☆ 4.8 Article

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

NATURE COMMUNICATIONS (2022)

Journal

NATURE COMMUNICATIONS

Volume 13, Issue 1, Pages -

Publisher

NATURE PORTFOLIO

DOI: 10.1038/s41467-021-27942-w

Keywords

Funding

Wellcome Trust [222903/Z/21/Z, 207498/Z/17/Z, 206298/B/17/Z]
University of Cambridge
National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre (BRC) at the Cambridge University Hospitals NHS Foundation Trust
UK Research and Innovation (UKRI) Fellowship [MR/S00291X/1]
Medical Research Council (MRC) [MC_UU_00002/11]
MRC [CSF MR/P008801/1]
NHSBT [WPA15-02]
Biotechnology and Biological Sciences Research Council (BBSRC)
BBSRC Institute Strategic Programme Microbes in the Food Chain [BB/R012504/1]
Quadram Institute Bioscience BBSRC [BBS/E/F/000PR10352, BB/CCG1860/1]
NIHR Cambridge BRC
MRC part of UK Research & Innovation (UKRI)
National Institute of Health Research
Genome Research Limited
Department of Health and Social Care, UK Government
Oxford Martin School
Wellcome Trust [206298/B/17/Z] Funding Source: Wellcome Trust

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Abstract

Understanding the transmission of SARS-CoV-2 in higher education settings is crucial in limiting spread among students and at-risk populations. A study conducted at the University of Cambridge analyzed viral isolates and found limited introductions of the virus into the university. Student cases were primarily linked to a single genetic cluster, likely originating from social gatherings outside of the university. Transmission was observed within student accommodations and courses but was effectively contained through local infection control measures and a national lockdown. The study highlights important factors in SARS-CoV-2 transmission and effective interventions in higher education settings.

Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our 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. In this study, Aggarwal and colleagues perform prospective sequencing of SARS-CoV-2 isolates derived from asymptomatic student screening and symptomatic testing of students and staff at the University of Cambridge. They identify important factors that contributed to within university transmission and onward spread into the wider community.

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Genomic Epidemiology of Early SARS-CoV-2 Transmission Dynamics, Gujarat, India

Jayna Raghwani, Louis du Plessis, John T. McCrone, Sarah C. Hill, Kris Parag, Julien Theze, Dinesh Kumar, Apurva Puvar, Ramesh Pandit, Oliver G. Pybus, Guillaume Fournie, Madhvi Joshi, Chaitanya Joshi

Summary: This study investigates the transmission dynamics of SARS-CoV-2 in Gujarat, India, and reveals that global and regional connectivity, as well as population density, are major drivers of the outbreak. The virus primarily spreads from densely populated urban centers to areas with lower population density.

EMERGING INFECTIOUS DISEASES (2022)