Genomic sequencing used to investigate university halls outbreak in new study

A new study from Public Health Scotland (PHS) in collaboration with the University of Glasgow and NHS Greater Glasgow and Clyde (external website), published today, investigates a large outbreak of COVID-19 among students resident at university accommodation in Scotland at the start of the autumn 2020 term. It clearly describes the potential for rapid spread of COVID-19 within and between university accommodation.

A total of 1,039 student cases of COVID-19 were identified in this study between September and November 2020, with 50% associated with the student halls. Whole genome sequencing of SARS-CoV-2, the virus that causes COVID-19 disease, combined with epidemiological information was used to provide a deep insight into this outbreak.

The study estimated that at least 11 independent introductions of SARS-CoV-2 into the student population had occurred, with four leading to large outbreaks, and with a complex picture of transmission within and between student halls. Data strongly indicated that for at least two of the four outbreaks, the virus had been imported from within Scotland, owing to a high proportion of students domiciled within Scotland.

Overall there was a strong indication that the infection spread via social activity and gatherings associated with Freshers’ Week. There was no evidence that the university outbreak had significantly impacted on transmission within the local community.

The higher education setting presents a risk for contributing to the winter burden of COVID-19. With rapid identification, and implementation of non-pharmaceutical control interventions, the impact of outbreaks arising in student halls on local communities may be limited. Public health guidance should consider regional differences in the domicile locations of student populations, and of university accommodation and social structures.

Whole genome sequencing is used to monitor the spread and movement of the virus as well as for detecting and tracking variants of COVID-19. Around 350,000 whole genome sequences have been generated in Scotland for COVID-19 to date, from COVID-19 Genomics UK (COG-UK) Consortium partner laboratories and Scotland’s NHS sequencing service. This study maximises these data to generate detailed intelligence on outbreaks.

The university outbreak occurred before the rollout of vaccination and the use of lateral flow devices for regular testing. The study highlights a number of findings which are now being used to support plans for students returning to universities at the start of the autumn term.

Dr Alison Smith-Palmer, Senior author of the study and Consultant in Public Health at PHS, said:

“Since the start of the pandemic, PHS has been using whole genome sequencing to help understand the transmission of the virus in the community and how it spreads in outbreaks, and to manage the risks of new variants or mutations. The data and information we gain through sequencing has played a crucial role in being able to look back at an outbreak such as this. It allows us to investigate it further for public health benefit and to support the overall response to COVID-19, as well as any future outbreaks of different viruses like flu.

Despite the scale at which this particular outbreak grew, it came to a rapid end following the swift action of the University and the local Public Health Protection Team at NHS Greater Glasgow and Clyde, along with an apparent high compliance from the students affected. These actions prevented any further rise in case numbers and also limited any impact on the surrounding community”.

Chris Illingworth, co-senior author and Senior Lecturer at the University of Glasgow, said:

“This study is a reminder that COVID-19 can spread extremely rapidly: Within a short time of the virus getting into the University more than 1,000 students were infected.  Prompt action to stop the spread of the virus was effective in bringing the outbreak to an end and preventing any long-term impact on the wider Glasgow community”.

Dr Catriona Milosevic, co-author of the study and Consultant in Public Health Medicine, NHS Greater Glasgow and Clyde, said:

“COVID-19 has presented us all with huge challenges. This study is a reminder of the impact the pandemic had on university students and staff, as well as adding to our understanding of transmission of infection in these settings. Our job is to assess an outbreak and work with partners to bring it to an end. We are grateful to colleagues at the University of Glasgow, PHS and in Environmental Health for the excellent support we received during this outbreak”.