Academic Journal

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

Bibliographic Details
Title: Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission
Authors: Aggarwal, D, Warne, B, Jahun, AS, Hamilton, WL, Fieldman, T, du Plessis, L, Hill, V, Blane, B, Watkins, E, Wright, E, Hall, G, Ludden, C, Myers, R, Hosmillo, M, Chaudhry, Y, Pinckert, ML, Georgana, I, Izuagbe, R, Leek, D, Nsonwu, O, Hughes, GJ, Packer, S, Page, AJ, Metaxaki, M, Fuller, S, Weale, G, Holgate, J, Brown, CA, Orton, A, Douthwaite, J, Rees, S, Brown, C, Clark, R, Jones, DR, Kuenzi, F, Rankin, J, Waddell, I, Maxwell, P, Matheson, N, Abell, C, Braithwaite, V, Brierley, C, Crowcroft, J, Dahal, A, Faulkner, K, Glover, M, Goodfellow, I, Greatorex, J, James, L, Lehner, P, Leslie, I, Liddell, K, Margolis, B, Morgan, S, Sheridan, L, Valletta, S, Vignoles, A, Vinnell, M, Wills, M, Hilborne, S, Berry, S, Kahkeshi, MB, Hancock, D, Winster, J, Enright, J, Samworth, R, Samtani, V, Ahmadi-Assalemi, G, Feather, T, Goodall, R, Hoensch, S, Johnson, D, Hunt, M, Mathieson, N, Nikitina, K, Sheldrake, Z, Keen, M, Sato, A, Connor, D, Tolhurst, J, Williman, J, Hollamby, V, Jordan, S, Fatseas, T, Taylor, P, Georgiou, C, Caspersz, M, McNulty, C, Davies, R, Clarke, R, Danaei, D, Dyer, R, Glew, R, Lambson, O, Gibbs, K, Mozdzen, B, Raub, G, Radecki, A, White, P, Hughes, R, Gransden, L, Ceaser, M, Sing, R, Wilson, K, Parlikad, A, Dhada, M, Ridgman, T, Mungovan, D, Matthews, S, Searle, P, Mills, J, Neely, A, Henderson, R, Murphy, E, Russell, M, Freeling, A, Poppitt, S, Tynan, J, Knapton, J, Marchetti, F, Angelis, DD, Feltwell, T, Hadjirin, NF, Jahun, A, Pinckert, M, Shaw, A, Chaudhry, A, Brown, NM, Mactavous, L, Hannan, S, Hosaja, A, Leong, C, Wright, J, Quinnell, N, Workman, C, Ferris, M, Wright, G, Brooks, E, Carabelli, AM, Churcher, CM, Galai, K, Girgis, ST, Gupta, RK, McManus, GM, Palmer, S, Peacock, SJ, Smith, KS, Allara, E, Bibby, D, Bishop, C, Bosworth, A, Bradshaw, D, Chalker, V, Chand, M, Dabrera, G, Ellaby, N, Gallagher, E, Groves, N, Harrison, I, Hartman, H, Hopes, R, Hubb, J, Hutchings, S, Lackenby, A, Ledesma, J, Lee, D, Manesis, N, Manso, C, Mbisa, T, Miah, S, Muir, P, Osman, H, Patel, V, Pearson, C, Platt, S, Pymont, HM, Ramsay, M, Robinson, E, Schaefer, U, Thornton, A, Twohig, KA, Vipond, IB, Williams, D, Aigrain, L, Alderton, A, Amato, R, Ariani, CV, Barrett, J, Bassett, AR, Beale, MA, Beaver, C, Bellis, KL, Betteridge, E, Bonfield, J, Bronner, IF, Chapman, MHS, Danesh, J, Dorman, MJ, Drury, E, Durham, J, Farr, BW, Foulser, L, Goncalves, S, Goodwin, S, Gourtovaia, M, Jackson, DK, James, K, Jamrozy, D, Johnston, I, Kane, L, Kay, S, Keatley, J-P, Kwiatkowski, D, Langford, CF, Lawniczak, M, Lensing, SV, Leonard, S, Letchford, L, Lewis, K, Liddle, J, Livett, R, Lo, S, Makunin, A, Martincorena, I, McCarthy, S, McGuigan, S, Moll, RJ, Nelson, R, Oliver, K, Park, NR, Patel, M, Prestwood, L, Puethe, C, Quail, MA, Rajan, D, Rajatileka, S, Redshaw, NM, Scott, C, Shirley, L, Sillitoe, J, Thurston, SAJ, Tonkin-Hill, G, Tovar-Corona, JM, Weldon, D, Whitwham, A, Attwood, SW, Zamudio, ME, Francois, S, Gutierrez, B, Kraemer, MUG, Raghwani, J, Vasylyeva, TI, Zarebski, AE, Alikhan, N-F, Aydin, A, Baker, DJ, de Oliveira Martins, L, Kay, GL, Le-Viet, T, Mather, AE, Meadows, L, O’Grady, J, Rudder, S, Trotter, AJ, Illingworth, CJ, Jackson, C, Aranday-Cortes, E, Asamaphan, P, Broos, A, Carmichael, SN, da Silva Filipe, A, Hughes, J, Jesudason, NG, Johnson, N, Li, KK, Mair, D, Nichols, J, Nickbakhsh, S, Niebel, MO, Nomikou, K, Orton, RJ, Robertson, DL, Shah, RN, Shepherd, JG, Singer, JB, Starinskij, I, Thomson, EC, Tong, L, Vattipally, S, Ash, A, Koshy, C, Cortes, N, Kidd, S, Lynch, J, Moore, N, Mori, M, Wise, E, Curran, T, Fairley, DJ, McKenna, JP, Adams, H, Bonsall, D, Fraser, C, Golubchik, T, Cogger, BJ, Hassan-Ibrahim, MO, Malone, CS, Reynolds, N, Wantoch, M, Afifi, S, Beer, R, John, M, Maksimovic, J, McCluggage, K, Spellman, K, Bresner, C, Connor, TR, Fuller, W, Guest, M, Gulliver, H, Kitchen, C, Marchbank, A, Merrick, I, Munn, R, Price, A, Southgate, J, Workman, T, Patel, A, Snell, LB, Batra, R, Charalampous, T, Edgeworth, J, Nebbia, G, Beckett, AH, Robson, SC, Aanensen, DM, Abudahab, K, Menegazzo, M, Taylor, BEW, Underwood, AP, Yeats, CA, Berry, L, Boswell, T, Clark, G, Fleming, VM, Howson-Wells, HC, Jones, C, Joseph, A, Khakh, M, Lister, MM, Smith, W, Willingham, I, Bird, P, Fallon, K, Helmer, T, Holmes, C, Tang, J, Blakey, V, Campbell, S, Raviprakash, V, Sheriff, N, Williams, L-A, Carlile, M, Debebe, J, Holmes, N, Loose, MW, Moore, C, Sang, F, Wright, V, Coll, F, Betancor, G, Signell, AW, Wilson, HD, Davis, T, Eldirdiri, S, Kenyon, A, Torok, ME, Lowe, H, Moses, S, Bedford, L, Moore, J, Stonehouse, S, Awan, AR, Fisher, CL, BoYes, J, Atkinson, L, Breuer, J, Brown, JR, Harris, KA, Lee, JCD, Shah, D, Storey, N, Flaviani, F, Alcolea-Medina, A, Vernet, G, Williams, R, Chapman, MR, Chatterton, W, Heaney, J, Levett, LJ, Pusok, M, Xu-McCrae, L, Bashton, M, Smith, DL, Young, GR, Bolt, F, Cox, A, Holmes, A, Madona, P, Mookerjee, S, Price, J, Randell, PA, Boyd, O, Nascimento, FF, Geidelberg, L, Johnson, R, Jorgensen, D, Ragonnet-Cronin, M, Rowan, A, Siveroni, I, Taylor, GP, Volz, EM, Smollett, KL, Loman, NJ, McMurray, C, McNally, A, Nicholls, S, Poplawski, R, Quick, J, Rowe, W, Stockton, J, Nunez, RTM, Breen, C, Cowell, A, Mason, J, O’Toole, E, Robinson, TI, Watts, J, Sluga, G, Ahmad, SSY, George, RP, Machin, NW, Halstead, F, Hogsden, W, Sivaprakasam, V, Carden, H, Hale, AD, Harper, KL, Macfarlane-Smith, LR, Burton-Fanning, S, Collins, J, Eltringham, G, Payne, BAI, Taha, Y, Waugh, S, O’Brien, S, Rushton, S, Blacow, R, Bradley, A, Maclean, A, Mollett, G, Dewar, R, McHugh, MP, Templeton, KE, Wastenge, E, Coupland, L, Dervisevic, S, Meader, EJ, Stanley, R, Smith, L, Barton, E, Graham, C, Padgett, D, Scott, G, Greenaway, J, Swindells, E, McCann, CM, Nelson, A, Yew, WC, Andersson, M, Crook, D, Eyre, D, Justice, A, Peto, T, Duckworth, N, Sloan, TJ, Walsh, S, Bicknell, K, Chauhan, AJ, Elliott, S, Glaysher, S, Impey, R, Lloyd, A, Wyllie, S, Levene, N, Monaghan, L, Bradley, DT, Wyatt, T, Curran, MD, Parmar, S, Holden, MTG, Shaaban, S, Adams, A, Asad, H, Birchley, A, Bull, M, Coombes, J, Corden, S, Cottrell, S, Craine, N, Cronin, M, Davies, A, Lacy, ED, Downing, F, Edwards, S, Evans, JM, Fina, L, Gaskin, A, Gatica-Wilcox, B, Gifford, L, Gilbert, L, Graham, L, Heyburn, D, Hilvers, E, Howe, R, Jones, H, Jones, R, Jones, S, Kumziene-SummerhaYes, S, McKerr, C, Morgan, M, Pacchiarini, N, Perry, M, Plimmer, A, Rey, S, Shankar, G, Taylor, S, Watkins, J, Williams, C, Casey, A, Ratcliffe, L, Acheson, E, Molnar, Z, Simpson, DA, Thompson, T, Auckland, C, Ellard, S, Jones, CR, Knight, BA, Masoli, JAH, Haque, T, Hart, J, Irish-Tavares, D, Mahungu, TW, Witele, E, Dadrah, A, Fenton, ML, Saluja, T, Symmonds, A, Bourgeois, Y, Scarlett, GP, Cook, K, Dent, H, Fearn, C, Goudarzi, S, Loveson, KF, Paul, H, Evans, C, Johnson, K, Partridge, DG, Raza, M, Baker, P, Bonner, S, Essex, S, Liggett, S, Lyons, RA, Mahanama, AIK, Saeed, K, Samaraweera, B, Silveira, S, Wilson-Davies, E, Emanuela, P, Bayzid, N, Cotic, M, Ensell, L, Hartley, JA, Jannoo, R, Karamani, A, Kristiansen, M, Lowe, HL, Roy, S, Westhorpe, AP, Williams, RJ, Williams, CA, Jeremiah, S, Prieto, JA, Grammatopoulos, D, Jones, K, Pandey, S, Beggs, A, Richter, A, Ashcroft, F, Best, A, Crawford, L, Cumley, N, Mayhew, M, Megram, O, Mirza, J, Moles-Garcia, E, Percival, B, Bucca, G, Hesketh, AR, Smith, CP, Davidson, RK, Balcazar, CE, Gallagher, MD, O’Toole, Á, Rambaut, A, Rooke, S, Stanton, TD, Williams, T, Williamson, KA, Bewshea, CM, Farbos, A, Harrison, JW, Jeffries, AR, Manley, R, Michell, SL, Michelsen, ML, Sambles, CM, Studholme, DJ, Temperton, B, Warwick-Dugdale, J, Darby, AC, Eccles, R, Gemmell, M, Gregory, R, Haldenby, ST, Hiscox, JA, Hughes, M, Iturriza-Gomara, M, Jackson, KA, Lucaci, AO, Nelson, C, Paterson, S, Rainbow, L, Turtle, L, Vamos, EE, Webster, HJ, Whitehead, M, Wierzbicki, C, Angyal, A, Brown, R, de Silva, TI, Freeman, TM, Gallis, M, Green, LR, Groves, DC, Keeley, AJ, Lindsey, BB, Louka, SF, Parker, MD, Parsons, PJ, Smith, N, Tucker, RM, Wang, D, Whiteley, M, Wyles, M, Zhang, P, Alam, MT, Baxter, L, Bridgewater, HE, Brown, PE, Cheng, JKJ, Constantinidou, C, Frost, LR, Ott, S, Stark, R, Taylor-Joyce, G, Unnikrishnan, M, Cerda, AC, Merrill, TV, Wilson, RE, Ball, J, Chappell, JG, McClure, PC, Tsoleridis, T, Buck, D, de Cesare, M, Green, A, MacIntyre-Cockett, G, Todd, JA, Trebes, A, Gunson, RN, Cormie, C, Dias, J, Forrest, S, Gill, HK, Higginson, EE, Kermack, LM, Maes, M, Ruis, C, Sridhar, S, Young, J, Howes, R, McFarlane, D, Dougan, G, Pybus, OG, Maxwell, PH, Weekes, MP, Illingworth, C, Harrison, EM, Matheson, NJ, Goodfellow, IG
Publisher Information: Nature Research (part of Springer Nature)
Publication Year: 2022
Collection: White Rose Research Online (Universities of Leeds, Sheffield & York)
Description: Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.
Document Type: article in journal/newspaper
File Description: text
Language: English
ISSN: 2041-1723
Relation: https://eprints.whiterose.ac.uk/id/eprint/183970/1/s41467-021-27942-w.pdf; Aggarwal, D, Warne, B, Jahun, AS et al. (725 more authors) (2022) Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13 (1). 751. ISSN: 2041-1723
Availability: https://eprints.whiterose.ac.uk/id/eprint/183970/
Rights: cc_by_4
Accession Number: edsbas.4637DB8B
Database: BASE
Description
ISSN:20411723