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

Abstract

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.

Metadata

Item Type:	Article
Authors/Creators:	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 Hamilton, WL 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 Wright, E Aggarwal, D Brooks, E Carabelli, AM Churcher, CM Galai, K Girgis, ST Gupta, RK Ludden, C 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 Hamilton, WL 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 Davies, R 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 Palmer, S 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 Hosmillo, M Attwood, SW du Plessis, L 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 Morgan, S 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 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, 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 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, 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 https://orcid.org/0000-0002-6498-9212 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 Angelis, DD Maxwell, PH Peacock, SJ Weekes, MP Illingworth, C Harrison, EM Matheson, NJ Goodfellow, IG
Copyright, Publisher and Additional Information:	© The Author(s) 2022. Open Access: 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:	COVID-19; Contact Tracing; Genome, Viral; Genomics; Humans; Phylogeny; RNA, Viral; Risk Factors; SARS-CoV-2; Students; United Kingdom; Universities
Dates:	Published: 8 February 2022 Published (online): 8 February 2022 Accepted: 17 December 2021
Institution:	The University of Sheffield
Academic Units:	The University of Sheffield > Faculty of Medicine, Dentistry and Health (Sheffield) > Department of Infection and Immunity (Sheffield)
Depositing User:	Symplectic Sheffield
Date Deposited:	23 Feb 2022 14:40
Last Modified:	23 Feb 2022 14:40
Status:	Published
Publisher:	Nature Research (part of Springer Nature)
Refereed:	Yes
Identification Number:	10.1038/s41467-021-27942-w
Related URLs:	PubMed URL
Open Archives Initiative ID (OAI ID):	oai:eprints.whiterose.ac.uk:183970

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

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