Skip to main content

Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning.

Nickbakhsh, S., Hughes, J., Christofidis, N., Griffiths, E., Shaaban, S., Enright, J., Smollett, K., Nomikou, K., Palmalux, N., Tong, L., Carmichael, S., Sreenu, V.B., Orton, R., Goldstein, E.J., Tomb, R.M., Robson, S.C., Connor, T.R., Loman, N.J., Golubchik, T., Nunez, R.T.M., Bonsall, D., Rambaut, A., Snell, L.B., Livett, R., Ludden, C., Corden, S., Nastouli, E., Nebbia, G., Johnston, I., Lythgoe, K., Torok, M.E., Goodfellow, I.G., Prieto, J.A., Saeed, K., Jackson, D.K., Houlihan, C., Frampton, D., Hamilton, W.L., Witney, A.A., Bucca, G., Pope, C.F., Moore, C., Thomson, E.C., Harrison, E.M., Smith, C.P., Rogan, F., Beckwith, S.M., Murray, A., Singleton, D., Eastick, K., Sheridan, L.A., Randell, P., Jackson, L.M., Ariani, C.V., Gonçalves, S., Fairley, D.J., Loose, M.W., Watkins, J., Moses, S., Nicholls, S., Bull, M., Amato, R., Smith, D.L., Aanensen, D.M., Barrett, J.C., Aggarwal, D., Shepherd, J.G., Curran, M.D., Parmar, S., Parker, M.D., Williams, C., Glaysher, S., Underwood, A.P., Bashton, M., Pacchiarini, N., Loveson, K.F., Byott, M., Carabelli, A.M., Templeton, K.E., de Silva, T.I., Wang, D., Langford, C.F., Sillitoe, J., Gunson, R.N., Cottrell, S., O’Grady, J., Kwiatkowski, D., Lillie, P.J., Cortes, N., Moore, N., Thomas, C., Burns, P.J., Mahungu, T.W., Liggett, S., Beckett, A.H., Holden, M.T.G., Levett, L.J., Osman, H., Hassan-Ibrahim, M.O., Simpson, D.A. and The COVID-19 Genomics UK (COG-UK) Consortium, , 2022. Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports, 12 (1), 11735.

Full text available as:

s41598-022-15661-1.pdf - Published Version
Available under License Creative Commons Attribution.


DOI: 10.1038/s41598-022-15661-1


Whole genome sequencing of SARS-CoV-2 has occurred at an unprecedented scale, and can be exploited for characterising outbreak risks at the fine-scale needed to inform control strategies. One setting at continued risk of COVID-19 outbreaks are higher education institutions, associated with student movements at the start of term, close living conditions within residential halls, and high social contact rates. Here we analysed SARS-CoV-2 whole genome sequences in combination with epidemiological data to investigate a large cluster of student cases associated with University of Glasgow accommodation in autumn 2020, Scotland. We identified 519 student cases of SARS-CoV-2 infection associated with this large cluster through contact tracing data, with 30% sequencing coverage for further analysis. We estimated at least 11 independent introductions of SARS-CoV-2 into the student population, with four comprising the majority of detected cases and consistent with separate outbreaks. These four outbreaks were curtailed within a week following implementation of control measures. The impact of student infections on the local community was short-term despite an underlying increase in community infections. Our study highlights the need for context-specific information in the formation of public health policy for higher educational settings.

Item Type:Article
Uncontrolled Keywords:COVID-19; Disease Outbreaks; Genomics; Health Planning; Humans; SARS-CoV-2; United States; Universities
Group:Faculty of Science & Technology
ID Code:37306
Deposited By: Symplectic RT2
Deposited On:01 Aug 2022 15:36
Last Modified:01 Aug 2022 15:36


Downloads per month over past year

More statistics for this item...
Repository Staff Only -