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Genomic reconstruction of the SARS-CoV-2 epidemic in England
Authors :
Vöhringer, HS Sanderson, T Sinnott, M De Maio, N Nguyen, T Goater, R Schwach, F Harrison, I Hellewell, J Ariani, CV Gonçalves, S Jackson, DK Johnston, I Jung, AW Saint, C Sillitoe, J Suciu, M Goldman, N Panovska-Griffiths, J Abnizova, I Aigrain, L Alderton, A Ali, M Allen, L Amato, R Anderson, R Ariani, C Austin-Guest, S Bala, S Barrett, J Bassett, A Battleday, K Beal, J Beale, M Beaver, C Bellany, S Bellerby, T Bellis, K Berger, D Berriman, M Betteridge, E Bevan, P Binley, S Bishop, J Blackburn, K Bonfield, J Boughton, N Bowker, S Brendler-Spaeth, T Bronner, I Brooklyn, T Buddenborg, SK Bush, R Caetano, C Cagan, A Carter, N Cartwright, J Monteiro, TC Chapman, L Chillingworth, TJ Clapham, P Clark, R Clarke, A Clarke, C Cole, D Cook, E Coppola, M Cornell, L Cornwell, C Corton, C Crackett, A Cranage, A Craven, H Craw, S Crawford, M Cutts, T Dabrowska, M Davies, M Davies, R Dawson, J Day, C Densem, A Dibling, T Dockree, C Dodd, D Dogga, S Dorman, M Dougan, G Dougherty, M Dove, A Drummond, L Drury, E Dudek, M Durham, J Durrant, L Easthope, E Eckert, S Ellis, P Farr, B Fenton, M Ferrero, M Flack, N Fordham, H Forsythe, G Foulser, L Francis, M Fraser, A Freeman, A Galvin, A Garcia-Casado, M Gedny, A Girgis, S Glover, J Goncalves, S Goodwin, S Gould, O Gourtovaia, M Gray, A Gray, E Griffiths, C Gu, Y Guerin, F Hamilton, W Hanks, H Harrison, E Harrott, A Harry, E Harvison, J Heath, P Hernandez-Koutoucheva, A Hobbs, R Holland, D Holmes, S Hornett, G Hough, N Huckle, L Hughes-Hallet, L Hunter, A Inglis, S Iqbal, S Jackson, A Jackson, D James, K Jamrozy, D Verdejo, CJ Jones, M Kallepally, K Kane, L Kay, K Kay, S Keatley, J Keith, A King, A Kitchin, L Kleanthous, M Klimekova, M Korlevic, P Krasheninnkova, K Lane, G Langford, C Laverack, A Law, K Lawniczak, M Lensing, S Leonard, S Letchford, L Lewis, K Lewis-Wade, A Liddle, J Lin, Q Lindsay, S Linsdell, S Livett, R Lo, S Long, R Lovell, J Ludden, C Mack, J Maddison, M Makunin, A Mamun, I Mansfield, J Marriott, N Martin, M Mayho, M McCarthy, S McClintock, J McGuigan, S McHugh, S McMinn, L Meadows, C Mobley, E Moll, R Morra, M Morrow, L Murie, K Nash, S Nathwani, C Naydenova, P Neaverson, A Nelson, R Nerou, E Nicholson, J Nimz, T Noell, GG O’Meara, S Ohan, V Oliver, K Olney, C Ormond, D Oszlanczi, A Palmer, S Pang, YF Pardubska, B Park, N Parmar, A Patel, G Patel, M Payne, M Peacock, S Petersen, A Plowman, D Preston, T Prestwood, L Puethe, C Quail, M Rajan, D Rajatileka, S Rance, R Rawlings, S Redshaw, N Reynolds, J Reynolds, M Rice, S Richardson, M Roberts, C Robinson, K Robinson, M Robinson, D Rogers, H Rojo, EM Roopra, D Rose, M Rudd, L Sadri, R Salmon, N Saul, D Scott, C Seekings, P Shirley, L Simms, A Sivadasan, S Siwek, B Sizer, D Skeldon, K Skelton, J Slater-Tunstill, J Sloper, L Smerdon, N Smith, C Smith, J Smith, K Smith, M Smith, S Smith, T Sneade, L Soria, CD Sousa, C Souster, E Sparkes, A Spencer-Chapman, M Squares, J Stanley, R Steed, C Stickland, T Still, I Stratton, MR Strickland, M Swann, A Swiatkowska, A Sycamore, N Swift, E Symons, E Szluha, S Taluy, E Tao, N Taylor, K Taylor, S Thompson, S Thompson, M Thomson, M Thomson, N Thurston, S Tonkin-Hill, G Toombs, D Topping, B Tovar-Corona, J Ungureanu, D Uphill, J Urbanova, J Van Vuuren, PJ Vancollie, V Voak, P Walker, D Walker, M Waller, M Ward, G Weatherhogg, C Webb, N Weldon, D Wells, A Wells, E Westwood, L Whipp, T Whiteley, T Whitton, G Whitwham, A Widaa, S Williams, M Wilson, M Wright, S Robson, SC Connor, TR Loman, NJ Golubchik, T Martinez Nunez, RT Bonsall, D Rambaut, A Snell, LB Corden, S Nastouli, E Nebbia, G Lythgoe, K Torok, ME Goodfellow, IG Prieto, JA Saeed, K Houlihan, C Frampton, D Hamilton, WL Witney, AA Bucca, G Pope, CF Moore, C Thomson, EC Harrison, EM Smith, CP Rogan, F Beckwith, SM Murray, A Singleton, D Eastick, K Sheridan, LA Randell, P Jackson, LM Fairley, DJ Loose, MW Watkins, J Moses, S Nicholls, S Bull, M Smith, DL Aanensen, DM Aggarwal, D Shepherd, JG Curran, MD Parmar, S Parker, MD Williams, C Glaysher, S Underwood, AP Bashton, M Pacchiarini, N Loveson, KF Byott, M Carabelli, AM Templeton, KE de Silva, TI Wang, D Langford, CF Gunson, RN Cottrell, S O’Grady, J Kwiatkowski, D Lillie, PJ Cortes, N Moore, N Thomas, C Burns, PJ Mahungu, TW Liggett, S Beckett, AH Holden, MTG Levett, LJ Osman, H Hassan-Ibrahim, MO Simpson, DA Chand, M Gupta, RK Darby, AC Paterson, S Pybus, OG Volz, EM de Angelis, D Robertson, DL Page, AJ Bassett, AR Wong, N Taha, Y Erkiert, MJ Spencer Chapman, MH Dewar, R McHugh, MP Mookerjee, S Aplin, S Harvey, M Sass, T Umpleby, H Wheeler, H McKenna, JP Warne, B Taylor, JF Chaudhry, Y Izuagbe, R Jahun, AS Young, GR McMurray, C McCann, CM Nelson, A Elliott, S Lowe, H Price, A Crown, MR Rey, S Roy, S Temperton, B Shaaban, S Hesketh, AR Laing, KG Monahan, IM Heaney, J Pelosi, E Silviera, S Wilson-Davies, E Fryer, H Adams, H du Plessis, L Johnson, R Harvey, WT Hughes, J Orton, RJ Spurgin, LG Bourgeois, Y Ruis, C O’Toole, Á Fraser, C Edgeworth, J Breuer, J Michell, SL Todd, JA John, M Buck, D Gajee, K Kay, GL Peacock, SJ Heyburn, D Kitchman, K McNally, A Pritchard, DT Dervisevic, S Muir, P Robinson, E Vipond, BB Ramadan, NA Jeanes, C Catalan, J Jones, N da Silva Filipe, A Fuchs, M Miskelly, J Jeffries, AR Park, NR Ash, A Koshy, C Barrow, M Buchan, SL Mantzouratou, A Clark, G Holmes, CW Campbell, S Davis, T Tan, NK Brown, JR Harris, KA Kidd, SP Grant, PR Xu-McCrae, L Cox, A Madona, P Pond, M Randell, PA Withell, KT Graham, C Denton-Smith, R Swindells, E Turnbull, R Sloan, TJ Bosworth, A Hutchings, S Pymont, HM Casey, A Ratcliffe, L Jones, CR Knight, BA Haque, T Hart, J Irish-Tavares, D Witele, E Mower, C Watson, LK Collins, J Eltringham, G Crudgington, D Macklin, B Iturriza-Gomara, M Lucaci, AO McClure, PC Carlile, M Holmes, N Storey, N Rooke, S Yebra, G Craine, N Perry, M Alikhan, NF Bridgett, S Cook, KF Fearn, C Goudarzi, S Lyons, RA Williams, T Haldenby, ST Davies, RM Batra, R Blane, B Spyer, MJ Smith, P Yavus, M Williams, RJ Mahanama, AIK Samaraweera, B Girgis, ST Hansford, SE Green, A Bellis, KL Dorman, MJ Quick, J Poplawski, R Reynolds, N Mack, A Morriss, A Whalley, T Patel, B Georgana, I Hosmillo, M Pinckert, ML Stockton, J Henderson, JH Hollis, A Stanley, W Yew, WC Myers, R Thornton, A Adams, A Annett, T Asad, H Birchley, A Coombes, J Evans, JM Fina, L Gatica-Wilcox, B Gilbert, L Graham, L Hey, J Hilvers, E Jones, S Jones, H Kumziene-Summerhayes, S McKerr, C Powell, J Pugh, G Trotter, AJ Williams, CA Kermack, LM Foulkes, BH Gallis, M Hornsby, HR Louka, SF Pohare, M Wolverson, P Zhang, P MacIntyre-Cockett, G Trebes, A Moll, RJ Ferguson, L Goldstein, EJ Maclean, A Tomb, R Starinskij, I Thomson, L Southgate, J Kraemer, MUG Raghwani, J Zarebski, AE Boyd, O Geidelberg, L Illingworth, CJ Jackson, C Pascall, D Vattipally, S Freeman, TM Hsu, SN Lindsey, BB Tovar-Corona, JM Cox, MG Abudahab, K Menegazzo, M Taylor, BEW Yeats, CA Mukaddas, A Wright, DW de Oliveira Martins, L Colquhoun, R Hill, V Jackson, B McCrone, JT Medd, N Scher, E Keatley, JP Curran, T Morgan, S Maxwell, P Eldirdiri, S Kenyon, A Holmes, AH Price, JR Wyatt, T Mather, AE Skvortsov, T Hartley, JA Guest, M Kitchen, C Merrick, I Munn, R Bertolusso, B Lynch, J Vernet, G Kirk, S Wastnedge, E Idle, G Bradley, DT Poyner, J Mori, M Jones, O Wright, V Brooks, E Churcher, CM Fragakis, M Galai, K Jermy, A Judges, S McManus, GM Smith, KS Westwick, E Attwood, SW Bolt, F Davies, A De Lacy, E Downing, F Edwards, S Meadows, L Jeremiah, S Smith, N Charalampous, T Patel, A Berry, L Boswell, T Fleming, VM Howson-Wells, HC Joseph, A Khakh, M Lister, MM Bird, PW Fallon, K Helmer, T McMurray, CL Odedra, M Shaw, J Tang, JW Willford, NJ Blakey, V Raviprakash, V Sheriff, N Williams, LA Feltwell, T Bedford, L Cargill, JS Hughes, W Moore, J Stonehouse, S Atkinson, L Lee, JCD Shah, D Alcolea, A Ohemeng-Kumi, N Ramble, J Sehmi, J Williams, R Chatterton, W Pusok, M Everson, W Castigador, A Macnaughton, E El Bouzidi, K Lampejo, T Sudhanva, M Breen, C Sluga, G Ahmad, SSY George, RP Machin, NW Binns, D James, V Blacow, R Coupland, L Smith, L Barton, E Padgett, D Scott, G Cross, A Mirfenderesky, M Greenaway, J Cole, K Clarke, P Duckworth, N Walsh, S Bicknell, K Impey, R Wyllie, S Hopes, R Bishop, C Chalker, V Gifford, L Molnar, Z Auckland, C Evans, C Johnson, K Partridge, DG Raza, M Baker, P Bonner, S Essex, S Murray, LJ Lawton, AI Burton-Fanning, S Payne, BAI Waugh, S Gomes, AN Kimuli, M Murray, DR Ashfield, P Dobie, D Ashford, F Best, A Crawford, L Cumley, N Mayhew, M Megram, O Mirza, J Moles-Garcia, E Percival, B Ensell, L Lowe, HL Maftei, L Mondani, M Chaloner, NJ Cogger, BJ Easton, LJ Huckson, H Lewis, J Lowdon, S Malone, CS Munemo, F Mutingwende, M Nicodemi, R Podplomyk, O Somassa, T Beggs, A Richter, A Cormie, C Dias, J Forrest, S Higginson, EE Maes, M Young, J Davidson, RK Jackson, KA Turtle, L Keeley, AJ Ball, J Byaruhanga, T Chappell, JG Dey, J Hill, JD Park, EJ Fanaie, A Hilson, RA Yaze, G Afifi, S Beer, R Maksimovic, J Masters, KMC Spellman, K Bresner, C Fuller, W Marchbank, A Workman, T Shelest, E Debebe, J Sang, F Zamudio, ME Francois, S Gutierrez, B Vasylyeva, TI Flaviani, F Ragonnet-Cronin, M Smollett, KL Broos, A Mair, D Nichols, J Nomikou, K Tong, L Tsatsani, I O’Brien, S Rushton, S Sanderson, R Perkins, J Cotton, S Gallagher, A Allara, E Pearson, C Bibby, D Dabrera, G Ellaby, N Gallagher, E Hubb, J Lackenby, A Lee, D Manesis, N Mbisa, T Platt, S Twohig, KA Morgan, M Aydin, A Baker, DJ Foster-Nyarko, E Prosolek, SJ Rudder, S Baxter, C Carvalho, SF Lavin, D Mariappan, A Radulescu, C Singh, A Tang, M Morcrette, H Bayzid, N Cotic, M Balcazar, CE Gallagher, MD Maloney, D Stanton, TD Williamson, KA Manley, R Michelsen, ML Sambles, CM Studholme, DJ Warwick-Dugdale, J Eccles, R Gemmell, M Gregory, R Hughes, M Nelson, C Rainbow, L Vamos, EE Webster, HJ Whitehead, M Wierzbicki, C Angyal, A Green, LR Whiteley, M Bronner, IF Farr, BW Lensing, SV McCarthy, SA Quail, MA Redshaw, NM Thurston, SAJ Rowe, W Gaskin, A Le-Viet, T Birney, E Volz, E Funk, S Martincorena, I Barrett, JC Gerstung, M Vöhringer, HS Sanderson, T Sinnott, M De Maio, N Nguyen, T Goater, R Schwach, F Harrison, I Hellewell, J Ariani, CV Gonçalves, S Jackson, DK Johnston, I Jung, AW Saint, C Sillitoe, J Suciu, M Goldman, N Panovska-Griffiths, J Abnizova, I Aigrain, L Alderton, A Ali, M Allen, L Amato, R Anderson, R Ariani, C Austin-Guest, S Bala, S Barrett, J Bassett, A Battleday, K Beal, J Beale, M Beaver, C Bellany, S Bellerby, T Bellis, K Berger, D Berriman, M Betteridge, E Bevan, P Binley, S Bishop, J Blackburn, K Bonfield, J Boughton, N Bowker, S Brendler-Spaeth, T Bronner, I Brooklyn, T Buddenborg, SK Bush, R Caetano, C Cagan, A Carter, N Cartwright, J Monteiro, TC Chapman, L Chillingworth, TJ Clapham, P Clark, R Clarke, A Clarke, C Cole, D Cook, E Coppola, M Cornell, L Cornwell, C Corton, C Crackett, A Cranage, A Craven, H Craw, S Crawford, M Cutts, T Dabrowska, M Davies, M Davies, R Dawson, J Day, C Densem, A Dibling, T Dockree, C Dodd, D Dogga, S Dorman, M Dougan, G Dougherty, M Dove, A Drummond, L Drury, E Dudek, M Durham, J Durrant, L Easthope, E Eckert, S Ellis, P Farr, B Fenton, M Ferrero, M Flack, N Fordham, H Forsythe, G Foulser, L Francis, M Fraser, A Freeman, A Galvin, A Garcia-Casado, M Gedny, A Girgis, S Glover, J Goncalves, S Goodwin, S Gould, O Gourtovaia, M Gray, A Gray, E Griffiths, C Gu, Y Guerin, F Hamilton, W Hanks, H Harrison, E Harrott, A Harry, E Harvison, J Heath, P Hernandez-Koutoucheva, A Hobbs, R Holland, D Holmes, S Hornett, G Hough, N Huckle, L Hughes-Hallet, L Hunter, A Inglis, S Iqbal, S Jackson, A Jackson, D James, K Jamrozy, D Verdejo, CJ Jones, M Kallepally, K Kane, L Kay, K Kay, S Keatley, J Keith, A King, A Kitchin, L Kleanthous, M Klimekova, M Korlevic, P Krasheninnkova, K Lane, G Langford, C Laverack, A Law, K Lawniczak, M Lensing, S Leonard, S Letchford, L Lewis, K Lewis-Wade, A Liddle, J Lin, Q Lindsay, S Linsdell, S Livett, R Lo, S Long, R Lovell, J Ludden, C Mack, J Maddison, M Makunin, A Mamun, I Mansfield, J Marriott, N Martin, M Mayho, M McCarthy, S McClintock, J McGuigan, S McHugh, S McMinn, L Meadows, C Mobley, E Moll, R Morra, M Morrow, L Murie, K Nash, S Nathwani, C Naydenova, P Neaverson, A Nelson, R Nerou, E Nicholson, J Nimz, T Noell, GG O’Meara, S Ohan, V Oliver, K Olney, C Ormond, D Oszlanczi, A Palmer, S Pang, YF Pardubska, B Park, N Parmar, A Patel, G Patel, M Payne, M Peacock, S Petersen, A Plowman, D Preston, T Prestwood, L Puethe, C Quail, M Rajan, D Rajatileka, S Rance, R Rawlings, S Redshaw, N Reynolds, J Reynolds, M Rice, S Richardson, M Roberts, C Robinson, K Robinson, M Robinson, D Rogers, H Rojo, EM Roopra, D Rose, M Rudd, L Sadri, R Salmon, N Saul, D Scott, C Seekings, P Shirley, L Simms, A Sivadasan, S Siwek, B Sizer, D Skeldon, K Skelton, J Slater-Tunstill, J Sloper, L Smerdon, N Smith, C Smith, J Smith, K Smith, M Smith, S Smith, T Sneade, L Soria, CD Sousa, C Souster, E Sparkes, A Spencer-Chapman, M Squares, J Stanley, R Steed, C Stickland, T Still, I Stratton, MR Strickland, M Swann, A Swiatkowska, A Sycamore, N Swift, E Symons, E Szluha, S Taluy, E Tao, N Taylor, K Taylor, S Thompson, S Thompson, M Thomson, M Thomson, N Thurston, S Tonkin-Hill, G Toombs, D Topping, B Tovar-Corona, J Ungureanu, D Uphill, J Urbanova, J Van Vuuren, PJ Vancollie, V Voak, P Walker, D Walker, M Waller, M Ward, G Weatherhogg, C Webb, N Weldon, D Wells, A Wells, E Westwood, L Whipp, T Whiteley, T Whitton, G Whitwham, A Widaa, S Williams, M Wilson, M Wright, S Robson, SC Connor, TR Loman, NJ Golubchik, T Martinez Nunez, RT Bonsall, D Rambaut, A Snell, LB Corden, S Nastouli, E Nebbia, G Lythgoe, K Torok, ME Goodfellow, IG Prieto, JA Saeed, K Houlihan, C Frampton, D Hamilton, WL Witney, AA Bucca, G Pope, CF Moore, C Thomson, EC Harrison, EM Smith, CP Rogan, F Beckwith, SM Murray, A Singleton, D Eastick, K Sheridan, LA Randell, P Jackson, LM Fairley, DJ Loose, MW Watkins, J Moses, S Nicholls, S Bull, M Smith, DL Aanensen, DM Aggarwal, D Shepherd, JG Curran, MD Parmar, S Parker, MD Williams, C Glaysher, S Underwood, AP Bashton, M Pacchiarini, N Loveson, KF Byott, M Carabelli, AM Templeton, KE de Silva, TI Wang, D Langford, CF Gunson, RN Cottrell, S O’Grady, J Kwiatkowski, D Lillie, PJ Cortes, N Moore, N Thomas, C Burns, PJ Mahungu, TW Liggett, S Beckett, AH Holden, MTG Levett, LJ Osman, H Hassan-Ibrahim, MO Simpson, DA Chand, M Gupta, RK Darby, AC Paterson, S Pybus, OG Volz, EM de Angelis, D Robertson, DL Page, AJ Bassett, AR Wong, N Taha, Y Erkiert, MJ Spencer Chapman, MH Dewar, R McHugh, MP Mookerjee, S Aplin, S Harvey, M Sass, T Umpleby, H Wheeler, H McKenna, JP Warne, B Taylor, JF Chaudhry, Y Izuagbe, R Jahun, AS Young, GR McMurray, C McCann, CM Nelson, A Elliott, S Lowe, H Price, A Crown, MR Rey, S Roy, S Temperton, B Shaaban, S Hesketh, AR Laing, KG Monahan, IM Heaney, J Pelosi, E Silviera, S Wilson-Davies, E Fryer, H Adams, H du Plessis, L Johnson, R Harvey, WT Hughes, J Orton, RJ Spurgin, LG Bourgeois, Y Ruis, C O’Toole, Á Fraser, C Edgeworth, J Breuer, J Michell, SL Todd, JA John, M Buck, D Gajee, K Kay, GL Peacock, SJ Heyburn, D Kitchman, K McNally, A Pritchard, DT Dervisevic, S Muir, P Robinson, E Vipond, BB Ramadan, NA Jeanes, C Catalan, J Jones, N da Silva Filipe, A Fuchs, M Miskelly, J Jeffries, AR Park, NR Ash, A Koshy, C Barrow, M Buchan, SL Mantzouratou, A Clark, G Holmes, CW Campbell, S Davis, T Tan, NK Brown, JR Harris, KA Kidd, SP Grant, PR Xu-McCrae, L Cox, A Madona, P Pond, M Randell, PA Withell, KT Graham, C Denton-Smith, R Swindells, E Turnbull, R Sloan, TJ Bosworth, A Hutchings, S Pymont, HM Casey, A Ratcliffe, L Jones, CR Knight, BA Haque, T Hart, J Irish-Tavares, D Witele, E Mower, C Watson, LK Collins, J Eltringham, G Crudgington, D Macklin, B Iturriza-Gomara, M Lucaci, AO McClure, PC Carlile, M Holmes, N Storey, N Rooke, S Yebra, G Craine, N Perry, M Alikhan, NF Bridgett, S Cook, KF Fearn, C Goudarzi, S Lyons, RA Williams, T Haldenby, ST Davies, RM Batra, R Blane, B Spyer, MJ Smith, P Yavus, M Williams, RJ Mahanama, AIK Samaraweera, B Girgis, ST Hansford, SE Green, A Bellis, KL Dorman, MJ Quick, J Poplawski, R Reynolds, N Mack, A Morriss, A Whalley, T Patel, B Georgana, I Hosmillo, M Pinckert, ML Stockton, J Henderson, JH Hollis, A Stanley, W Yew, WC Myers, R Thornton, A Adams, A Annett, T Asad, H Birchley, A Coombes, J Evans, JM Fina, L Gatica-Wilcox, B Gilbert, L Graham, L Hey, J Hilvers, E Jones, S Jones, H Kumziene-Summerhayes, S McKerr, C Powell, J Pugh, G Trotter, AJ Williams, CA Kermack, LM Foulkes, BH Gallis, M Hornsby, HR Louka, SF Pohare, M Wolverson, P Zhang, P MacIntyre-Cockett, G Trebes, A Moll, RJ Ferguson, L Goldstein, EJ Maclean, A Tomb, R Starinskij, I Thomson, L Southgate, J Kraemer, MUG Raghwani, J Zarebski, AE Boyd, O Geidelberg, L Illingworth, CJ Jackson, C Pascall, D Vattipally, S Freeman, TM Hsu, SN Lindsey, BB Tovar-Corona, JM Cox, MG Abudahab, K Menegazzo, M Taylor, BEW Yeats, CA Mukaddas, A Wright, DW de Oliveira Martins, L Colquhoun, R Hill, V Jackson, B McCrone, JT Medd, N Scher, E Keatley, JP Curran, T Morgan, S Maxwell, P Eldirdiri, S Kenyon, A Holmes, AH Price, JR Wyatt, T Mather, AE Skvortsov, T Hartley, JA Guest, M Kitchen, C Merrick, I Munn, R Bertolusso, B Lynch, J Vernet, G Kirk, S Wastnedge, E Idle, G Bradley, DT Poyner, J Mori, M Jones, O Wright, V Brooks, E Churcher, CM Fragakis, M Galai, K Jermy, A Judges, S McManus, GM Smith, KS Westwick, E Attwood, SW Bolt, F Davies, A De Lacy, E Downing, F Edwards, S Meadows, L Jeremiah, S Smith, N Charalampous, T Patel, A Berry, L Boswell, T Fleming, VM Howson-Wells, HC Joseph, A Khakh, M Lister, MM Bird, PW Fallon, K Helmer, T McMurray, CL Odedra, M Shaw, J Tang, JW Willford, NJ Blakey, V Raviprakash, V Sheriff, N Williams, LA Feltwell, T Bedford, L Cargill, JS Hughes, W Moore, J Stonehouse, S Atkinson, L Lee, JCD Shah, D Alcolea, A Ohemeng-Kumi, N Ramble, J Sehmi, J Williams, R Chatterton, W Pusok, M Everson, W Castigador, A Macnaughton, E El Bouzidi, K Lampejo, T Sudhanva, M Breen, C Sluga, G Ahmad, SSY George, RP Machin, NW Binns, D James, V Blacow, R Coupland, L Smith, L Barton, E Padgett, D Scott, G Cross, A Mirfenderesky, M Greenaway, J Cole, K Clarke, P Duckworth, N Walsh, S Bicknell, K Impey, R Wyllie, S Hopes, R Bishop, C Chalker, V Gifford, L Molnar, Z Auckland, C Evans, C Johnson, K Partridge, DG Raza, M Baker, P Bonner, S Essex, S Murray, LJ Lawton, AI Burton-Fanning, S Payne, BAI Waugh, S Gomes, AN Kimuli, M Murray, DR Ashfield, P Dobie, D Ashford, F Best, A Crawford, L Cumley, N Mayhew, M Megram, O Mirza, J Moles-Garcia, E Percival, B Ensell, L Lowe, HL Maftei, L Mondani, M Chaloner, NJ Cogger, BJ Easton, LJ Huckson, H Lewis, J Lowdon, S Malone, CS Munemo, F Mutingwende, M Nicodemi, R Podplomyk, O Somassa, T Beggs, A Richter, A Cormie, C Dias, J Forrest, S Higginson, EE Maes, M Young, J Davidson, RK Jackson, KA Turtle, L Keeley, AJ Ball, J Byaruhanga, T Chappell, JG Dey, J Hill, JD Park, EJ Fanaie, A Hilson, RA Yaze, G Afifi, S Beer, R Maksimovic, J Masters, KMC Spellman, K Bresner, C Fuller, W Marchbank, A Workman, T Shelest, E Debebe, J Sang, F Zamudio, ME Francois, S Gutierrez, B Vasylyeva, TI Flaviani, F Ragonnet-Cronin, M Smollett, KL Broos, A Mair, D Nichols, J Nomikou, K Tong, L Tsatsani, I O’Brien, S Rushton, S Sanderson, R Perkins, J Cotton, S Gallagher, A Allara, E Pearson, C Bibby, D Dabrera, G Ellaby, N Gallagher, E Hubb, J Lackenby, A Lee, D Manesis, N Mbisa, T Platt, S Twohig, KA Morgan, M Aydin, A Baker, DJ Foster-Nyarko, E Prosolek, SJ Rudder, S Baxter, C Carvalho, SF Lavin, D Mariappan, A Radulescu, C Singh, A Tang, M Morcrette, H Bayzid, N Cotic, M Balcazar, CE Gallagher, MD Maloney, D Stanton, TD Williamson, KA Manley, R Michelsen, ML Sambles, CM Studholme, DJ Warwick-Dugdale, J Eccles, R Gemmell, M Gregory, R Hughes, M Nelson, C Rainbow, L Vamos, EE Webster, HJ Whitehead, M Wierzbicki, C Angyal, A Green, LR Whiteley, M Bronner, IF Farr, BW Lensing, SV McCarthy, SA Quail, MA Redshaw, NM Thurston, SAJ Rowe, W Gaskin, A Le-Viet, T Birney, E Volz, E Funk, S Martincorena, I Barrett, JC Gerstung, M
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.
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application/pdf, Vöhringer, H., Sanderson, T, Sinnott, M, De Maio, N, Nguyen, T, Goater, R, Schwach, F, Harrison, I, Hellewell, J, Ariani, C., Gonçalves, S, Jackson, D., Johnston, I, Jung, A., Saint, C, Sillitoe, J, Suciu, M, Goldman, N, Panovska-Griffiths, J, Abnizova, I, Aigrain, L, Alderton, A, Ali, M, Allen, L, Amato, R, Anderson, R, Ariani, C, Austin-Guest, S, Bala, S, Barrett, J, Bassett, A, Battleday, K, Beal, J, Beale, M, Beaver, C, Bellany, S, Bellerby, T, Bellis, K, Berger, D, Berriman, M, Betteridge, E, Bevan, P, Binley, S, Bishop, J, Blackburn, K, Bonfield, J, Boughton, N, Bowker, S, Brendler-Spaeth, T, Bronner, I, Brooklyn, T, Buddenborg, S., Bush, R, Caetano, C, Cagan, A, Carter, N, Cartwright, J, Monteiro, T., Chapman, L, Chillingworth, T., Clapham, P, Clark, R, Clarke, A, Clarke, C, Cole, D, Cook, E, Coppola, M, Cornell, L, Cornwell, C, Corton, C, Crackett, A, Cranage, A, Craven, H, Craw, S, Crawford, M, Cutts, T, Dabrowska, M, Davies, M, Davies, R, Dawson, J, Day, C, Densem, A, Dibling, T, Dockree, C, Dodd, D, Dogga, S, Dorman, M, Dougan, G, Dougherty, M, Dove, A, Drummond, L, Drury, E, Dudek, M, Durham, J, Durrant, L, Easthope, E, Eckert, S, Ellis, P, Farr, B, Fenton, M, Ferrero, M, Flack, N, Fordham, H, Forsythe, G, Foulser, L, Francis, M, Fraser, A, Freeman, A, Galvin, A, Garcia-Casado, M, Gedny, A, Girgis, S, Glover, J, Goncalves, S, Goodwin, S, Gould, O, Gourtovaia, M, Gray, A, Gray, E, Griffiths, C, Gu, Y, Guerin, F, Hamilton, W, Hanks, H, Harrison, E, Harrott, A, Harry, E, Harvison, J, Heath, P, Hernandez-Koutoucheva, A, Hobbs, R, Holland, D, Holmes, S, Hornett, G, Hough, N, Huckle, L, Hughes-Hallet, L, Hunter, A, Inglis, S, Iqbal, S, Jackson, A, Jackson, D, James, K, Jamrozy, D, Verdejo, C., Jones, M, Kallepally, K, Kane, L, Kay, K, Kay, S, Keatley, J, Keith, A, King, A, Kitchin, L, Kleanthous, M, Klimekova, M, Korlevic, P, Krasheninnkova, K, Lane, G, Langford, C, Laverack, A, Law, K, Lawniczak, M, Lensing, S, Leonard, S, Letchford, L, Lewis, K, Lewis-Wade, English
Publication Type :
Electronic Resource
Accession number :
edsoai.on1401082980
Document Type :
Electronic Resource