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

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