@article{Aggarwal_D-2022_60009,
title = {Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission},
author = {Aggarwal, D. and Warne, B. and Jahun, A. and Hamilton, W. and Fieldman, T. and du Plessis, L. and Hill, V. and Blane, B. and Watkins, E. and Wright, E. and Hall, G. and Ludden, C. and Myers, R. and Hosmillo, M. and Chaudhry, Y. and Pinckert, M. and Georgana, I. and Izuagbe, R. and Leek, D. and Nsonwu, O. and Hughes, G. and Packer, S. and Page, A. and Metaxaki, M. and Fuller, S. and Weale, G. and Holgate, J. and Brown, C. and Howes, R. and McFarlane, D. and Dougan, G. and Pybus, O. and Angelis, D. and Maxwell, P. and Peacock, S. and Weekes, M. and Illingworth, C. and Harrison, E. and Matheson, N. and Goodfellow, I. and Orton, A. and Douthwaite, J. and Rees, S. and Brown, C. and Clark, R. and Jones, D. and Kuenzi, F. and Rankin, J. and Waddell, I. and Maxwell, P. and Matheson, N. and Abell, C. and Braithwaite, V. and Brierley, C. and Crowcroft, J. and Dahal, A. and Faulkner, K. and Glover, M. and Goodfellow, I. and Greatorex, J. and James, L. and Lehner, P. and Leslie, I. and Liddell, K. and Margolis, B. and Morgan, S. and Sheridan, L. and Valletta, S. and Vignoles, A. and Vinnell, M. and Wills, M. and Hilborne, S. and Berry, S. and Kahkeshi, M. and Hancock, D. and Winster, J. and Enright, J. and Samworth, R. and Samtani, V. and Ahmadi-Assalemi, G. and Feather, T. and Goodall, R. and Hoensch, S. and Johnson, D. and Hunt, M. and Mathieson, N. and Nikitina, K. and Sheldrake, Z. and Keen, M. and Sato, A. and Connor, D. and Tolhurst, J. and Williman, J. and Hollamby, V. and Jordan, S. and Fatseas, T. and Taylor, P. and Georgiou, C. and Caspersz, M. and McNulty, C. and Davies, R. and Clarke, R. and Danaei, D. and Dyer, R. and Glew, R. and Lambson, O. and Gibbs, K. and Mozdzen, B. and Raub, G. and Radecki, A. and White, P. and Hughes, R. and Gransden, L. and Ceaser, M. and Sing, R. and Wilson, K. and Parlikad, A. and Dhada, M. and Ridgman, T. and Mungovan, D. and Matthews, S. and Searle, P. and Mills, J. and Neely, A. and Henderson, R. and Murphy, E. and Russell, M. and Freeling, A. and Poppitt, S. and Tynan, J. and Knapton, J. and Marchetti, F. and Angelis, D. and Feltwell, T. and Hadjirin, N. and Hamilton, W. and Jahun, A. and Pinckert, M. and Shaw, A. and Chaudhry, A. and Brown, N. and Mactavous, L. and Hannan, S. and Hosaja, A. and Leong, C. and Wright, J. and Quinnell, N. and Workman, C. and Ferris, M. and Wright, G. and Aggarwal, D. and Brooks, E. and Carabelli, A. and Churcher, C. and Galai, K. and Girgis, S. and Gupta, R. and McManus, G. and Palmer, S. and Peacock, S. and Smith, K. and Allara, E. and Bibby, D. and Bishop, C. and Bosworth, A. and Bradshaw, D. and Chalker, V. and Chand, M. and Dabrera, G. and Ellaby, N. and Gallagher, E. and Groves, N. and Harrison, I. and Hartman, H. and Hopes, R. and Hubb, J. and Hutchings, S. and Lackenby, A. and Ledesma, J. and Lee, D. and Manesis, N. and Manso, C. and Mbisa, T. and Miah, S. and Muir, P. and Osman, H. and Patel, V. and Pearson, C. and Platt, S. and Pymont, H. and Ramsay, M. and Robinson, E. and Schaefer, U. and Thornton, A. and Twohig, K. and Vipond, I. and Williams, D. and Aigrain, L. and Alderton, A. and Amato, R. and Ariani, C. and Barrett, J. and Bassett, A. and Beale, M. and Beaver, C. and Bellis, K. and Betteridge, E. and Bonfield, J. and Bronner, I. and Chapman, M. and Danesh, J. and Davies, R. and Dorman, M. and Drury, E. and Durham, J. and Farr, B. and Foulser, L. and Gonçalves, S. and Goodwin, S. and Gourtovaia, M. and Jackson, D. and James, K. and Jamrozy, D. and Johnston, I. and Kane, L. and Kay, S. and Keatley, J. and Kwiatkowski, D. and Langford, C. and Lawniczak, M. and Lensing, S. and Leonard, S. and Letchford, L. and Lewis, K. and Liddle, J. and Livett, R. and Lo, S. and Makunin, A. and Martincorena, I. and McCarthy, S. and McGuigan, S. and Moll, R. and Nelson, R. and Oliver, K. and Palmer, S. and Park, N. and Patel, M. and Prestwood, L. and Puethe, C. and Quail, M. and Rajan, D. and Rajatileka, S. and Redshaw, N. and Scott, C. and Shirley, L. and Sillitoe, J. and Thurston, S. and Tonkin-Hill, G. and Tovar-Corona, J. and Weldon, D. and Whitwham, A. and Attwood, S. and Escalera-Zamudio, M. and Francois, S. and Gutierrez, B. and Kraemer, M. and Raghwani, J. and Vasylyeva, T. and Zarebski, A. and Alikhan, N. and Aydin, A. and Baker, D. and de Oliveira Martins, L. and Kay, G. and Le-Viet, T. and Mather, A. and Meadows, L. and O'Grady, J. and Rudder, S. and Trotter, A. and Illingworth, C. and Jackson, C. and Aranday-Cortes, E. and Asamaphan, P. and Broos, A. and Carmichael, S. and da Silva Filipe, A. and Hughes, J. and Jesudason, N. and Johnson, N. and Li, K. and Mair, D. and Nichols, J. and Nickbakhsh, S. and Niebel, M. and Nomikou, K. and Orton, R. and Robertson, D. and Shah, R. and Shepherd, J. and Singer, J. and Starinskij, I. and Thomson, E. and Tong, L. and Vattipally, S. and Ash, A. and Koshy, C. and Cortes, N. and Kidd, S. and Lynch, J. and Moore, N. and Mori, M. and Wise, E. and Curran, T. and Fairley, D. and McKenna, J. and Adams, H. and Bonsall, D. and Fraser, C. and Golubchik, T. and Cogger, B. and Hassan-Ibrahim, M. and Malone, C. and Reynolds, N. and Wantoch, M. and Afifi, S. and Beer, R. and John, M. and Maksimovic, J. and McCluggage, K. and Morgan, S. and Spellman, K. and Bresner, C. and Connor, T. and Fuller, W. and Guest, M. and Gulliver, H. and Kitchen, C. and Marchbank, A. and Merrick, I. and Munn, R. and Price, A. and Southgate, J. and Workman, T. and Patel, A. and Snell, L. and Batra, R. and Charalampous, T. and Edgeworth, J. and Nebbia, G. and Beckett, A. and Robson, S. and Aanensen, D. and Abu-Dahab, K. and Menegazzo, M. and Taylor, B. and Underwood, A. and Yeats, C. and Berry, L. and Boswell, T. and Clark, G. and Fleming, V. and Howson-Wells, H. and Jones, C. and Joseph, A. and Khakh, M. and Lister, M. and Smith, W. and Willingham, I. and Bird, P. and Fallon, K. and Helmer, T. and Holmes, C. and Tang, J. and Blakey, V. and Campbell, S. and Raviprakash, V. and Sheriff, N. and Williams, L. and Carlile, M. and Debebe, J. and Holmes, N. and Loose, M. and Moore, C. and Sang, F. and Wright, V. and Coll, F. and Betancor, G. and Signell, A. and Wilson, H. and Davis, T. and Eldirdiri, S. and Kenyon, A. and Torok, M. and Lowe, H. and Moses, S. and Bedford, L. and Moore, J. and Stonehouse, S. and Awan, A. and Fisher, C. and BoYes, J. and Atkinson, L. and Breuer, J. and Brown, J. and Harris, K. and Lee, J. and Shah, D. and Storey, N. and Flaviani, F. and Alcolea-Medina, A. and Vernet, G. and Williams, R. and Chapman, M. and Chatterton, W. and Heaney, J. and Levett, L. and Pusok, M. and Xu-McCrae, L. and Bashton, M. and Smith, D. and Young, G. and Bolt, F. and Cox, A. and Holmes, A. and Madona, P. and Mookerjee, S. and Price, J. and Randell, P. and Boyd, O. and Nascimento, F. and Geidelberg, L. and Johnson, R. and Jorgensen, D. and Ragonnet-Cronin, M. and Rowan, A. and Siveroni, I. and Taylor, G. and Volz, E. and Smollett, K. and Loman, N. and McMurray, C. and McNally, A. and Nicholls, S. and Poplawski, R. and Quick, J. and Rowe, W. and Stockton, J. and Nunez, R. and Breen, C. and Cowell, A. and Mason, J. and O'Toole, E. and Robinson, T. and Watts, J. and Sluga, G. and Ahmad, S. and George, R. and Machin, N. and Halstead, F. and Hogsden, W. and Sivaprakasam, V. and Carden, H. and Hale, A. and Harper, K. and Macfarlane-Smith, L. and Burton-Fanning, S. and Collins, J. and Eltringham, G. and Payne, B. and Taha, Y. and Waugh, S. and O'Brien, S. and Rushton, S. and Blacow, R. and Bradley, A. and MacLean, A. and Mollett, G. and Dewar, R. and McHugh, M. and Templeton, K. and Wastenge, E. and Coupland, L. and Dervisevic, S. and Meader, E. and Stanley, R. and Smith, L. and Barton, E. and Graham, C. and Padgett, D. and Scott, G. and Greenaway, J. and Swindells, E. and McCann, C. and Nelson, A. and Yew, W. and Andersson, M. and Crook, D. and Eyre, D. and Justice, A. and Peto, T. and Duckworth, N. and Sloan, T. and Walsh, S. and Bicknell, K. and Chauhan, A. and Elliott, S. and Glaysher, S. and Impey, R. and Lloyd, A. and Wyllie, S. and Levene, N. and Monaghan, L. and Bradley, D. and Wyatt, T. and Curran, M. and Parmar, S. and Holden, M. and Shaaban, S. and Adams, A. and Asad, H. and Birchley, A. and Bull, M. and Coombes, J. and Corden, S. and Cottrell, S. and Craine, N. and Cronin, M. and Davies, A. and De Lacy, E. and Downing, F. and Edwards, S. and Evans, J. and Fina, L. and Gaskin, A. and Gatica-Wilcox, B. and Gifford, L. and Gilbert, L. and Graham, L. and Heyburn, D. and Hilvers, E. and Howe, R. and Jones, H. and Jones, R. and Jones, S. and Kumziene-Summerhayes, S. and McKerr, C. and Moore, C. and Morgan, M. and Pacchiarini, N. and Perry, M. and Plimmer, A. and Rey, S. and Shankar, G. and Taylor, S. and Watkins, J. and Williams, C. and Casey, A. and Ratcliffe, L. and Acheson, E. and Molnar, Z. and Simpson, D. and Thompson, T. and Auckland, C. and Ellard, S. and Jones, C. and Knight, B. and Masoli, J. and Haque, T. and Hart, J. and Irish-Tavares, D. and Mahungu, T. and Witele, E. and Dadrah, A. and Fenton, M. and Saluja, T. and Symmonds, A. and Bourgeois, Y. and Scarlett, G. and Cook, K. and Dent, H. and Fearn, C. and Goudarzi, S. and Loveson, K. and Paul, H. and Evans, C. and Johnson, K. and Partridge, D. and Raza, M. and Baker, P. and Bonner, S. and Essex, S. and Liggett, S. and Lyons, R. and Mahanama, A. and Saeed, K. and Samaraweera, B. and Silveira, S. and Wilson-Davies, E. and Emanuela, P. and Bayzid, N. and Cotic, M. and Ensell, L. and Hartley, J. and Jannoo, R. and Karamani, A. and Kristiansen, M. and Lowe, H. and Roy, S. and Westhorpe, A. and Williams, R. and Williams, C. and Jeremiah, S. and Prieto, J. and Berry, L. and Grammatopoulos, D. and Jones, K. and Pandey, S. and Beggs, A. and Richter, A. and Ashcroft, F. and Best, A. and Crawford, L. and Cumley, N. and Mayhew, M. and Megram, O. and Mirza, J. and Moles-Garcia, E. and Percival, B. and Bucca, G. and Hesketh, A. and Smith, C. and Davidson, R. and Balcazar, C. and Gallagher, M. and O'Toole, Á. and Rambaut, A. and Rooke, S. and Stanton, T. and Williams, T. and Williamson, K. and Bewshea, C. and Farbos, A. and Harrison, J. and Jeffries, A. and Manley, R. and Michell, S. and Michelsen, M. and Sambles, C. and Studholme, D. and Temperton, B. and Warwick-Dugdale, J. and Darby, A. and Eccles, R. and Gemmell, M. and Gregory, R. and Haldenby, S. and Hiscox, J. and Hughes, M. and Iturriza-Gomara, M. and Jackson, K. and Lucaci, A. and Nelson, C. and Paterson, S. and Rainbow, L. and Turtle, L. and Vamos, E. and Webster, H. and Whitehead, M. and Wierzbicki, C. and Angyal, A. and Brown, R. and de Silva, T. and Freeman, T. and Gallis, M. and Green, L. and Groves, D. and Keeley, A. and Lindsey, B. and Louka, S. and Parker, M. and Parsons, P. and Smith, N. and Tucker, R. and Wang, D. and Whiteley, M. and Wyles, M. and Zhang, P. and Alam, M. and Baxter, L. and Bridgewater, H. and Brown, P. and Cheng, J. and Constantinidou, C. and Frost, L. and Ott, S. and Stark, R. and Taylor-Joyce, G. and Unnikrishnan, M. and Cerda, A. and Merrill, T. and Wilson, R. and Ball, J. and Chappell, J. and McClure, P. and Tsoleridis, T. and Buck, D. and de Cesare, M. and Green, A. and MacIntyre-Cockett, G. and Todd, J. and Trebes, A. and Gunson, R. and Cormie, C. and Dias, J. and Forrest, S. and Gill, H. and Higginson, E. and Kermack, L. and Maes, M. and Ruis, C. and Sridhar, S. and Young, J.},
month = {feb},
year = {2022},
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.},
volume = {13},
issue = {751},
journal = {Nature Communications},
publisher = {Springer Nature},
url = {https://doi.org/10.1038/s41467-021-27942-w},
}
