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

Aggarwal, D. orcid.org/0000-0002-5938-8172, Warne, B. orcid.org/0000-0003-1326-0373, Jahun, A.S. orcid.org/0000-0002-4585-1701 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

Abstract

Metadata

Item Type: Article
Authors/Creators:
  • Aggarwal, D. ORCID logo https://orcid.org/0000-0002-5938-8172
  • Warne, B. ORCID logo https://orcid.org/0000-0003-1326-0373
  • Jahun, A.S. ORCID logo https://orcid.org/0000-0002-4585-1701
  • Hamilton, W.L. ORCID logo https://orcid.org/0000-0002-3330-353X
  • Fieldman, T.
  • du Plessis, L. ORCID logo https://orcid.org/0000-0003-0352-6289
  • Hill, V. ORCID logo https://orcid.org/0000-0002-3509-8146
  • Blane, B. ORCID logo https://orcid.org/0000-0002-0996-9091
  • Watkins, E.
  • Wright, E. ORCID logo https://orcid.org/0000-0002-8378-9072
  • Hall, G. ORCID logo https://orcid.org/0000-0003-3928-3979
  • Ludden, C.
  • Myers, R.
  • Hosmillo, M.
  • Chaudhry, Y. ORCID logo https://orcid.org/0000-0002-2386-3269
  • Pinckert, M.L. ORCID logo https://orcid.org/0000-0002-6072-5949
  • Georgana, I.
  • Izuagbe, R. ORCID logo https://orcid.org/0000-0001-8080-2510
  • Leek, D.
  • Nsonwu, O. ORCID logo https://orcid.org/0000-0002-3024-700X
  • Hughes, G.J. ORCID logo https://orcid.org/0000-0002-3781-0117
  • Packer, S. ORCID logo https://orcid.org/0000-0002-9157-3650
  • Page, A.J. ORCID logo https://orcid.org/0000-0001-6919-6062
  • Metaxaki, M. ORCID logo https://orcid.org/0000-0002-4552-1622
  • Fuller, S.
  • Weale, G. ORCID logo https://orcid.org/0000-0003-4728-5915
  • Holgate, J.
  • Brown, C.A. ORCID logo https://orcid.org/0000-0001-7773-0878
  • Orton, A.
  • Douthwaite, J.
  • Rees, S.
  • Brown, C.
  • Clark, R.
  • Jones, D.R.
  • 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, M.B.
  • 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, D.D.
  • Feltwell, T.
  • Hadjirin, N.F.
  • Hamilton, W.L.
  • Jahun, A.
  • Pinckert, M.
  • Shaw, A.
  • Chaudhry, A.
  • Brown, N.M.
  • Mactavous, L.
  • Hannan, S.
  • Hosaja, A.
  • Leong, C.
  • Wright, J.
  • Quinnell, N.
  • Workman, C.
  • Ferris, M.
  • Wright, G.
  • Wright, E. ORCID logo https://orcid.org/0000-0002-8378-9072
  • Aggarwal, D. ORCID logo https://orcid.org/0000-0002-5938-8172
  • Brooks, E.
  • Carabelli, A.M.
  • Churcher, C.M.
  • Galai, K.
  • Girgis, S.T.
  • Gupta, R.K.
  • Ludden, C.
  • McManus, G.M.
  • Palmer, S.
  • Peacock, S.J. ORCID logo https://orcid.org/0000-0002-1718-2782
  • Smith, K.S.
  • 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, H.M.
  • Ramsay, M.
  • Robinson, E.
  • Schaefer, U.
  • Thornton, A.
  • Twohig, K.A.
  • Vipond, I.B.
  • Williams, D.
  • Hamilton, W.L. ORCID logo https://orcid.org/0000-0002-3330-353X
  • Aigrain, L.
  • Alderton, A.
  • Amato, R.
  • Ariani, C.V.
  • Barrett, J.
  • Bassett, A.R.
  • Beale, M.A.
  • Beaver, C.
  • Bellis, K.L.
  • Betteridge, E.
  • Bonfield, J.
  • Bronner, I.F.
  • Chapman, M.H.S.
  • Danesh, J.
  • Davies, R.
  • Dorman, M.J.
  • Drury, E.
  • Durham, J.
  • Farr, B.W.
  • Foulser, L.
  • Goncalves, S.
  • Goodwin, S.
  • Gourtovaia, M.
  • Jackson, D.K.
  • James, K.
  • Jamrozy, D.
  • Johnston, I.
  • Kane, L.
  • Kay, S.
  • Keatley, J.-P.
  • Kwiatkowski, D.
  • Langford, C.F.
  • Lawniczak, M.
  • Lensing, S.V.
  • Leonard, S.
  • Letchford, L.
  • Lewis, K.
  • Liddle, J.
  • Livett, R.
  • Lo, S.
  • Makunin, A.
  • Martincorena, I.
  • McCarthy, S.
  • McGuigan, S.
  • Moll, R.J.
  • Nelson, R.
  • Oliver, K.
  • Palmer, S.
  • Park, N.R.
  • Patel, M.
  • Prestwood, L.
  • Puethe, C.
  • Quail, M.A.
  • Rajan, D.
  • Rajatileka, S.
  • Redshaw, N.M.
  • Scott, C.
  • Shirley, L.
  • Sillitoe, J.
  • Thurston, S.A.J.
  • Tonkin-Hill, G.
  • Tovar-Corona, J.M.
  • Weldon, D.
  • Whitwham, A.
  • Hosmillo, M.
  • Attwood, S.W.
  • du Plessis, L. ORCID logo https://orcid.org/0000-0003-0352-6289
  • Zamudio, M.E.
  • Francois, S.
  • Gutierrez, B.
  • Kraemer, M.U.G.
  • Raghwani, J.
  • Vasylyeva, T.I.
  • Zarebski, A.E.
  • Alikhan, N.-F.
  • Aydin, A.
  • Baker, D.J.
  • de Oliveira Martins, L.
  • Kay, G.L.
  • Le-Viet, T.
  • Mather, A.E.
  • Meadows, L.
  • O’Grady, J.
  • Rudder, S.
  • Trotter, A.J.
  • Illingworth, C.J.
  • Jackson, C.
  • Aranday-Cortes, E.
  • Asamaphan, P.
  • Broos, A.
  • Carmichael, S.N.
  • da Silva Filipe, A.
  • Hughes, J.
  • Jesudason, N.G.
  • Johnson, N.
  • Li, K.K.
  • Mair, D.
  • Nichols, J.
  • Nickbakhsh, S.
  • Niebel, M.O.
  • Nomikou, K.
  • Orton, R.J.
  • Robertson, D.L.
  • Shah, R.N.
  • Shepherd, J.G.
  • Singer, J.B.
  • Starinskij, I.
  • Thomson, E.C.
  • Tong, L.
  • Vattipally, S.
  • Ash, A.
  • Koshy, C.
  • Cortes, N.
  • Kidd, S.
  • Lynch, J.
  • Moore, N.
  • Mori, M.
  • Wise, E.
  • Curran, T.
  • Fairley, D.J.
  • McKenna, J.P.
  • Adams, H.
  • Bonsall, D.
  • Fraser, C.
  • Golubchik, T.
  • Cogger, B.J.
  • Hassan-Ibrahim, M.O.
  • Malone, C.S.
  • Reynolds, N.
  • Wantoch, M.
  • Afifi, S.
  • Beer, R.
  • John, M.
  • Maksimovic, J.
  • McCluggage, K.
  • Morgan, S.
  • Spellman, K.
  • Bresner, C.
  • Connor, T.R.
  • Fuller, W.
  • Guest, M.
  • Gulliver, H.
  • Kitchen, C.
  • Marchbank, A.
  • Merrick, I.
  • Munn, R.
  • Price, A.
  • Southgate, J.
  • Workman, T.
  • Patel, A.
  • Snell, L.B.
  • Batra, R.
  • Charalampous, T.
  • Edgeworth, J.
  • Nebbia, G.
  • Beckett, A.H.
  • Robson, S.C.
  • Aanensen, D.M.
  • Abudahab, K.
  • Menegazzo, M.
  • Taylor, B.E.W.
  • Underwood, A.P.
  • Yeats, C.A.
  • Berry, L.
  • Boswell, T.
  • Clark, G.
  • Fleming, V.M.
  • Howson-Wells, H.C.
  • Jones, C.
  • Joseph, A.
  • Khakh, M.
  • Lister, M.M.
  • 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, M.W.
  • Moore, C.
  • Sang, F.
  • Wright, V.
  • Coll, F.
  • Betancor, G.
  • Signell, A.W.
  • Wilson, H.D.
  • Davis, T.
  • Eldirdiri, S.
  • Kenyon, A.
  • Torok, M.E.
  • Lowe, H.
  • Moses, S.
  • Bedford, L.
  • Moore, J.
  • Stonehouse, S.
  • Awan, A.R.
  • Fisher, C.L.
  • BoYes, J.
  • Atkinson, L.
  • Breuer, J.
  • Brown, J.R.
  • Harris, K.A.
  • Lee, J.C.D.
  • Shah, D.
  • Storey, N.
  • Flaviani, F.
  • Alcolea-Medina, A.
  • Vernet, G.
  • Williams, R.
  • Chapman, M.R.
  • Chatterton, W.
  • Heaney, J.
  • Levett, L.J.
  • Pusok, M.
  • Xu-McCrae, L.
  • Bashton, M.
  • Smith, D.L.
  • Young, G.R.
  • Bolt, F.
  • Cox, A.
  • Holmes, A.
  • Madona, P.
  • Mookerjee, S.
  • Price, J.
  • Randell, P.A.
  • Boyd, O.
  • Nascimento, F.F.
  • Geidelberg, L.
  • Johnson, R.
  • Jorgensen, D.
  • Ragonnet-Cronin, M.
  • Rowan, A.
  • Siveroni, I.
  • Taylor, G.P.
  • Volz, E.M.
  • Smollett, K.L.
  • Loman, N.J.
  • McMurray, C.
  • McNally, A.
  • Nicholls, S.
  • Poplawski, R.
  • Quick, J.
  • Rowe, W.
  • Stockton, J.
  • Nunez, R.T.M.
  • Breen, C.
  • Cowell, A.
  • Mason, J.
  • O’Toole, E.
  • Robinson, T.I.
  • Watts, J.
  • Sluga, G.
  • Ahmad, S.S.Y.
  • George, R.P.
  • Machin, N.W.
  • Halstead, F.
  • Hogsden, W.
  • Sivaprakasam, V.
  • Carden, H.
  • Hale, A.D.
  • Harper, K.L.
  • Macfarlane-Smith, L.R.
  • Burton-Fanning, S.
  • Collins, J.
  • Eltringham, G.
  • Payne, B.A.I.
  • Taha, Y.
  • Waugh, S.
  • O’Brien, S.
  • Rushton, S.
  • Blacow, R.
  • Bradley, A.
  • Maclean, A.
  • Mollett, G.
  • Dewar, R.
  • McHugh, M.P.
  • Templeton, K.E.
  • Wastenge, E.
  • Coupland, L.
  • Dervisevic, S.
  • Meader, E.J.
  • Stanley, R.
  • Smith, L.
  • Barton, E.
  • Graham, C.
  • Padgett, D.
  • Scott, G.
  • Greenaway, J.
  • Swindells, E.
  • McCann, C.M.
  • Nelson, A.
  • Yew, W.C.
  • Andersson, M.
  • Crook, D.
  • Eyre, D.
  • Justice, A.
  • Peto, T.
  • Duckworth, N.
  • Sloan, T.J.
  • Walsh, S.
  • Bicknell, K.
  • Chauhan, A.J.
  • Elliott, S.
  • Glaysher, S.
  • Impey, R.
  • Lloyd, A.
  • Wyllie, S.
  • Levene, N.
  • Monaghan, L.
  • Bradley, D.T.
  • Wyatt, T.
  • Curran, M.D.
  • Parmar, S.
  • Holden, M.T.G.
  • Shaaban, S.
  • Adams, A.
  • Asad, H.
  • Birchley, A.
  • Bull, M.
  • Coombes, J.
  • Corden, S.
  • Cottrell, S.
  • Craine, N.
  • Cronin, M.
  • Davies, A.
  • Lacy, E.D.
  • Downing, F.
  • Edwards, S.
  • Evans, J.M.
  • 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.
  • Moore, 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, D.A.
  • Thompson, T.
  • Auckland, C.
  • Ellard, S.
  • Jones, C.R.
  • Knight, B.A.
  • Masoli, J.A.H.
  • Haque, T.
  • Hart, J.
  • Irish-Tavares, D.
  • Mahungu, T.W.
  • Witele, E.
  • Dadrah, A.
  • Fenton, M.L.
  • Saluja, T.
  • Symmonds, A.
  • Bourgeois, Y.
  • Scarlett, G.P.
  • Cook, K.
  • Dent, H.
  • Fearn, C.
  • Goudarzi, S.
  • Loveson, K.F.
  • Paul, H.
  • Evans, C.
  • Johnson, K.
  • Partridge, D.G.
  • Raza, M.
  • Baker, P.
  • Bonner, S.
  • Essex, S.
  • Liggett, S.
  • Lyons, R.A.
  • Mahanama, A.I.K.
  • Saeed, K.
  • Samaraweera, B.
  • Silveira, S.
  • Wilson-Davies, E.
  • Emanuela, P.
  • Bayzid, N.
  • Cotic, M.
  • Ensell, L.
  • Hartley, J.A.
  • Jannoo, R.
  • Karamani, A.
  • Kristiansen, M.
  • Lowe, H.L.
  • Roy, S.
  • Westhorpe, A.P.
  • Williams, R.J.
  • Williams, C.A.
  • Jeremiah, S.
  • Prieto, J.A.
  • Berry, L.
  • 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, A.R.
  • Smith, C.P.
  • Davidson, R.K.
  • Balcazar, C.E.
  • Gallagher, M.D.
  • O’Toole, Á
  • Rambaut, A.
  • Rooke, S.
  • Stanton, T.D.
  • Williams, T.
  • Williamson, K.A.
  • Bewshea, C.M.
  • Farbos, A.
  • Harrison, J.W.
  • Jeffries, A.R.
  • Manley, R.
  • Michell, S.L.
  • Michelsen, M.L.
  • Sambles, C.M.
  • Studholme, D.J.
  • Temperton, B.
  • Warwick-Dugdale, J.
  • Darby, A.C.
  • Eccles, R.
  • Gemmell, M.
  • Gregory, R.
  • Haldenby, S.T.
  • Hiscox, J.A.
  • Hughes, M.
  • Iturriza-Gomara, M.
  • Jackson, K.A.
  • Lucaci, A.O.
  • Nelson, C.
  • Paterson, S.
  • Rainbow, L.
  • Turtle, L.
  • Vamos, E.E.
  • Webster, H.J.
  • Whitehead, M.
  • Wierzbicki, C.
  • Angyal, A.
  • Brown, R.
  • de Silva, T.I.
  • Freeman, T.M.
  • Gallis, M.
  • Green, L.R.
  • Groves, D.C.
  • Keeley, A.J.
  • Lindsey, B.B.
  • Louka, S.F.
  • Parker, M.D.
  • Parsons, P.J.
  • Smith, N.
  • Tucker, R.M.
  • Wang, D.
  • Whiteley, M.
  • Wyles, M.
  • Zhang, P.
  • Alam, M.T.
  • Baxter, L.
  • Bridgewater, H.E.
  • Brown, P.E.
  • Cheng, J.K.J.
  • Constantinidou, C.
  • Frost, L.R.
  • Ott, S.
  • Stark, R.
  • Taylor-Joyce, G.
  • Unnikrishnan, M.
  • Cerda, A.C.
  • Merrill, T.V.
  • Wilson, R.E.
  • Ball, J.
  • Chappell, J.G.
  • McClure, P.C.
  • Tsoleridis, T.
  • Buck, D.
  • de Cesare, M.
  • Green, A.
  • MacIntyre-Cockett, G.
  • Todd, J.A.
  • Trebes, A.
  • Gunson, R.N.
  • Cormie, C.
  • Dias, J.
  • Forrest, S.
  • Gill, H.K.
  • Higginson, E.E.
  • Kermack, L.M.
  • Maes, M.
  • Ruis, C.
  • Sridhar, S.
  • Young, J.
  • Howes, R.
  • McFarlane, D.
  • Dougan, G.
  • Pybus, O.G. ORCID logo https://orcid.org/0000-0002-8797-2667
  • Angelis, D.D.
  • Maxwell, P.H.
  • Peacock, S.J. ORCID logo https://orcid.org/0000-0002-1718-2782
  • Weekes, M.P. ORCID logo https://orcid.org/0000-0003-3196-5545
  • Illingworth, C.
  • Harrison, E.M. ORCID logo https://orcid.org/0000-0003-2720-0507
  • Matheson, N.J. ORCID logo https://orcid.org/0000-0002-3318-1851
  • Goodfellow, I.G. ORCID logo https://orcid.org/0000-0002-9483-510X
Copyright, Publisher and Additional Information:

© The Author(s) 2022. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/ licenses/by/4.0/.

Keywords: Cambridge Covid-19 testing Centre; University of Cambridge Asymptomatic COVID-19 Screening Programme Consortium; COVID-19 Genomics UK (COG-UK) Consortium; Humans; RNA, Viral; Contact Tracing; Risk Factors; Genomics; Phylogeny; Genome, Viral; Students; Universities; United Kingdom; COVID-19; SARS-CoV-2
Dates:
  • Accepted: 17 December 2021
  • Published (online): 8 February 2022
  • Published: 8 February 2022
Institution: The University of Leeds
Academic Units: The University of Leeds > Faculty of Biological Sciences (Leeds) > School of Molecular and Cellular Biology (Leeds) > Molecular Biology (Leeds)
Depositing User: Symplectic Publications
Date Deposited: 25 Apr 2024 14:44
Last Modified: 25 Apr 2024 14:44
Published Version: https://www.nature.com/articles/s41467-021-27942-w
Status: Published
Publisher: Springer
Identification Number: https://doi.org/10.1038/s41467-021-27942-w
Related URLs:

Export

Statistics