Asymptomatic screening and genome sequencing help Cambridge understand spread of SARS-CoV-2 among its students

Initial results suggest that the screening programme, together with the University’s public health measures and responsible student behaviour, has helped limit the spread of the virus.

Now, the team running the programme has joined up with researchers at the COVID-19 Genomics UK Consortium (COG-UK) to track how infections spread among the student population. They have shown how a small number of transmission events early on were likely responsible for most of the infections at the University and found little evidence of substantial transmission of SARS-CoV-2 between students and the local Cambridge community in the first five weeks of term.

Around 12,000 students living in College accommodation (80% of eligible students) signed up to the asymptomatic screening programme, which uses a pooled sample approach to reduce the number of tests to fewer than 2,000 per week. In the first weeks of term, 1-2 students from each ‘household’ were tested each week; this has now increased to all participating students being tested each week. In addition, the University offers tests to students and staff who show symptoms of potential COVID-19.

The University is also playing a leading role in COG-UK, which is sequencing the genetic code of samples of the virus isolated from infected individuals to help better understand the spread of infection. As a virus spreads, its genetic code acquires mutations. By comparing the genetic code of samples, it is possible to plot a genetic ‘family tree’ known as phylogenetic tree and to say, coupled with epidemiological information, whether two cases are related – identical or almost-identical samples are likely to be closely related, while genomes with a larger number of genetic differences are less likely to be related.

As part of this work, COG-UK is analysing virus samples from students identified as positive through the University of Cambridge’s testing programmes and comparing them to samples taken from people in the wider Cambridge community. COG-UK and the University have released their interim report, covering the first five weeks of term.

The analysis showed that in week two, 90% of infections were confined to three lineages (related viral genomes). This lack of diversity suggests that a small number of transmission events at the start of term led to the majority of infections in the University.

Outbreaks that have largely been restricted to single Colleges appear to have been contained, suggesting that measures to prevent spread of the virus were successful. In one of the largest clusters (which included 32 cases by week three), half of the students were asymptomatic, highlighting the importance of screening programmes in helping identify infected individuals.

The largest cluster of cases (139 cases by week five, including 135 students, 1 staff member and 3 individuals from the local community) was the source of ongoing transmission within the University. It included students from a number of Colleges, courses and years of study. However, it is not clear whether these can be traced back to a single event that led to dispersion amongst colleges and courses.

Dr Dinesh Aggarwal from the Department of Medicine at the University of Cambridge and a member of COG-UK said: “It appears that a few instances of the virus being introduced to the University account for the majority of cases of established transmission. This suggests to us that in most cases, when a virus was introduced, students behaving responsibly and complying with infection control measures helped stop the virus in its tracks.

“We hope it will be particularly reassuring that so far we have not found evidence of substantial transmission between our students and the local community.”

Dr Ben Warne, a Clinical Research Fellow and one of the leads on the University’s asymptomatic screening programme, added: “It’s clear we need to better understand how the virus spreads between students on different courses and at different Colleges. Once established, these widely-distributed outbreaks are more challenging to control, potentially resulting in continued spread. Genomics should help us piece together this puzzle and help us target prevention strategies.”

The team say their findings appear to suggest that a regular screening programme to detect asymptomatic infection and robust containment measures can be effective at limiting transmission both within the University and to the wider community. This will be particularly important with the emergence of a new, more transmissible variant and substantially higher levels of transmission within the community.

Patrick Maxwell, Regius Professor of Physic at the University of Cambridge, said: “Getting our screening programme up and running in time for the start of term was no small order, but we believe it has paid off. Asymptomatic screening can help identify cases of infection early, including where students are unaware of infection, and inform infection control measures. This has never been more urgent, with the emergence of the new variant.”

The University recently announced that while it will remain open, almost all teaching and learning for undergraduate and postgraduate taught students will move online for the entirety of the Lent term. Undergraduate and postgraduate taught students have been asked to remain where they are currently staying, other than for certain exceptions.