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

Abstract

Understanding the drivers for spread of SARS-CoV-2 in higher education settings is important to limit transmission between students, and onward spread into at-risk populations. In this study, we prospectively sequenced 482 SARS-CoV-2 isolates derived from asymptomatic student screening and symptomatic testing of students and staff at the University of Cambridge from 5 October to 6 December 2020. We performed a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. After a limited number of viral introductions into the university, the majority of student cases were linked to a single genetic cluster, likely dispersed across the university following social gatherings at a venue outside the university. We identified considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and dramatically reduced following a national lockdown. We observed that transmission clusters were largely segregated within the university or within the community. This 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.

Large university with high COVID-19 incidence is not associated with excess cases in non-student population

“…The outbreak in students was asynchronous with the outbreak in non-students in Centre County and led the reported cases in the non-student residents of Centre County. Other studies of university populations also noted little genomic evidence for spread between student populations with high incidence and surrounding non-student communities 19 , 20 . The outbreak in Centre County’s non-students was synchronous with outbreaks in surrounding counties.…”

Effect of Returning University Students on COVID-19 Infections in England, 2020

“…This percentage decreased to 73% (4,844) of 6,632 students 18 years of age who attended university. For all case-patients living in student accommodations, the median age was 19 (interquartile range [IQR] 18-20]) years, which was slightly younger than the age of student case-patients living in other types of accommodation (median age 20 [IQR [19][20][21][22]) years. This age profile reflects the common nature of student accommodations being used by first-year students who then move on to privately rented accommodations.…”

An iteratively optimised process for improving the efficiency and effectiveness of an industrial SARS-CoV-2 diagnostic facility

“…The CCTC is unique in many ways to other local and national COVID-19 diagnostic laboratories, as in addition to processing the normal single swab samples, the centre also evolved a process for pooled patient swab samples from the University of Cambridge Asymptomatic Testing Programme for its students 12,13 and testing of staff samples from the local NHS Trust hospital (Addenbrooke's Hospitalthe largest in the East of England). The centre also employed a dedicated technology development team involved in research activities leading to pioneering innovations for improving the safety, e ciency, robustness, and portability of the COVID-19 screening process.…”