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

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Title: 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
Publication Year: 2021
Collection: Bournemouth University Research Online (BURO)
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.
Document Type: article in journal/newspaper
File Description: application/pdf
Language: English
Relation: https://eprints.bournemouth.ac.uk/38888/1/s41586-021-04069-y.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, A, Liddle, J, Lin, Q, Lindsay, S, Linsdell, S, Livett, R, Lo, S, Long, R, Lovell, J, 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, G., O’Meara, S, Ohan, V, Oliver, K, Olney, C, Ormond, D, Oszlanczi, A, Palmer, S, Pang, Y., 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, E., Roopra, D, Rose, M, Rudd, L, Sadri, R, Salmon, N, Saul, D, Scott, C, Seekings, P, Shirley, L, Simms, A, Sinnott, M, Sivadasan, S, Siwek, B, Sizer, D, Skeldon, K, Skelton, J, Slater-Tunstill, J, Sloper, L, Smerdon, N, Smith, C, Smith, C, Smith, J, Smith, K, Smith, M, Smith, S, Smith, T, Sneade, L, Soria, C., Sousa, C, Souster, E, Sparkes, A, Spencer-Chapman, M, Squares, J, Stanley, R, Steed, C, Stickland, T, Still, I, Stratton, M., 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, P., 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, S., Connor, T., Loman, N., Golubchik, T, Martinez Nunez, R., Bonsall, D, Rambaut, A, Snell, L., Ludden, C, Corden, S, Nastouli, E, Nebbia, G, Lythgoe, K, Torok, M., Goodfellow, I., Prieto, J., Saeed, K, Houlihan, C, Frampton, D, Hamilton, W., Witney, A., Bucca, G, Pope, C., Moore, C, Thomson, E., Harrison, E., Smith, C., Rogan, F, Beckwith, S., Murray, A, Singleton, D, Eastick, K, Sheridan, L., Randell, P, Jackson, L., Gonçalves, S, Fairley, D., Loose, M., Watkins, J, Moses, S, Nicholls, S, Bull, M, Smith, D., Aanensen, D., Aggarwal, D, Shepherd, J., Curran, M., Parmar, S, Parker, M., Williams, C, Glaysher, S, Underwood, A., Bashton, M, Pacchiarini, N, Loveson, K., Byott, M, Carabelli, A., Templeton, K., de Silva, T., Wang, D, Langford, C., Gunson, R., Cottrell, S, O’Grady, J, Kwiatkowski, D, Lillie, P., Cortes, N, Moore, N, Thomas, C, Burns, P., Mahungu, T., Liggett, S, Beckett, A., Holden, M., Levett, L., Osman, H, Hassan-Ibrahim, M., Simpson, D., Chand, M, Gupta, R., Darby, A., Paterson, S, Pybus, O., Volz, E., de Angelis, D, Robertson, D., Page, A., Bassett, A., Wong, N, Taha, Y, Erkiert, M., Spencer Chapman, M., Dewar, R, McHugh, M., Mookerjee, S, Aplin, S, Harvey, M, Sass, T, Umpleby, H, Wheeler, H, McKenna, J., Warne, B, Taylor, J., Chaudhry, Y, Izuagbe, R, Jahun, A., Young, G., McMurray, C, McCann, C., Nelson, A, Elliott, S, Lowe, H, Price, A, Crown, M., Rey, S, Roy, S, Temperton, B, Shaaban, S, Hesketh, A., Laing, K., Monahan, I., Heaney, J, Pelosi, E, Silviera, S, Wilson-Davies, E, Fryer, H, Adams, H, du Plessis, L, Johnson, R, Harvey, W., Hughes, J, Orton, R., Spurgin, L., Bourgeois, Y, Ruis, C, O’Toole, Á, Sanderson, T, Fraser, C, Edgeworth, J, Breuer, J, Michell, S., Todd, J., John, M, Buck, D, Gajee, K, Kay, G., Peacock, S., Heyburn, D, Kitchman, K, McNally, A, Pritchard, D., Dervisevic, S, Muir, P, Robinson, E, Vipond, B., Ramadan, N., Jeanes, C, Catalan, J, Jones, N, da Silva Filipe, A, Williams, C, Fuchs, M, Miskelly, J, Jeffries, A., Park, N., Ash, A, Koshy, C, Barrow, M, Buchan, S., Mantzouratou, A, Clark, G, Holmes, C., Campbell, S, Davis, T, Tan, N., Brown, J., Harris, K., Kidd, S., Grant, P., Xu-McCrae, L, Cox, A, Madona, P, Pond, M, Randell, P., Withell, K., Williams, C, Graham, C, Denton-Smith, R, Swindells, E, Turnbull, R, Sloan, T., Bosworth, A, Hutchings, S, Pymont, H., Casey, A, Ratcliffe, L, Jones, C., Knight, B., Haque, T, Hart, J, Irish-Tavares, D, Witele, E, Mower, C, Watson, L., Collins, J, Eltringham, G, Crudgington, D, Macklin, B, Iturriza-Gomara, M, Lucaci, A., McClure, P., Carlile, M, Holmes, N, Moore, C, Storey, N, Rooke, S, Yebra, G, Craine, N, Perry, M, Alikhan, N., Bridgett, S, Cook, K., Fearn, C, Goudarzi, S, Lyons, R., Williams, T, Haldenby, S., Davies, R., Batra, R, Blane, B, Spyer, M., Smith, P, Yavus, M, Williams, R., Mahanama, A., Samaraweera, B, Girgis, S., Hansford, S., Green, A, Bellis, K., Dorman, M., Quick, J, Poplawski, R, Reynolds, N, Mack, A, Morriss, A, Whalley, T, Patel, B, Georgana, I, Hosmillo, M, Pinckert, M., Stockton, J, Henderson, J., Hollis, A, Stanley, W, Yew, W., 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Items – Name: Title
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  Data: Genomic reconstruction of the SARS-CoV-2 epidemic in England
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M</searchLink><br /><searchLink fieldCode="AR" term="%22Payne%2C+M%22">Payne, M</searchLink><br /><searchLink fieldCode="AR" term="%22Peacock%2C+S%22">Peacock, S</searchLink><br /><searchLink fieldCode="AR" term="%22Petersen%2C+A%22">Petersen, A</searchLink><br /><searchLink fieldCode="AR" term="%22Plowman%2C+D%22">Plowman, D</searchLink><br /><searchLink fieldCode="AR" term="%22Preston%2C+T%22">Preston, T</searchLink><br /><searchLink fieldCode="AR" term="%22Prestwood%2C+L%22">Prestwood, L</searchLink><br /><searchLink fieldCode="AR" term="%22Puethe%2C+C%22">Puethe, C</searchLink><br /><searchLink fieldCode="AR" term="%22Quail%2C+M%22">Quail, M</searchLink><br /><searchLink fieldCode="AR" term="%22Rajan%2C+D%22">Rajan, D</searchLink><br /><searchLink fieldCode="AR" term="%22Rajatileka%2C+S%22">Rajatileka, S</searchLink><br /><searchLink fieldCode="AR" term="%22Rance%2C+R%22">Rance, R</searchLink><br /><searchLink fieldCode="AR" term="%22Rawlings%2C+S%22">Rawlings, S</searchLink><br 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K</searchLink><br /><searchLink fieldCode="AR" term="%22Skelton%2C+J%22">Skelton, J</searchLink><br /><searchLink fieldCode="AR" term="%22Slater-Tunstill%2C+J%22">Slater-Tunstill, J</searchLink><br /><searchLink fieldCode="AR" term="%22Sloper%2C+L%22">Sloper, L</searchLink><br /><searchLink fieldCode="AR" term="%22Smerdon%2C+N%22">Smerdon, N</searchLink><br /><searchLink fieldCode="AR" term="%22Smith%2C+C%22">Smith, C</searchLink><br /><searchLink fieldCode="AR" term="%22Smith%2C+J%22">Smith, J</searchLink><br /><searchLink fieldCode="AR" term="%22Smith%2C+K%22">Smith, K</searchLink><br /><searchLink fieldCode="AR" term="%22Smith%2C+M%22">Smith, M</searchLink><br /><searchLink fieldCode="AR" term="%22Smith%2C+S%22">Smith, S</searchLink><br /><searchLink fieldCode="AR" term="%22Smith%2C+T%22">Smith, T</searchLink><br /><searchLink fieldCode="AR" term="%22Sneade%2C+L%22">Sneade, L</searchLink><br /><searchLink fieldCode="AR" term="%22Soria%2C+CD%22">Soria, CD</searchLink><br 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T</searchLink><br /><searchLink fieldCode="AR" term="%22Morgan%2C+S%22">Morgan, S</searchLink><br /><searchLink fieldCode="AR" term="%22Maxwell%2C+P%22">Maxwell, P</searchLink><br /><searchLink fieldCode="AR" term="%22Eldirdiri%2C+S%22">Eldirdiri, S</searchLink><br /><searchLink fieldCode="AR" term="%22Kenyon%2C+A%22">Kenyon, A</searchLink><br /><searchLink fieldCode="AR" term="%22Holmes%2C+AH%22">Holmes, AH</searchLink><br /><searchLink fieldCode="AR" term="%22Price%2C+JR%22">Price, JR</searchLink><br /><searchLink fieldCode="AR" term="%22Wyatt%2C+T%22">Wyatt, T</searchLink><br /><searchLink fieldCode="AR" term="%22Mather%2C+AE%22">Mather, AE</searchLink><br /><searchLink fieldCode="AR" term="%22Skvortsov%2C+T%22">Skvortsov, T</searchLink><br /><searchLink fieldCode="AR" term="%22Hartley%2C+JA%22">Hartley, JA</searchLink><br /><searchLink fieldCode="AR" term="%22Guest%2C+M%22">Guest, M</searchLink><br /><searchLink fieldCode="AR" term="%22Kitchen%2C+C%22">Kitchen, C</searchLink><br 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term="%22Davies%2C+A%22">Davies, A</searchLink><br /><searchLink fieldCode="AR" term="%22De+Lacy%2C+E%22">De Lacy, E</searchLink><br /><searchLink fieldCode="AR" term="%22Downing%2C+F%22">Downing, F</searchLink><br /><searchLink fieldCode="AR" term="%22Edwards%2C+S%22">Edwards, S</searchLink><br /><searchLink fieldCode="AR" term="%22Meadows%2C+L%22">Meadows, L</searchLink><br /><searchLink fieldCode="AR" term="%22Jeremiah%2C+S%22">Jeremiah, S</searchLink><br /><searchLink fieldCode="AR" term="%22Smith%2C+N%22">Smith, N</searchLink><br /><searchLink fieldCode="AR" term="%22Charalampous%2C+T%22">Charalampous, T</searchLink><br /><searchLink fieldCode="AR" term="%22Patel%2C+A%22">Patel, A</searchLink><br /><searchLink fieldCode="AR" term="%22Berry%2C+L%22">Berry, L</searchLink><br /><searchLink fieldCode="AR" term="%22Boswell%2C+T%22">Boswell, T</searchLink><br /><searchLink fieldCode="AR" term="%22Fleming%2C+VM%22">Fleming, VM</searchLink><br /><searchLink fieldCode="AR" term="%22Howson-Wells%2C+HC%22">Howson-Wells, HC</searchLink><br /><searchLink fieldCode="AR" term="%22Joseph%2C+A%22">Joseph, A</searchLink><br /><searchLink fieldCode="AR" term="%22Khakh%2C+M%22">Khakh, M</searchLink><br /><searchLink fieldCode="AR" term="%22Lister%2C+MM%22">Lister, MM</searchLink><br /><searchLink fieldCode="AR" term="%22Bird%2C+PW%22">Bird, PW</searchLink><br /><searchLink fieldCode="AR" term="%22Fallon%2C+K%22">Fallon, K</searchLink><br /><searchLink fieldCode="AR" term="%22Helmer%2C+T%22">Helmer, T</searchLink><br /><searchLink fieldCode="AR" term="%22McMurray%2C+CL%22">McMurray, CL</searchLink><br /><searchLink fieldCode="AR" term="%22Odedra%2C+M%22">Odedra, M</searchLink><br /><searchLink fieldCode="AR" term="%22Shaw%2C+J%22">Shaw, J</searchLink><br /><searchLink fieldCode="AR" term="%22Tang%2C+JW%22">Tang, JW</searchLink><br /><searchLink fieldCode="AR" term="%22Willford%2C+NJ%22">Willford, NJ</searchLink><br /><searchLink fieldCode="AR" 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term="%22Shah%2C+D%22">Shah, D</searchLink><br /><searchLink fieldCode="AR" term="%22Alcolea%2C+A%22">Alcolea, A</searchLink><br /><searchLink fieldCode="AR" term="%22Ohemeng-Kumi%2C+N%22">Ohemeng-Kumi, N</searchLink><br /><searchLink fieldCode="AR" term="%22Ramble%2C+J%22">Ramble, J</searchLink><br /><searchLink fieldCode="AR" term="%22Sehmi%2C+J%22">Sehmi, J</searchLink><br /><searchLink fieldCode="AR" term="%22Williams%2C+R%22">Williams, R</searchLink><br /><searchLink fieldCode="AR" term="%22Chatterton%2C+W%22">Chatterton, W</searchLink><br /><searchLink fieldCode="AR" term="%22Pusok%2C+M%22">Pusok, M</searchLink><br /><searchLink fieldCode="AR" term="%22Everson%2C+W%22">Everson, W</searchLink><br /><searchLink fieldCode="AR" term="%22Castigador%2C+A%22">Castigador, A</searchLink><br /><searchLink fieldCode="AR" term="%22Macnaughton%2C+E%22">Macnaughton, E</searchLink><br /><searchLink fieldCode="AR" term="%22El+Bouzidi%2C+K%22">El Bouzidi, K</searchLink><br /><searchLink 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S</searchLink><br /><searchLink fieldCode="AR" term="%22Essex%2C+S%22">Essex, S</searchLink><br /><searchLink fieldCode="AR" term="%22Murray%2C+LJ%22">Murray, LJ</searchLink><br /><searchLink fieldCode="AR" term="%22Lawton%2C+AI%22">Lawton, AI</searchLink><br /><searchLink fieldCode="AR" term="%22Burton-Fanning%2C+S%22">Burton-Fanning, S</searchLink><br /><searchLink fieldCode="AR" term="%22Payne%2C+BAI%22">Payne, BAI</searchLink><br /><searchLink fieldCode="AR" term="%22Waugh%2C+S%22">Waugh, S</searchLink><br /><searchLink fieldCode="AR" term="%22Gomes%2C+AN%22">Gomes, AN</searchLink><br /><searchLink fieldCode="AR" term="%22Kimuli%2C+M%22">Kimuli, M</searchLink><br /><searchLink fieldCode="AR" term="%22Murray%2C+DR%22">Murray, DR</searchLink><br /><searchLink fieldCode="AR" term="%22Ashfield%2C+P%22">Ashfield, P</searchLink><br /><searchLink fieldCode="AR" term="%22Dobie%2C+D%22">Dobie, D</searchLink><br /><searchLink fieldCode="AR" term="%22Ashford%2C+F%22">Ashford, F</searchLink><br /><searchLink fieldCode="AR" term="%22Best%2C+A%22">Best, A</searchLink><br /><searchLink fieldCode="AR" term="%22Crawford%2C+L%22">Crawford, L</searchLink><br /><searchLink fieldCode="AR" term="%22Cumley%2C+N%22">Cumley, N</searchLink><br /><searchLink fieldCode="AR" term="%22Mayhew%2C+M%22">Mayhew, M</searchLink><br /><searchLink fieldCode="AR" term="%22Megram%2C+O%22">Megram, O</searchLink><br /><searchLink fieldCode="AR" term="%22Mirza%2C+J%22">Mirza, J</searchLink><br /><searchLink fieldCode="AR" term="%22Moles-Garcia%2C+E%22">Moles-Garcia, E</searchLink><br /><searchLink fieldCode="AR" term="%22Percival%2C+B%22">Percival, B</searchLink><br /><searchLink fieldCode="AR" term="%22Ensell%2C+L%22">Ensell, L</searchLink><br /><searchLink fieldCode="AR" term="%22Lowe%2C+HL%22">Lowe, HL</searchLink><br /><searchLink fieldCode="AR" term="%22Maftei%2C+L%22">Maftei, L</searchLink><br /><searchLink fieldCode="AR" term="%22Mondani%2C+M%22">Mondani, M</searchLink><br 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– Name: DatePubCY
  Label: Publication Year
  Group: Date
  Data: 2021
– Name: Subset
  Label: Collection
  Group: HoldingsInfo
  Data: Bournemouth University Research Online (BURO)
– Name: Abstract
  Label: Description
  Group: Ab
  Data: 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.
– Name: TypeDocument
  Label: Document Type
  Group: TypDoc
  Data: article in journal/newspaper
– Name: Format
  Label: File Description
  Group: SrcInfo
  Data: application/pdf
– Name: Language
  Label: Language
  Group: Lang
  Data: English
– Name: NoteTitleSource
  Label: Relation
  Group: SrcInfo
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Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600 (7889), 506-511.
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  Data: https://eprints.bournemouth.ac.uk/38888/
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      – TitleFull: Genomic reconstruction of the SARS-CoV-2 epidemic in England
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      – PersonEntity:
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      – PersonEntity:
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