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

Journal article

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.

Authors: Nickbakhsh, S; Hughes, J; Christofidis, N; Griffiths, E; Shaaban, S

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Nature Research
• Journal: Scientific Reports
• Volume: 12
• Issue: 1
• Pages: 11735-11735
• Article number: 11735
• Publication date: 2022-07-19
• DOI: 10.1038/s41598-022-15661-1
• EISSN: 2045-2322
• ISSN: 2045-2322
• Language: English
• Keywords: Contact tracing; Scale (ratio); Virology; Environmental health; Outbreak; Geography; Cluster (spacecraft); Public health; Computer science; Coronavirus disease 2019 (COVID-19); Epidemiology; Population; Infectious disease (medical specialty); Pathology; Medicine; Context (archaeology); Disease