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

Aggarwal, D. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13, 751. (doi: 10.1038/s41467-021-27942-w) (PMID:35136068) (PMCID:PMC8826310)

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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.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Shah, Dr Rajiv and Li, Dr Kathy and Aranday-Cortes, Dr Elihu and Robertson, Professor David and Singer, Dr Josh and Asamaphan, Dr Patawee and Nickbakhsh, Dr Sema and Tong, Dr Lily and Mair, Mr Daniel and Orton, Dr Richard and Jesudason, Dr Natasha and Gunson, Dr Rory and Blacow, Dr Rachel and Shepherd, Dr James and Da Silva Filipe, Dr Ana and Hughes, Dr Joseph and Mollett, Mr Guy and Broos, Ms Alice and Vattipally, Dr Sreenu and Nichols, Mrs Jenna and Carmichael, Dr Stephen and Nomikou, Dr Kyriaki and Illingworth, Dr Chris and Thomson, Professor Emma and Bradley-Stewart, Dr Amanda and Johnson, Miss Natasha and Enright, Dr Jessica and Smollett, Dr Katherine and MacLean, Dr Alasdair and Niebel, Mr Marc
Authors: Aggarwal, D., Warne, B., Jahun, A. S., Hamilton, W. L., Fieldman, T., du Plessis, L., Hill, V., Blane, B., Watkins, E., Wright, E., Hall, G., Ludden, C., Myers, R., Hosmillo, M., Chaudhry, Y., Pinckert, M. L., Georgana, I., Izuagbe, R., Leek, D., Nsonwu, O., Hughes, G. J., Packer, S., Page, A. J., Metaxaki, M., Fuller, S., Weale, G., Holgate, J., Brown, C. A., Howes, R., McFarlane, D., Dougan, G., Pybus, O. G., Angelis, D. D., Maxwell, P. H., Peacock, S. J., Weekes, M. P., Illingworth, C., Harrison, E. M., Matheson, N. J., Goodfellow, I. G., 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., Aggarwal, D., Brooks, E., Carabelli, A. M., Churcher, C. M., Galai, K., Girgis, S. T., Gupta, R. K., McManus, G. M., Palmer, S., Peacock, S. J., 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., 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., Attwood, S. W., 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. 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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., and Young, J.
College/School:College of Medical Veterinary and Life Sciences > School of Infection & Immunity
College of Science and Engineering > School of Computing Science
College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
Journal Name:Nature Communications
Publisher:Nature Research
ISSN:2041-1723
ISSN (Online):2041-1723
Copyright Holders:Copyright © 2022 The Authors
First Published:First published in Nature Communications 13: 751
Publisher Policy:Reproduced under a Creative Commons License

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