961x</orcid><order>8</order></author><author><firstname>Joel</firstname><surname>Hellewell</surname><orcid>0000-0003-2683-0849</orcid><order>9</order></author><author><firstname>Cristina V.</firstname><surname>Ariani</surname><order>10</order></author><author><firstname>Sonia</firstname><surname>Gonçalves</surname><order>11</order></author><author><firstname>David K.</firstname><surname>Jackson</surname><orcid>0000-0002-8090-9462</orcid><order>12</order></author><author><firstname>Ian</firstname><surname>Johnston</surname><order>13</order></author><author><firstname>Alexander W.</firstname><surname>Jung</surname><order>14</order></author><author><firstname>Callum</firstname><surname>Saint</surname><orcid>0000-0001-8720-9736</orcid><order>15</order></author><author><firstname>John</firstname><surname>Sillitoe</surname><order>16</order></author><author><firstname>Maria</firstname><surname>Suciu</surname><order>17</order></author><author><firstname>Nick</firstname><surname>Goldman</surname><orcid>0000-0001-8486-2211</orcid><order>18</order></author><author><firstname>Jasmina</firstname><surname>Panovska-Griffiths</surname><orcid>0000-0002-7720-1121</orcid><order>19</order></author><author><firstname>Irina</firstname><surname>Abnizova</surname><order>20</order></author><author><firstname>Louise</firstname><surname>Aigrain</surname><order>21</order></author><author><firstname>Alex</firstname><surname>Alderton</surname><order>22</order></author><author><firstname>Mozam</firstname><surname>Ali</surname><order>23</order></author><author><firstname>Laura</firstname><surname>Allen</surname><order>24</order></author><author><firstname>Roberto</firstname><surname>Amato</surname><order>25</order></author><author><firstname>Ralph</firstname><surname>Anderson</surname><order>26</order></author><author><firstname>Cristina</firstname><surname>Ariani</surname><order>27</order></author><author><firstname>Siobhan</firstname><surname>Austin-Guest</surname><order>28</order></author><author><firstname>Sendu</firstname><surname>Bala</surname><order>29</order></author><author><firstname>Jeffrey</firstname><surname>Barrett</surname><order>30</order></author><author><firstname>Andrew</firstname><surname>Bassett</surname><order>31</order></author><author><firstname>Kristina</firstname><surname>Battleday</surname><order>32</order></author><author><firstname>James</firstname><surname>Beal</surname><order>33</order></author><author><firstname>Mathew</firstname><surname>Beale</surname><order>34</order></author><author><firstname>Charlotte</firstname><surname>Beaver</surname><order>35</order></author><author><firstname>Sam</firstname><surname>Bellany</surname><order>36</order></author><author><firstname>Tristram</firstname><surname>Bellerby</surname><order>37</order></author><author><firstname>Katie</firstname><surname>Bellis</surname><order>38</order></author><author><firstname>Duncan</firstname><surname>Berger</surname><order>39</order></author><author><firstname>Matt</firstname><surname>Berriman</surname><order>40</order></author><author><firstname>Emma</firstname><surname>Betteridge</surname><order>41</order></author><author><firstname>Paul</firstname><surname>Bevan</surname><order>42</order></author><author><firstname>Simon</firstname><surname>Binley</surname><order>43</order></author><author><firstname>Jason</firstname><surname>Bishop</surname><order>44</order></author><author><firstname>Kirsty</firstname><surname>Blackburn</surname><order>45</order></author><author><firstname>James</firstname><surname>Bonfield</surname><order>46</order></author><author><firstname>Nick</firstname><surname>Boughton</surname><order>47</order></author><author><firstname>Sam</firstname><surname>Bowker</surname><order>48</order></author><author><firstname>Timothy</firstname><surname>Brendler-Spaeth</surname><order>49</order></author><author><firstname>Iraad</firstname><surname>Bronner</surname><order>50</order></author><author><firstname>Tanya</firstname><surname>Brooklyn</surname><order>51</order></author><author><firstname>Sarah Kay</firstname><surname>Buddenborg</surname><order>52</order></author><author><firstname>Robert</firstname><surname>Bush</surname><order>53</order></author><author><firstname>Catarina</firstname><surname>Caetano</surname><order>54</order></author><author><firstname>Alex</firstname><surname>Cagan</surname><order>55</order></author><author><firstname>Nicola</firstname><surname>Carter</surname><order>56</order></author><author><firstname>Joanna</firstname><surname>Cartwright</surname><order>57</order></author><author><firstname>Tiago Carvalho</firstname><surname>Monteiro</surname><order>58</order></author><author><firstname>Liz</firstname><surname>Chapman</surname><order>59</order></author><author><firstname>Tracey-Jane</firstname><surname>Chillingworth</surname><order>60</order></author><author><firstname>Peter</firstname><surname>Clapham</surname><order>61</order></author><author><firstname>Richard</firstname><surname>Clark</surname><order>62</order></author><author><firstname>Adrian</firstname><surname>Clarke</surname><order>63</order></author><author><firstname>Catriona</firstname><surname>Clarke</surname><order>64</order></author><author><firstname>Daryl</firstname><surname>Cole</surname><order>65</order></author><author><firstname>Elizabeth</firstname><surname>Cook</surname><order>66</order></author><author><firstname>Maria</firstname><surname>Coppola</surname><order>67</order></author><author><firstname>Linda</firstname><surname>Cornell</surname><order>68</order></author><author><firstname>Clare</firstname><surname>Cornwell</surname><order>69</order></author><author><firstname>Craig</firstname><surname>Corton</surname><order>70</order></author><author><firstname>Abby</firstname><surname>Crackett</surname><order>71</order></author><author><firstname>Alison</firstname><surname>Cranage</surname><order>72</order></author><author><firstname>Harriet</firstname><surname>Craven</surname><order>73</order></author><author><firstname>Sarah</firstname><surname>Craw</surname><order>74</order></author><author><firstname>Mark</firstname><surname>Crawford</surname><order>75</order></author><author><firstname>Tim</firstname><surname>Cutts</surname><order>76</order></author><author><firstname>Monika</firstname><surname>Dabrowska</surname><order>77</order></author><author><firstname>Matt</firstname><surname>Davies</surname><order>78</order></author><author><firstname>Robert</firstname><surname>Davies</surname><order>79</order></author><author><firstname>Joseph</firstname><surname>Dawson</surname><order>80</order></author><author><firstname>Callum</firstname><surname>Day</surname><order>81</order></author><author><firstname>Aiden</firstname><surname>Densem</surname><order>82</order></author><author><firstname>Thomas</firstname><surname>Dibling</surname><order>83</order></author><author><firstname>Cat</firstname><surname>Dockree</surname><order>84</order></author><author><firstname>David</firstname><surname>Dodd</surname><order>85</order></author><author><firstname>Sunil</firstname><surname>Dogga</surname><order>86</order></author><author><firstname>Matthew</firstname><surname>Dorman</surname><order>87</order></author><author><firstname>Gordon</firstname><surname>Dougan</surname><order>88</order></author><author><firstname>Martin</firstname><surname>Dougherty</surname><order>89</order></author><author><firstname>Alexander</firstname><surname>Dove</surname><order>90</order></author><author><firstname>Lucy</firstname><surname>Drummond</surname><order>91</order></author><author><firstname>Eleanor</firstname><surname>Drury</surname><order>92</order></author><author><firstname>Monika</firstname><surname>Dudek</surname><order>93</order></author><author><firstname>Jillian</firstname><surname>Durham</surname><order>94</order></author><author><firstname>Laura</firstname><surname>Durrant</surname><order>95</order></author><author><firstname>Elizabeth</firstname><surname>Easthope</surname><order>96</order></author><author><firstname>Sabine</firstname><surname>Eckert</surname><order>97</order></author><author><firstname>Pete</firstname><surname>Ellis</surname><order>98</order></author><author><firstname>Ben</firstname><surname>Farr</surname><order>99</order></author><author><firstname>Michael</firstname><surname>Fenton</surname><order>100</order></author><author><firstname>Marcella</firstname><surname>Ferrero</surname><order>101</order></author><author><firstname>Neil</firstname><surname>Flack</surname><order>102</order></author><author><firstname>Howerd</firstname><surname>Fordham</surname><order>103</order></author><author><firstname>Grace</firstname><surname>Forsythe</surname><order>104</order></author><author><firstname>Luke</firstname><surname>Foulser</surname><order>105</order></author><author><firstname>Matt</firstname><surname>Francis</surname><order>106</order></author><author><firstname>Audrey</firstname><surname>Fraser</surname><order>107</order></author><author><firstname>Adam</firstname><surname>Freeman</surname><order>108</order></author><author><firstname>Anastasia</firstname><surname>Galvin</surname><order>109</order></author><author><firstname>Maria</firstname><surname>Garcia-Casado</surname><order>110</order></author><author><firstname>Alex</firstname><surname>Gedny</surname><order>111</order></author><author><firstname>Sophia</firstname><surname>Girgis</surname><order>112</order></author><author><firstname>James</firstname><surname>Glover</surname><order>113</order></author><author><firstname>Sonia</firstname><surname>Goncalves</surname><order>114</order></author><author><firstname>Scott</firstname><surname>Goodwin</surname><order>115</order></author><author><firstname>Oliver</firstname><surname>Gould</surname><order>116</order></author><author><firstname>Marina</firstname><surname>Gourtovaia</surname><order>117</order></author><author><firstname>Andy</firstname><surname>Gray</surname><order>118</order></author><author><firstname>Emma</firstname><surname>Gray</surname><order>119</order></author><author><firstname>Coline</firstname><surname>Griffiths</surname><order>120</order></author><author><firstname>Yong</firstname><surname>Gu</surname><order>121</order></author><author><firstname>Florence</firstname><surname>Guerin</surname><order>122</order></author><author><firstname>Will</firstname><surname>Hamilton</surname><order>123</order></author><author><firstname>Hannah</firstname><surname>Hanks</surname><order>124</order></author><author><firstname>Ewan</firstname><surname>Harrison</surname><order>125</order></author><author><firstname>Alexandria</firstname><surname>Harrott</surname><order>126</order></author><author><firstname>Edward</firstname><surname>Harry</surname><order>127</order></author><author><firstname>Julia</firstname><surname>Harvison</surname><order>128</order></author><author><firstname>Paul</firstname><surname>Heath</surname><order>129</order></author><author><firstname>Anastasia</firstname><surname>Hernandez-Koutoucheva</surname><order>130</order></author><author><firstname>Rhiannon</firstname><surname>Hobbs</surname><order>131</order></author><author><firstname>Dave</firstname><surname>Holland</surname><order>132</order></author><author><firstname>Sarah</firstname><surname>Holmes</surname><order>133</order></author><author><firstname>Gary</firstname><surname>Hornett</surname><order>134</order></author><author><firstname>Nicholas</firstname><surname>Hough</surname><order>135</order></author><author><firstname>Liz</firstname><surname>Huckle</surname><order>136</order></author><author><firstname>Lena</firstname><surname>Hughes-Hallet</surname><order>137</order></author><author><firstname>Adam</firstname><surname>Hunter</surname><order>138</order></author><author><firstname>Stephen</firstname><surname>Inglis</surname><order>139</order></author><author><firstname>Sameena</firstname><surname>Iqbal</surname><order>140</order></author><author><firstname>Adam</firstname><surname>Jackson</surname><order>141</order></author><author><firstname>David</firstname><surname>Jackson</surname><order>142</order></author><author><firstname>Keith</firstname><surname>James</surname><order>143</order></author><author><firstname>Dorota</firstname><surname>Jamrozy</surname><order>144</order></author><author><firstname>Carlos Jimenez</firstname><surname>Verdejo</surname><order>145</order></author><author><firstname>Matthew</firstname><surname>Jones</surname><order>146</order></author><author><firstname>Kalyan</firstname><surname>Kallepally</surname><order>147</order></author><author><firstname>Leanne</firstname><surname>Kane</surname><order>148</order></author><author><firstname>Keely</firstname><surname>Kay</surname><order>149</order></author><author><firstname>Sally</firstname><surname>Kay</surname><order>150</order></author><author><firstname>Jon</firstname><surname>Keatley</surname><order>151</order></author><author><firstname>Alan</firstname><surname>Keith</surname><order>152</order></author><author><firstname>Alison</firstname><surname>King</surname><order>153</order></author><author><firstname>Lucy</firstname><surname>Kitchin</surname><order>154</order></author><author><firstname>Matt</firstname><surname>Kleanthous</surname><order>155</order></author><author><firstname>Martina</firstname><surname>Klimekova</surname><order>156</order></author><author><firstname>Petra</firstname><surname>Korlevic</surname><order>157</order></author><author><firstname>Ksenia</firstname><surname>Krasheninnkova</surname><order>158</order></author><author><firstname>Greg</firstname><surname>Lane</surname><order>159</order></author><author><firstname>Cordelia</firstname><surname>Langford</surname><order>160</order></author><author><firstname>Adam</firstname><surname>Laverack</surname><order>161</order></author><author><firstname>Katharine</firstname><surname>Law</surname><order>162</order></author><author><firstname>Mara</firstname><surname>Lawniczak</surname><order>163</order></author><author><firstname>Stefanie</firstname><surname>Lensing</surname><order>164</order></author><author><firstname>Steven</firstname><surname>Leonard</surname><order>165</order></author><author><firstname>Laura</firstname><surname>Letchford</surname><order>166</order></author><author><firstname>Kevin</firstname><surname>Lewis</surname><order>167</order></author><author><firstname>Amanah</firstname><surname>Lewis-Wade</surname><order>168</order></author><author><firstname>Jennifer</firstname><surname>Liddle</surname><order>169</order></author><author><firstname>Quan</firstname><surname>Lin</surname><order>170</order></author><author><firstname>Sarah</firstname><surname>Lindsay</surname><order>171</order></author><author><firstname>Sally</firstname><surname>Linsdell</surname><order>172</order></author><author><firstname>Rich</firstname><surname>Livett</surname><order>173</order></author><author><firstname>Stephanie</firstname><surname>Lo</surname><order>174</order></author><author><firstname>Rhona</firstname><surname>Long</surname><order>175</order></author><author><firstname>Jamie</firstname><surname>Lovell</surname><order>176</order></author><author><firstname>Jon</firstname><surname>Lovell</surname><order>177</order></author><author><firstname>Catherine</firstname><surname>Ludden</surname><order>178</order></author><author><firstname>James</firstname><surname>Mack</surname><order>179</order></author><author><firstname>Mark</firstname><surname>Maddison</surname><order>180</order></author><author><firstname>Aleksei</firstname><surname>Makunin</surname><order>181</order></author><author><firstname>Irfan</firstname><surname>Mamun</surname><order>182</order></author><author><firstname>Jenny</firstname><surname>Mansfield</surname><order>183</order></author><author><firstname>Neil</firstname><surname>Marriott</surname><order>184</order></author><author><firstname>Matt</firstname><surname>Martin</surname><order>185</order></author><author><firstname>Matthew</firstname><surname>Mayho</surname><order>186</order></author><author><firstname>Shane</firstname><surname>McCarthy</surname><order>187</order></author><author><firstname>Jo</firstname><surname>McClintock</surname><order>188</order></author><author><firstname>Samantha</firstname><surname>McGuigan</surname><order>189</order></author><author><firstname>Sandra</firstname><surname>McHugh</surname><order>190</order></author><author><firstname>Liz</firstname><surname>McMinn</surname><order>191</order></author><author><firstname>Carl</firstname><surname>Meadows</surname><order>192</order></author><author><firstname>Emily</firstname><surname>Mobley</surname><order>193</order></author><author><firstname>Robin</firstname><surname>Moll</surname><order>194</order></author><author><firstname>Maria</firstname><surname>Morra</surname><order>195</order></author><author><firstname>Leanne</firstname><surname>Morrow</surname><order>196</order></author><author><firstname>Kathryn</firstname><surname>Murie</surname><order>197</order></author><author><firstname>Sian</firstname><surname>Nash</surname><order>198</order></author><author><firstname>Claire</firstname><surname>Nathwani</surname><order>199</order></author><author><firstname>Plamena</firstname><surname>Naydenova</surname><order>200</order></author><author><firstname>Alexandra</firstname><surname>Neaverson</surname><order>201</order></author><author><firstname>Rachel</firstname><surname>Nelson</surname><order>202</order></author><author><firstname>Ed</firstname><surname>Nerou</surname><order>203</order></author><author><firstname>Jon</firstname><surname>Nicholson</surname><order>204</order></author><author><firstname>Tabea</firstname><surname>Nimz</surname><order>205</order></author><author><firstname>Guillaume G.</firstname><surname>Noell</surname><order>206</order></author><author><firstname>Sarah</firstname><surname>O’Meara</surname><order>207</order></author><author><firstname>Valeriu</firstname><surname>Ohan</surname><order>208</order></author><author><firstname>Karen</firstname><surname>Oliver</surname><order>209</order></author><author><firstname>Charles</firstname><surname>Olney</surname><order>210</order></author><author><firstname>Doug</firstname><surname>Ormond</surname><order>211</order></author><author><firstname>Agnes</firstname><surname>Oszlanczi</surname><order>212</order></author><author><firstname>Steve</firstname><surname>Palmer</surname><order>213</order></author><author><firstname>Yoke Fei</firstname><surname>Pang</surname><order>214</order></author><author><firstname>Barbora</firstname><surname>Pardubska</surname><order>215</order></author><author><firstname>Naomi</firstname><surname>Park</surname><order>216</order></author><author><firstname>Aaron</firstname><surname>Parmar</surname><order>217</order></author><author><firstname>Gaurang</firstname><surname>Patel</surname><order>218</order></author><author><firstname>Minal</firstname><surname>Patel</surname><order>219</order></author><author><firstname>Maggie</firstname><surname>Payne</surname><order>220</order></author><author><firstname>Sharon</firstname><surname>Peacock</surname><order>221</order></author><author><firstname>Arabella</firstname><surname>Petersen</surname><order>222</order></author><author><firstname>Deborah</firstname><surname>Plowman</surname><order>223</order></author><author><firstname>Tom</firstname><surname>Preston</surname><order>224</order></author><author><firstname>Liam</firstname><surname>Prestwood</surname><order>225</order></author><author><firstname>Christoph</firstname><surname>Puethe</surname><order>226</order></author><author><firstname>Michael</firstname><surname>Quail</surname><order>227</order></author><author><firstname>Diana</firstname><surname>Rajan</surname><order>228</order></author><author><firstname>Shavanthi</firstname><surname>Rajatileka</surname><order>229</order></author><author><firstname>Richard</firstname><surname>Rance</surname><order>230</order></author><author><firstname>Suzannah</firstname><surname>Rawlings</surname><order>231</order></author><author><firstname>Nicholas</firstname><surname>Redshaw</surname><order>232</order></author><author><firstname>Joe</firstname><surname>Reynolds</surname><order>233</order></author><author><firstname>Mark</firstname><surname>Reynolds</surname><order>234</order></author><author><firstname>Simon</firstname><surname>Rice</surname><order>235</order></author><author><firstname>Matt</firstname><surname>Richardson</surname><order>236</order></author><author><firstname>Connor</firstname><surname>Roberts</surname><order>237</order></author><author><firstname>Katrina</firstname><surname>Robinson</surname><order>238</order></author><author><firstname>Melanie</firstname><surname>Robinson</surname><order>239</order></author><author><firstname>David</firstname><surname>Robinson</surname><order>240</order></author><author><firstname>Hazel</firstname><surname>Rogers</surname><order>241</order></author><author><firstname>Eduardo Martin</firstname><surname>Rojo</surname><order>242</order></author><author><firstname>Daljit</firstname><surname>Roopra</surname><order>243</order></author><author><firstname>Mark</firstname><surname>Rose</surname><order>244</order></author><author><firstname>Luke</firstname><surname>Rudd</surname><order>245</order></author><author><firstname>Ramin</firstname><surname>Sadri</surname><order>246</order></author><author><firstname>Nicholas</firstname><surname>Salmon</surname><order>247</order></author><author><firstname>David</firstname><surname>Saul</surname><order>248</order></author><author><firstname>Frank</firstname><surname>Schwach</surname><order>249</order></author><author><firstname>Carol</firstname><surname>Scott</surname><order>250</order></author><author><firstname>Phil</firstname><surname>Seekings</surname><order>251</order></author><author><firstname>Lesley</firstname><surname>Shirley</surname><order>252</order></author><author><firstname>Alison</firstname><surname>Simms</surname><order>253</order></author><author><firstname>Matthew</firstname><surname>Sinnott</surname><order>254</order></author><author><firstname>Shanthi</firstname><surname>Sivadasan</surname><order>255</order></author><author><firstname>Bart</firstname><surname>Siwek</surname><order>256</order></author><author><firstname>Dale</firstname><surname>Sizer</surname><order>257</order></author><author><firstname>Kenneth</firstname><surname>Skeldon</surname><order>258</order></author><author><firstname>Jason</firstname><surname>Skelton</surname><order>259</order></author><author><firstname>Joanna</firstname><surname>Slater-Tunstill</surname><order>260</order></author><author><firstname>Lisa</firstname><surname>Sloper</surname><order>261</order></author><author><firstname>Nathalie</firstname><surname>Smerdon</surname><order>262</order></author><author><firstname>Chris</firstname><surname>Smith</surname><order>263</order></author><author><firstname>Christen</firstname><surname>Smith</surname><order>264</order></author><author><firstname>James</firstname><surname>Smith</surname><order>265</order></author><author><firstname>Katie</firstname><surname>Smith</surname><order>266</order></author><author><firstname>Michelle</firstname><surname>Smith</surname><order>267</order></author><author><firstname>Sean</firstname><surname>Smith</surname><order>268</order></author><author><firstname>Tina</firstname><surname>Smith</surname><order>269</order></author><author><firstname>Leighton</firstname><surname>Sneade</surname><order>270</order></author><author><firstname>Carmen Diaz</firstname><surname>Soria</surname><order>271</order></author><author><firstname>Catarina</firstname><surname>Sousa</surname><order>272</order></author><author><firstname>Emily</firstname><surname>Souster</surname><order>273</order></author><author><firstname>Andrew</firstname><surname>Sparkes</surname><order>274</order></author><author><firstname>Michael</firstname><surname>Spencer-Chapman</surname><order>275</order></author><author><firstname>Janet</firstname><surname>Squares</surname><order>276</order></author><author><firstname>Robert</firstname><surname>Stanley</surname><order>277</order></author><author><firstname>Claire</firstname><surname>Steed</surname><order>278</order></author><author><firstname>Tim</firstname><surname>Stickland</surname><order>279</order></author><author><firstname>Ian</firstname><surname>Still</surname><order>280</order></author><author><firstname>Michael R.</firstname><surname>Stratton</surname><order>281</order></author><author><firstname>Michelle</firstname><surname>Strickland</surname><order>282</order></author><author><firstname>Allen</firstname><surname>Swann</surname><order>283</order></author><author><firstname>Agnieszka</firstname><surname>Swiatkowska</surname><order>284</order></author><author><firstname>Neil</firstname><surname>Sycamore</surname><order>285</order></author><author><firstname>Emma</firstname><surname>Swift</surname><order>286</order></author><author><firstname>Edward</firstname><surname>Symons</surname><order>287</order></author><author><firstname>Suzanne</firstname><surname>Szluha</surname><order>288</order></author><author><firstname>Emma</firstname><surname>Taluy</surname><order>289</order></author><author><firstname>Nunu</firstname><surname>Tao</surname><order>290</order></author><author><firstname>Katy</firstname><surname>Taylor</surname><order>291</order></author><author><firstname>Sam</firstname><surname>Taylor</surname><order>292</order></author><author><firstname>Stacey</firstname><surname>Thompson</surname><order>293</order></author><author><firstname>Mark</firstname><surname>Thompson</surname><order>294</order></author><author><firstname>Mark</firstname><surname>Thomson</surname><order>295</order></author><author><firstname>Nicholas</firstname><surname>Thomson</surname><order>296</order></author><author><firstname>Scott</firstname><surname>Thurston</surname><order>297</order></author><author><firstname>Gerry</firstname><surname>Tonkin-Hill</surname><order>298</order></author><author><firstname>Dee</firstname><surname>Toombs</surname><order>299</order></author><author><firstname>Benjamin</firstname><surname>Topping</surname><order>300</order></author><author><firstname>Jaime</firstname><surname>Tovar-Corona</surname><order>301</order></author><author><firstname>Daniel</firstname><surname>Ungureanu</surname><order>302</order></author><author><firstname>James</firstname><surname>Uphill</surname><order>303</order></author><author><firstname>Jana</firstname><surname>Urbanova</surname><order>304</order></author><author><firstname>Philip Jansen Van</firstname><surname>Vuuren</surname><order>305</order></author><author><firstname>Valerie</firstname><surname>Vancollie</surname><order>306</order></author><author><firstname>Paul</firstname><surname>Voak</surname><order>307</order></author><author><firstname>Danielle</firstname><surname>Walker</surname><order>308</order></author><author><firstname>Matthew</firstname><surname>Walker</surname><order>309</order></author><author><firstname>Matt</firstname><surname>Waller</surname><order>310</order></author><author><firstname>Gary</firstname><surname>Ward</surname><order>311</order></author><author><firstname>Charlie</firstname><surname>Weatherhogg</surname><order>312</order></author><author><firstname>Niki</firstname><surname>Webb</surname><order>313</order></author><author><firstname>Danni</firstname><surname>Weldon</surname><order>314</order></author><author><firstname>Alan</firstname><surname>Wells</surname><order>315</order></author><author><firstname>Eloise</firstname><surname>Wells</surname><order>316</order></author><author><firstname>Luke</firstname><surname>Westwood</surname><order>317</order></author><author><firstname>Theo</firstname><surname>Whipp</surname><order>318</order></author><author><firstname>Thomas</firstname><surname>Whiteley</surname><order>319</order></author><author><firstname>Georgia</firstname><surname>Whitton</surname><order>320</order></author><author><firstname>Andrew</firstname><surname>Whitwham</surname><order>321</order></author><author><firstname>Sara</firstname><surname>Widaa</surname><order>322</order></author><author><firstname>Mia</firstname><surname>Williams</surname><order>323</order></author><author><firstname>Mark</firstname><surname>Wilson</surname><order>324</order></author><author><firstname>Sean</firstname><surname>Wright</surname><order>325</order></author><author><firstname>Samuel 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Martinez</firstname><surname>Nunez</surname><order>330</order></author><author><firstname>David</firstname><surname>Bonsall</surname><order>331</order></author><author><firstname>Andrew</firstname><surname>Rambaut</surname><order>332</order></author><author><firstname>Luke B.</firstname><surname>Snell</surname><order>333</order></author><author><firstname>Catherine</firstname><surname>Ludden</surname><order>334</order></author><author><firstname>Sally</firstname><surname>Corden</surname><order>335</order></author><author><firstname>Eleni</firstname><surname>Nastouli</surname><order>336</order></author><author><firstname>Gaia</firstname><surname>Nebbia</surname><order>337</order></author><author><firstname>Katrina</firstname><surname>Lythgoe</surname><order>338</order></author><author><firstname>M. Estee</firstname><surname>Torok</surname><order>339</order></author><author><firstname>Ian G.</firstname><surname>Goodfellow</surname><order>340</order></author><author><firstname>Jacqui A.</firstname><surname>Prieto</surname><order>341</order></author><author><firstname>Kordo</firstname><surname>Saeed</surname><order>342</order></author><author><firstname>Catherine</firstname><surname>Houlihan</surname><order>343</order></author><author><firstname>Dan</firstname><surname>Frampton</surname><order>344</order></author><author><firstname>William L.</firstname><surname>Hamilton</surname><order>345</order></author><author><firstname>Adam A.</firstname><surname>Witney</surname><order>346</order></author><author><firstname>Giselda</firstname><surname>Bucca</surname><order>347</order></author><author><firstname>Cassie F.</firstname><surname>Pope</surname><order>348</order></author><author><firstname>Catherine</firstname><surname>Moore</surname><order>349</order></author><author><firstname>Emma 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M.</firstname><surname>Jackson</surname><order>360</order></author><author><firstname>Sónia</firstname><surname>Gonçalves</surname><order>361</order></author><author><firstname>Derek J.</firstname><surname>Fairley</surname><order>362</order></author><author><firstname>Matthew W.</firstname><surname>Loose</surname><order>363</order></author><author><firstname>Joanne</firstname><surname>Watkins</surname><order>364</order></author><author><firstname>Samuel</firstname><surname>Moses</surname><order>365</order></author><author><firstname>Sam</firstname><surname>Nicholls</surname><order>366</order></author><author><firstname>Matthew</firstname><surname>Bull</surname><order>367</order></author><author><firstname>Darren L.</firstname><surname>Smith</surname><order>368</order></author><author><firstname>David M.</firstname><surname>Aanensen</surname><order>369</order></author><author><firstname>Dinesh</firstname><surname>Aggarwal</surname><order>370</order></author><author><firstname>James 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R.</firstname><surname>Crown</surname><order>439</order></author><author><firstname>Sara</firstname><surname>Rey</surname><order>440</order></author><author><firstname>Sunando</firstname><surname>Roy</surname><order>441</order></author><author><firstname>Ben</firstname><surname>Temperton</surname><order>442</order></author><author><firstname>Sharif</firstname><surname>Shaaban</surname><order>443</order></author><author><firstname>Andrew R.</firstname><surname>Hesketh</surname><order>444</order></author><author><firstname>Kenneth G.</firstname><surname>Laing</surname><order>445</order></author><author><firstname>Irene 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T.</firstname><surname>Pritchard</surname><order>476</order></author><author><firstname>Samir</firstname><surname>Dervisevic</surname><order>477</order></author><author><firstname>Peter</firstname><surname>Muir</surname><order>478</order></author><author><firstname>Esther</firstname><surname>Robinson</surname><order>479</order></author><author><firstname>Barry B.</firstname><surname>Vipond</surname><order>480</order></author><author><firstname>Newara A.</firstname><surname>Ramadan</surname><order>481</order></author><author><firstname>Christopher</firstname><surname>Jeanes</surname><order>482</order></author><author><firstname>Jana</firstname><surname>Catalan</surname><order>483</order></author><author><firstname>Neil</firstname><surname>Jones</surname><order>484</order></author><author><firstname>Ana da Silva</firstname><surname>Filipe</surname><order>485</order></author><author><firstname>Chris</firstname><surname>Williams</surname><order>486</order></author><author><firstname>Marc</firstname><surname>Fuchs</surname><order>487</order></author><author><firstname>Julia</firstname><surname>Miskelly</surname><order>488</order></author><author><firstname>Aaron R.</firstname><surname>Jeffries</surname><order>489</order></author><author><firstname>Naomi R.</firstname><surname>Park</surname><order>490</order></author><author><firstname>Amy</firstname><surname>Ash</surname><order>491</order></author><author><firstname>Cherian</firstname><surname>Koshy</surname><order>492</order></author><author><firstname>Magdalena</firstname><surname>Barrow</surname><order>493</order></author><author><firstname>Sarah L.</firstname><surname>Buchan</surname><order>494</order></author><author><firstname>Anna</firstname><surname>Mantzouratou</surname><order>495</order></author><author><firstname>Gemma</firstname><surname>Clark</surname><order>496</order></author><author><firstname>Christopher W.</firstname><surname>Holmes</surname><order>497</order></author><author><firstname>Sharon</firstname><surname>Campbell</surname><order>498</order></author><author><firstname>Thomas</firstname><surname>Davis</surname><order>499</order></author><author><firstname>Ngee Keong</firstname><surname>Tan</surname><order>500</order></author><author><firstname>Julianne R.</firstname><surname>Brown</surname><order>501</order></author><author><firstname>Kathryn A.</firstname><surname>Harris</surname><order>502</order></author><author><firstname>Stephen P.</firstname><surname>Kidd</surname><order>503</order></author><author><firstname>Paul 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spelling v2 66422 2024-05-15 Genomic reconstruction of the SARS-CoV-2 epidemic in England 83efcf2a9dfcf8b55586999d3d152ac6 0000-0001-5225-000X Ronan Lyons Ronan Lyons true false 2024-05-15 MEDS 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. Journal Article Nature 600 7889 506 511 Springer Science and Business Media LLC 0028-0836 1476-4687 16 12 2021 2021-12-16 10.1038/s41586-021-04069-y Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England available at https://doi.org/10.1038/s41586-022-04887-8 COLLEGE NANME Medical School COLLEGE CODE MEDS Swansea University Open access funding provided by Deutsches Krebsforschungszentrum (DKFZ). 2024-06-24T12:29:31.9625493 2024-05-15T08:23:25.2739890 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Health Data Science Harald S. Vöhringer 1 Theo Sanderson 2 Matthew Sinnott 0000-0002-3054-7846 3 Nicola De Maio 4 Thuy Nguyen 5 Richard Goater 0000-0001-9954-841x 6 Frank Schwach 7 Ian Harrison 0000-0003-4117-961x 8 Joel Hellewell 0000-0003-2683-0849 9 Cristina V. Ariani 10 Sonia Gonçalves 11 David K. Jackson 0000-0002-8090-9462 12 Ian Johnston 13 Alexander W. Jung 14 Callum Saint 0000-0001-8720-9736 15 John Sillitoe 16 Maria Suciu 17 Nick Goldman 0000-0001-8486-2211 18 Jasmina Panovska-Griffiths 0000-0002-7720-1121 19 Irina Abnizova 20 Louise Aigrain 21 Alex Alderton 22 Mozam Ali 23 Laura Allen 24 Roberto Amato 25 Ralph Anderson 26 Cristina Ariani 27 Siobhan Austin-Guest 28 Sendu Bala 29 Jeffrey Barrett 30 Andrew Bassett 31 Kristina Battleday 32 James Beal 33 Mathew Beale 34 Charlotte Beaver 35 Sam Bellany 36 Tristram Bellerby 37 Katie Bellis 38 Duncan Berger 39 Matt Berriman 40 Emma Betteridge 41 Paul Bevan 42 Simon Binley 43 Jason Bishop 44 Kirsty Blackburn 45 James Bonfield 46 Nick Boughton 47 Sam Bowker 48 Timothy Brendler-Spaeth 49 Iraad Bronner 50 Tanya Brooklyn 51 Sarah Kay Buddenborg 52 Robert Bush 53 Catarina Caetano 54 Alex Cagan 55 Nicola Carter 56 Joanna Cartwright 57 Tiago Carvalho Monteiro 58 Liz Chapman 59 Tracey-Jane Chillingworth 60 Peter Clapham 61 Richard Clark 62 Adrian Clarke 63 Catriona Clarke 64 Daryl Cole 65 Elizabeth Cook 66 Maria Coppola 67 Linda Cornell 68 Clare Cornwell 69 Craig Corton 70 Abby Crackett 71 Alison Cranage 72 Harriet Craven 73 Sarah Craw 74 Mark Crawford 75 Tim Cutts 76 Monika Dabrowska 77 Matt Davies 78 Robert Davies 79 Joseph Dawson 80 Callum Day 81 Aiden Densem 82 Thomas Dibling 83 Cat Dockree 84 David Dodd 85 Sunil Dogga 86 Matthew Dorman 87 Gordon Dougan 88 Martin Dougherty 89 Alexander Dove 90 Lucy Drummond 91 Eleanor Drury 92 Monika Dudek 93 Jillian Durham 94 Laura Durrant 95 Elizabeth Easthope 96 Sabine Eckert 97 Pete Ellis 98 Ben Farr 99 Michael Fenton 100 Marcella Ferrero 101 Neil Flack 102 Howerd Fordham 103 Grace Forsythe 104 Luke Foulser 105 Matt Francis 106 Audrey Fraser 107 Adam Freeman 108 Anastasia Galvin 109 Maria Garcia-Casado 110 Alex Gedny 111 Sophia Girgis 112 James Glover 113 Sonia Goncalves 114 Scott Goodwin 115 Oliver Gould 116 Marina Gourtovaia 117 Andy Gray 118 Emma Gray 119 Coline Griffiths 120 Yong Gu 121 Florence Guerin 122 Will Hamilton 123 Hannah Hanks 124 Ewan Harrison 125 Alexandria Harrott 126 Edward Harry 127 Julia Harvison 128 Paul Heath 129 Anastasia Hernandez-Koutoucheva 130 Rhiannon Hobbs 131 Dave Holland 132 Sarah Holmes 133 Gary Hornett 134 Nicholas Hough 135 Liz Huckle 136 Lena Hughes-Hallet 137 Adam Hunter 138 Stephen Inglis 139 Sameena Iqbal 140 Adam Jackson 141 David Jackson 142 Keith James 143 Dorota Jamrozy 144 Carlos Jimenez Verdejo 145 Matthew Jones 146 Kalyan Kallepally 147 Leanne Kane 148 Keely Kay 149 Sally Kay 150 Jon Keatley 151 Alan Keith 152 Alison King 153 Lucy Kitchin 154 Matt Kleanthous 155 Martina Klimekova 156 Petra Korlevic 157 Ksenia Krasheninnkova 158 Greg Lane 159 Cordelia Langford 160 Adam Laverack 161 Katharine Law 162 Mara Lawniczak 163 Stefanie Lensing 164 Steven Leonard 165 Laura Letchford 166 Kevin Lewis 167 Amanah Lewis-Wade 168 Jennifer Liddle 169 Quan Lin 170 Sarah Lindsay 171 Sally Linsdell 172 Rich Livett 173 Stephanie Lo 174 Rhona Long 175 Jamie Lovell 176 Jon Lovell 177 Catherine Ludden 178 James Mack 179 Mark Maddison 180 Aleksei Makunin 181 Irfan Mamun 182 Jenny Mansfield 183 Neil Marriott 184 Matt Martin 185 Matthew Mayho 186 Shane McCarthy 187 Jo McClintock 188 Samantha McGuigan 189 Sandra McHugh 190 Liz McMinn 191 Carl Meadows 192 Emily Mobley 193 Robin Moll 194 Maria Morra 195 Leanne Morrow 196 Kathryn Murie 197 Sian Nash 198 Claire Nathwani 199 Plamena Naydenova 200 Alexandra Neaverson 201 Rachel Nelson 202 Ed Nerou 203 Jon Nicholson 204 Tabea Nimz 205 Guillaume G. Noell 206 Sarah O’Meara 207 Valeriu Ohan 208 Karen Oliver 209 Charles Olney 210 Doug Ormond 211 Agnes Oszlanczi 212 Steve Palmer 213 Yoke Fei Pang 214 Barbora Pardubska 215 Naomi Park 216 Aaron Parmar 217 Gaurang Patel 218 Minal Patel 219 Maggie Payne 220 Sharon Peacock 221 Arabella Petersen 222 Deborah Plowman 223 Tom Preston 224 Liam Prestwood 225 Christoph Puethe 226 Michael Quail 227 Diana Rajan 228 Shavanthi Rajatileka 229 Richard Rance 230 Suzannah Rawlings 231 Nicholas Redshaw 232 Joe Reynolds 233 Mark Reynolds 234 Simon Rice 235 Matt Richardson 236 Connor Roberts 237 Katrina Robinson 238 Melanie Robinson 239 David Robinson 240 Hazel Rogers 241 Eduardo Martin Rojo 242 Daljit Roopra 243 Mark Rose 244 Luke Rudd 245 Ramin Sadri 246 Nicholas Salmon 247 David Saul 248 Frank Schwach 249 Carol Scott 250 Phil Seekings 251 Lesley Shirley 252 Alison Simms 253 Matthew Sinnott 254 Shanthi Sivadasan 255 Bart Siwek 256 Dale Sizer 257 Kenneth Skeldon 258 Jason Skelton 259 Joanna Slater-Tunstill 260 Lisa Sloper 261 Nathalie Smerdon 262 Chris Smith 263 Christen Smith 264 James Smith 265 Katie Smith 266 Michelle Smith 267 Sean Smith 268 Tina Smith 269 Leighton Sneade 270 Carmen Diaz Soria 271 Catarina Sousa 272 Emily Souster 273 Andrew Sparkes 274 Michael Spencer-Chapman 275 Janet Squares 276 Robert Stanley 277 Claire Steed 278 Tim Stickland 279 Ian Still 280 Michael R. Stratton 281 Michelle Strickland 282 Allen Swann 283 Agnieszka Swiatkowska 284 Neil Sycamore 285 Emma Swift 286 Edward Symons 287 Suzanne Szluha 288 Emma Taluy 289 Nunu Tao 290 Katy Taylor 291 Sam Taylor 292 Stacey Thompson 293 Mark Thompson 294 Mark Thomson 295 Nicholas Thomson 296 Scott Thurston 297 Gerry Tonkin-Hill 298 Dee Toombs 299 Benjamin Topping 300 Jaime Tovar-Corona 301 Daniel Ungureanu 302 James Uphill 303 Jana Urbanova 304 Philip Jansen Van Vuuren 305 Valerie Vancollie 306 Paul Voak 307 Danielle Walker 308 Matthew Walker 309 Matt Waller 310 Gary Ward 311 Charlie Weatherhogg 312 Niki Webb 313 Danni Weldon 314 Alan Wells 315 Eloise Wells 316 Luke Westwood 317 Theo Whipp 318 Thomas Whiteley 319 Georgia Whitton 320 Andrew Whitwham 321 Sara Widaa 322 Mia Williams 323 Mark Wilson 324 Sean Wright 325 Samuel C. Robson 326 Thomas R. Connor 327 Nicholas J. Loman 328 Tanya Golubchik 329 Rocio T. Martinez Nunez 330 David Bonsall 331 Andrew Rambaut 332 Luke B. Snell 333 Catherine Ludden 334 Sally Corden 335 Eleni Nastouli 336 Gaia Nebbia 337 Katrina Lythgoe 338 M. Estee Torok 339 Ian G. Goodfellow 340 Jacqui A. Prieto 341 Kordo Saeed 342 Catherine Houlihan 343 Dan Frampton 344 William L. Hamilton 345 Adam A. Witney 346 Giselda Bucca 347 Cassie F. Pope 348 Catherine Moore 349 Emma C. Thomson 350 Ewan M. Harrison 351 Colin P. Smith 352 Fiona Rogan 353 Shaun M. Beckwith 354 Abigail Murray 355 Dawn Singleton 356 Kirstine Eastick 357 Liz A. Sheridan 358 Paul Randell 359 Leigh M. Jackson 360 Sónia Gonçalves 361 Derek J. Fairley 362 Matthew W. Loose 363 Joanne Watkins 364 Samuel Moses 365 Sam Nicholls 366 Matthew Bull 367 Darren L. Smith 368 David M. Aanensen 369 Dinesh Aggarwal 370 James G. Shepherd 371 Martin D. Curran 372 Surendra Parmar 373 Matthew D. Parker 374 Catryn Williams 375 Sharon Glaysher 376 Anthony P. Underwood 377 Matthew Bashton 378 Nicole Pacchiarini 379 Katie F. Loveson 380 Matthew Byott 381 Alessandro M. Carabelli 382 Kate E. Templeton 383 Thushan I. de Silva 384 Dennis Wang 385 Cordelia F. Langford 386 Rory N. Gunson 387 Simon Cottrell 388 Justin O’Grady 389 Dominic Kwiatkowski 390 Patrick J. Lillie 391 Nicholas Cortes 392 Nathan Moore 393 Claire Thomas 394 Phillipa J. Burns 395 Tabitha W. Mahungu 396 Steven Liggett 397 Angela H. Beckett 398 Matthew T. G. Holden 399 Lisa J. Levett 400 Husam Osman 401 Mohammed O. Hassan-Ibrahim 402 David A. Simpson 403 Meera Chand 404 Ravi K. Gupta 405 Alistair C. Darby 406 Steve Paterson 407 Oliver G. Pybus 408 Erik Volz 409 Daniela de Angelis 410 David L. Robertson 411 Andrew J. Page 412 Andrew R. Bassett 413 Nick Wong 414 Yusri Taha 415 Michelle J. Erkiert 416 Michael H. Spencer Chapman 417 Rebecca Dewar 418 Martin P. McHugh 419 Siddharth Mookerjee 420 Stephen Aplin 421 Matthew Harvey 422 Thea Sass 423 Helen Umpleby 424 Helen Wheeler 425 James P. McKenna 426 Ben Warne 427 Joshua F. Taylor 428 Yasmin Chaudhry 429 Rhys Izuagbe 430 Aminu S. Jahun 431 Gregory R. Young 432 Claire McMurray 433 Clare M. McCann 434 Andrew Nelson 435 Scott Elliott 436 Hannah Lowe 437 Anna Price 438 Matthew R. Crown 439 Sara Rey 440 Sunando Roy 441 Ben Temperton 442 Sharif Shaaban 443 Andrew R. Hesketh 444 Kenneth G. Laing 445 Irene M. Monahan 446 Judith Heaney 447 Emanuela Pelosi 448 Siona Silviera 449 Eleri Wilson-Davies 450 Helen Fryer 451 Helen Adams 452 Louis du Plessis 453 Rob Johnson 454 William T. Harvey 455 Joseph Hughes 456 Richard J. Orton 457 Lewis G. Spurgin 458 Yann Bourgeois 459 Chris Ruis 460 Áine O’Toole 461 Theo Sanderson 462 Christophe Fraser 463 Jonathan Edgeworth 464 Judith Breuer 465 Stephen L. Michell 466 John A. Todd 467 Michaela John 468 David Buck 469 Kavitha Gajee 470 Gemma L. Kay 471 Sharon J. Peacock 472 David Heyburn 473 Katie Kitchman 474 Alan McNally 475 David T. Pritchard 476 Samir Dervisevic 477 Peter Muir 478 Esther Robinson 479 Barry B. Vipond 480 Newara A. Ramadan 481 Christopher Jeanes 482 Jana Catalan 483 Neil Jones 484 Ana da Silva Filipe 485 Chris Williams 486 Marc Fuchs 487 Julia Miskelly 488 Aaron R. Jeffries 489 Naomi R. Park 490 Amy Ash 491 Cherian Koshy 492 Magdalena Barrow 493 Sarah L. Buchan 494 Anna Mantzouratou 495 Gemma Clark 496 Christopher W. Holmes 497 Sharon Campbell 498 Thomas Davis 499 Ngee Keong Tan 500 Julianne R. Brown 501 Kathryn A. Harris 502 Stephen P. Kidd 503 Paul R. Grant 504 Li Xu-McCrae 505 Alison Cox 506 Pinglawathee Madona 507 Marcus Pond 508 Paul A. Randell 509 Karen T. Withell 510 Cheryl Williams 511 Clive Graham 512 Rebecca Denton-Smith 513 Emma Swindells 514 Robyn Turnbull 515 Tim J. Sloan 516 Andrew Bosworth 517 Stephanie Hutchings 518 Hannah M. Pymont 519 Anna Casey 520 Liz Ratcliffe 521 Christopher R. Jones 522 Bridget A. Knight 523 Tanzina Haque 524 Jennifer Hart 525 Dianne Irish-Tavares 526 Eric Witele 527 Craig Mower 528 Louisa K. Watson 529 Jennifer Collins 530 Gary Eltringham 531 Dorian Crudgington 532 Ben Macklin 533 Miren Iturriza-Gomara 534 Anita O. Lucaci 535 Patrick C. McClure 536 Matthew Carlile 537 Nadine Holmes 538 Christopher Moore 539 Nathaniel Storey 540 Stefan Rooke 541 Gonzalo Yebra 542 Noel Craine 543 Malorie Perry 544 Nabil-Fareed Alikhan 545 Stephen Bridgett 546 Kate F. Cook 547 Christopher Fearn 548 Salman Goudarzi 549 Ronan A. Lyons 550 Thomas Williams 551 Sam T. Haldenby 552 Robert M. Davies 553 Rahul Batra 554 Beth Blane 555 Moira J. Spyer 556 Perminder Smith 557 Mehmet Yavus 558 Rachel J. Williams 559 Adhyana I. K. Mahanama 560 Buddhini Samaraweera 561 Sophia T. Girgis 562 Samantha E. Hansford 563 Angie Green 564 Katherine L. Bellis 565 Matthew J. Dorman 566 Joshua Quick 567 Radoslaw Poplawski 568 Nicola Reynolds 569 Andrew Mack 570 Arthur Morriss 571 Thomas Whalley 572 Bindi Patel 573 Iliana Georgana 574 Myra Hosmillo 575 Malte L. Pinckert 576 Joanne Stockton 577 John H. Henderson 578 Amy Hollis 579 William Stanley 580 Wen C. Yew 581 Richard Myers 582 Alicia Thornton 583 Alexander Adams 584 Tara Annett 585 Hibo Asad 586 Alec Birchley 587 Jason Coombes 588 Johnathan M. Evans 589 Laia Fina 590 Bree Gatica-Wilcox 591 Lauren Gilbert 592 Lee Graham 593 Jessica Hey 594 Ember Hilvers 595 Sophie Jones 596 Hannah Jones 597 Sara Kumziene-Summerhayes 598 Caoimhe McKerr 599 Jessica Powell 600 Georgia Pugh 601 Sarah Taylor 602 Alexander J. Trotter 603 Charlotte A. Williams 604 Leanne M. Kermack 605 Benjamin H. Foulkes 606 Marta Gallis 607 Hailey R. Hornsby 608 Stavroula F. Louka 609 Manoj Pohare 610 Paige Wolverson 611 Peijun Zhang 612 George MacIntyre-Cockett 613 Amy Trebes 614 Robin J. Moll 615 Lynne Ferguson 616 Emily J. Goldstein 617 Alasdair Maclean 618 Rachael Tomb 619 Igor Starinskij 620 Laura Thomson 621 Joel Southgate 622 Moritz U. G. Kraemer 623 Jayna Raghwani 624 Alex E. Zarebski 625 Olivia Boyd 626 Lily Geidelberg 627 Chris J. Illingworth 628 Chris Jackson 629 David Pascall 630 Sreenu Vattipally 631 Timothy M. Freeman 632 Sharon N. Hsu 633 Benjamin B. Lindsey 634 Jaime M. Tovar-Corona 635 MacGregor Cox 636 Khalil Abudahab 637 Mirko Menegazzo 638 Ben E. W. Taylor 639 Corin A. Yeats 640 Afrida Mukaddas 641 Derek W. Wright 642 Leonardo de Oliveira Martins 643 Rachel Colquhoun 644 Verity Hill 645 Ben Jackson 646 J. T. McCrone 647 Nathan Medd 648 Emily Scher 649 Jon-Paul Keatley 650 Tanya Curran 651 Sian Morgan 652 Patrick Maxwell 653 Ken Smith 654 Sahar Eldirdiri 655 Anita Kenyon 656 Alison H. Holmes 657 James R. Price 658 Tim Wyatt 659 Alison E. Mather 660 Timofey Skvortsov 661 John A. Hartley 662 Martyn Guest 663 Christine Kitchen 664 Ian Merrick 665 Robert Munn 666 Beatrice Bertolusso 667 Jessica Lynch 668 Gabrielle Vernet 669 Stuart Kirk 670 Elizabeth Wastnedge 671 Rachael Stanley 672 Giles Idle 673 Declan T. Bradley 674 Jennifer Poyner 675 Matilde Mori 676 Owen Jones 677 Victoria Wright 678 Ellena Brooks 679 Carol M. Churcher 680 Mireille Fragakis 681 Katerina Galai 682 Andrew Jermy 683 Sarah Judges 684 Georgina M. McManus 685 Kim S. Smith 686 Elaine Westwick 687 Stephen W. Attwood 688 Frances Bolt 689 Alisha Davies 690 Elen De Lacy 691 Fatima Downing 692 Sue Edwards 693 Lizzie Meadows 694 Sarah Jeremiah 695 Nikki Smith 696 Themoula Charalampous 697 Amita Patel 698 Louise Berry 699 Tim Boswell 700 Vicki M. Fleming 701 Hannah C. Howson-Wells 702 Amelia Joseph 703 Manjinder Khakh 704 Michelle M. Lister 705 Paul W. Bird 706 Karlie Fallon 707 Thomas Helmer 708 Claire L. McMurray 709 Mina Odedra 710 Jessica Shaw 711 Julian W. Tang 712 Nicholas J. Willford 713 Victoria Blakey 714 Veena Raviprakash 715 Nicola Sheriff 716 Lesley-Anne Williams 717 Theresa Feltwell 718 Luke Bedford 719 James S. Cargill 720 Warwick Hughes 721 Jonathan Moore 722 Susanne Stonehouse 723 Laura Atkinson 724 Jack C. D. Lee 725 Divya Shah 726 Adela Alcolea 727 Natasha Ohemeng-Kumi 728 John Ramble 729 Jasveen Sehmi 730 Rebecca Williams 731 Wendy Chatterton 732 Monika Pusok 733 William Everson 734 Anibolina Castigador 735 Emily Macnaughton 736 Kate El Bouzidi 737 Temi Lampejo 738 Malur Sudhanva 739 Cassie Breen 740 Graciela Sluga 741 Shazaad S. Y. Ahmad 742 Ryan P. George 743 Nicholas W. Machin 744 Debbie Binns 745 Victoria James 746 Rachel Blacow 747 Lindsay Coupland 748 Louise Smith 749 Edward Barton 750 Debra Padgett 751 Garren Scott 752 Aidan Cross 753 Mariyam Mirfenderesky 754 Jane Greenaway 755 Kevin Cole 756 Phillip Clarke 757 Nichola Duckworth 758 Sarah Walsh 759 Kelly Bicknell 760 Robert Impey 761 Sarah Wyllie 762 Richard Hopes 763 Chloe Bishop 764 Vicki Chalker 765 Laura Gifford 766 Zoltan Molnar 767 Cressida Auckland 768 Cariad Evans 769 Kate Johnson 770 David G. Partridge 771 Mohammad Raza 772 Paul Baker 773 Stephen Bonner 774 Sarah Essex 775 Leanne J. Murray 776 Andrew I. Lawton 777 Shirelle Burton-Fanning 778 Brendan A. I. Payne 779 Sheila Waugh 780 Andrea N. Gomes 781 Maimuna Kimuli 782 Darren R. Murray 783 Paula Ashfield 784 Donald Dobie 785 Fiona Ashford 786 Angus Best 787 Liam Crawford 788 Nicola Cumley 789 Megan Mayhew 790 Oliver Megram 791 Jeremy Mirza 792 Emma Moles-Garcia 793 Benita Percival 794 Leah Ensell 795 Helen L. Lowe 796 Laurentiu Maftei 797 Matteo Mondani 798 Nicola J. Chaloner 799 Benjamin J. Cogger 800 Lisa J. Easton 801 Hannah Huckson 802 Jonathan Lewis 803 Sarah Lowdon 804 Cassandra S. Malone 805 Florence Munemo 806 Manasa Mutingwende 807 Roberto Nicodemi 808 Olga Podplomyk 809 Thomas Somassa 810 Andrew Beggs 811 Alex Richter 812 Claire Cormie 813 Joana Dias 814 Sally Forrest 815 Ellen E. Higginson 816 Mailis Maes 817 Jamie Young 818 Rose K. Davidson 819 Kathryn A. Jackson 820 Lance Turtle 821 Alexander J. Keeley 822 Jonathan Ball 823 Timothy Byaruhanga 824 Joseph G. Chappell 825 Jayasree Dey 826 Jack D. Hill 827 Emily J. Park 828 Arezou Fanaie 829 Rachel A. Hilson 830 Geraldine Yaze 831 Safiah Afifi 832 Robert Beer 833 Joshua Maksimovic 834 Kathryn McCluggage Masters 835 Karla Spellman 836 Catherine Bresner 837 William Fuller 838 Angela Marchbank 839 Trudy Workman 840 Ekaterina Shelest 841 Johnny Debebe 842 Fei Sang 843 Marina Escalera Zamudio 844 Sarah Francois 845 Bernardo Gutierrez 846 Tetyana I. Vasylyeva 847 Flavia Flaviani 848 Manon Ragonnet-Cronin 849 Katherine L. Smollett 850 Alice Broos 851 Daniel Mair 852 Jenna Nichols 853 Kyriaki Nomikou 854 Lily Tong 855 Ioulia Tsatsani 856 Sarah O’Brien 857 Steven Rushton 858 Roy Sanderson 859 Jon Perkins 860 Seb Cotton 861 Abbie Gallagher 862 Elias Allara 863 Clare Pearson 864 David Bibby 865 Gavin Dabrera 866 Nicholas Ellaby 867 Eileen Gallagher 868 Jonathan Hubb 869 Angie Lackenby 870 David Lee 871 Nikos Manesis 872 Tamyo Mbisa 873 Steven Platt 874 Katherine A. Twohig 875 Mari Morgan 876 Alp Aydin 877 David J. Baker 878 Ebenezer Foster-Nyarko 879 Sophie J. Prosolek 880 Steven Rudder 881 Chris Baxter 882 Sílvia F. Carvalho 883 Deborah Lavin 884 Arun Mariappan 885 Clara Radulescu 886 Aditi Singh 887 Miao Tang 888 Helen Morcrette 889 Nadua Bayzid 890 Marius Cotic 891 Carlos E. Balcazar 892 Michael D. Gallagher 893 Daniel Maloney 894 Thomas D. Stanton 895 Kathleen A. Williamson 896 Robin Manley 897 Michelle L. Michelsen 898 Christine M. Sambles 899 David J. Studholme 900 Joanna Warwick-Dugdale 901 Richard Eccles 902 Matthew Gemmell 903 Richard Gregory 904 Margaret Hughes 905 Charlotte Nelson 906 Lucille Rainbow 907 Edith E. Vamos 908 Hermione J. Webster 909 Mark Whitehead 910 Claudia Wierzbicki 911 Adrienn Angyal 912 Luke R. Green 913 Max Whiteley 914 Iraad F. Bronner 915 Ben W. Farr 916 Stefanie V. Lensing 917 Shane A. McCarthy 918 Michael A. Quail 919 Nicholas M. Redshaw 920 Scott A. J. Thurston 921 Will Rowe 922 Amy Gaskin 923 Thanh Le-Viet 924 Jennifier Liddle 925 Ewan Birney 0000-0001-8314-8497 926 Erik Volz 0000-0001-6268-8937 927 Sebastian Funk 0000-0002-2842-3406 928 Dominic Kwiatkowski 0000-0002-5023-0176 929 Meera Chand 930 Inigo Martincorena 0000-0003-1122-4416 931 Jeffrey C. Barrett 0000-0002-1152-370x 932 Moritz Gerstung 0000-0001-6709-963x 933 (The Wellcome Sanger Institute COVID-19 Surveillance Team) 934 (The COVID-19 Genomics UK (COG-UK) Consortium*) 935 (Funding acquisition, leadership and supervision, metadata curation, project administration, samples and logistics, sequencing and analysis, software and analysis tools, and visualization) 936 (Funding acquisition, leadership and supervision, metadata curation, project administration, samples and logistics, sequencing and analysis, and software and analysis tools) 937 (Leadership and supervision, metadata curation, project administration, samples and logistics, sequencing and analysis, software and analysis tools, and visualization) 938 (Funding acquisition, leadership and supervision, metadata curation, samples and logistics, sequencing and analysis, and visualization) 939 (Funding acquisition, leadership and supervision, project administration, samples and logistics, sequencing and analysis, and software and analysis tools) 940 (Funding acquisition, leadership and supervision, project administration, sequencing and analysis, software and analysis tools, and visualization) 941 (Funding acquisition, metadata curation, project administration, samples and logistics, sequencing and analysis, and software and analysis tools) 942 (Leadership and supervision, metadata curation, project administration, samples and logistics, software and analysis tools, and visualization) 943 (Funding acquisition, leadership and supervision, metadata curation, project administration, and samples and logistics) 944 (Funding acquisition, leadership and supervision, metadata curation, samples and logistics, and sequencing and analysis) 945 (Funding acquisition, leadership and supervision, metadata curation, sequencing and analysis, and software and analysis tools) 946 (Funding acquisition, leadership and supervision, project administration, samples and logistics, and sequencing and analysis) 947 (Leadership and supervision, metadata curation, project administration, samples and logistics, and sequencing and analysis) 948 (Leadership and supervision, metadata curation, project administration, samples and logistics, and visualization) 949 (Leadership and supervision, metadata curation, project administration, sequencing and analysis, and software and analysis tools) 950 (Leadership and supervision, metadata curation, samples and logistics, sequencing and analysis, and visualization) 951 (Leadership and supervision, metadata curation, sequencing and analysis, software and analysis tools, and visualization) 952 (Metadata curation, project administration, samples and logistics, sequencing and analysis, and software and analysis tools) 953 (Funding acquisition, samples and logistics, sequencing and analysis, and visualization) 954 (Funding acquisition, leadership and supervision, metadata curation and project administration) 955 (Funding acquisition, leadership and supervision, metadata curation, and samples and logistics) 956 (Funding acquisition, leadership and supervision, metadata curation, and sequencing and analysis) 957 (Funding acquisition, leadership and supervision, project administration, and samples and logistics) 958 (Funding acquisition, leadership and supervision, sequencing and analysis, and visualization) 959 (Leadership and supervision, metadata curation, project administration, and sequencing and analysis) 960 (Leadership and supervision, metadata curation, project administration, and samples and logistics) 961 (Leadership and supervision, metadata curation, samples and logistics, and sequencing and analysis) 962 (Leadership and supervision, metadata curation, samples and logistics, and visualization) 963 (Leadership and supervision, metadata curation, sequencing and analysis, and software and analysis tools) 964 (Leadership and supervision, project administration, samples and logistics, and sequencing and analysis) 965 (Leadership and 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samples and logistics, and sequencing and analysis) 989 (Metadata curation, samples and logistics, and visualization) 990 (Metadata curation, sequencing and analysis, and software and analysis tools) 991 (Metadata curation, sequencing and analysis, and visualization) 992 (Project administration, samples and logistics, and sequencing and analysis) 993 (Project administration, samples and logistics, and visualization) 994 (Samples and logistics, software and analysis tools, and visualization) 995 (Sequencing and analysis, software and analysis tools, and visualization) 996 (Funding acquisition, and leadership and supervision) 997 (Funding acquisition and project administration) 998 (Leadership and supervision, and metadata curation) 999 (Leadership and supervision, and project administration) 1000 (Leadership and supervision, and samples and logistics) 1001 (Leadership and supervision, and sequencing and analysis) 1002 (Metadata curation, and samples and logistics) 1003 (Metadata curation, and sequencing and analysis) 1004 (Metadata curation, and software and analysis tools) 1005 (Project administration, and samples and logistics) 1006 (Project administration, and sequencing and analysis) 1007 (Project administration, and software and analysis tools) 1008 (Samples and logistics, and sequencing and analysis) 1009 (Samples and logistics, and software and analysis tools) 1010 (Sequencing and analysis, and software and analysis tools) 1011 (Sequencing and analysis, and visualization) 1012 (Software and analysis tools, and visualization) 1013 (Leadership and supervision) 1014 (Metadata curation) 1015 (Project administration) 1016 (Samples and logistics) 1017 (Sequencing and analysis) 1018 (Software and analysis tools) 1019 Ronan Lyons 0000-0001-5225-000X 1020 66422__30370__957b95ce96544597a61d9d846848ae6d.pdf 66422.pdf 2024-05-15T08:28:06.6267312 Output 13299713 application/pdf Version of Record true This article is licensed under a Creative Commons Attribution 4.0 International License. true eng https://creativecommons.org/licenses/by/4.0/
title Genomic reconstruction of the SARS-CoV-2 epidemic in England
spellingShingle Genomic reconstruction of the SARS-CoV-2 epidemic in England
Ronan Lyons
title_short Genomic reconstruction of the SARS-CoV-2 epidemic in England
title_full Genomic reconstruction of the SARS-CoV-2 epidemic in England
title_fullStr Genomic reconstruction of the SARS-CoV-2 epidemic in England
title_full_unstemmed Genomic reconstruction of the SARS-CoV-2 epidemic in England
title_sort Genomic reconstruction of the SARS-CoV-2 epidemic in England
author_id_str_mv 83efcf2a9dfcf8b55586999d3d152ac6
author_id_fullname_str_mv 83efcf2a9dfcf8b55586999d3d152ac6_***_Ronan Lyons
author Ronan Lyons
author2 Harald S. Vöhringer
Theo Sanderson
Matthew Sinnott
Nicola De Maio
Thuy Nguyen
Richard Goater
Frank Schwach
Ian Harrison
Joel Hellewell
Cristina V. Ariani
Sonia 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 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
Erik Volz
Sebastian Funk
Dominic Kwiatkowski
Meera Chand
Inigo Martincorena
Jeffrey C. Barrett
Moritz Gerstung
(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, samples and logistics, and sequencing and analysis)
(Leadership and supervision, metadata curation, project administration, samples and logistics, and visualization)
(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)
(Leadership and supervision, metadata curation, sequencing and analysis, software and analysis tools, and visualization)
(Metadata curation, project administration, samples and logistics, sequencing and analysis, and software and analysis tools)
(Funding acquisition, samples and logistics, sequencing and analysis, and visualization)
(Funding acquisition, leadership and supervision, metadata curation and project administration)
(Funding acquisition, leadership and supervision, metadata curation, and samples and logistics)
(Funding acquisition, leadership and supervision, 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
format Journal article
container_title Nature
container_volume 600
container_issue 7889
container_start_page 506
publishDate 2021
institution Swansea University
issn 0028-0836
1476-4687
doi_str_mv 10.1038/s41586-021-04069-y
publisher Springer Science and Business Media LLC
college_str Faculty of Medicine, Health and Life Sciences
hierarchytype
hierarchy_top_id facultyofmedicinehealthandlifesciences
hierarchy_top_title Faculty of Medicine, Health and Life Sciences
hierarchy_parent_id facultyofmedicinehealthandlifesciences
hierarchy_parent_title Faculty of Medicine, Health and Life Sciences
department_str Swansea University Medical School - Health Data Science{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Health Data Science
document_store_str 1
active_str 0
description 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.
published_date 2021-12-16T12:29:35Z
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