Skip to main content

Research Repository

Advanced Search

The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks

Francis, Rodric V.; Billam, Harriet; Clarke, Mitch; Yates, Carl; Tsoleridis, Theocharis; Berry, Louise; Mahida, Nikunj; Irving, William L.; Moore, Christopher; Holmes, Nadine; Ball, Jonathan K.; Loose, Matthew; McClure, C. Patrick


Rodric V. Francis

Harriet Billam

Mitch Clarke

Carl Yates

Louise Berry

Nikunj Mahida

Christopher Moore

Nadine Holmes

Professor of Molecular Virology

Professor of Developmental and Computational Biology


Nosocomial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have severely affected bed capacity and patient flow. We utilized whole-genome sequencing (WGS) to identify outbreaks and focus infection control resources and intervention during the United Kingdom's second pandemic wave in late 2020. Phylogenetic analysis of WGS and epidemiological data pinpointed an initial transmission event to an admission ward, with immediate prior community infection linkage documented. High incidence of asymptomatic staff infection with genetically identical viral sequences was also observed, which may have contributed to the propagation of the outbreak. WGS allowed timely nosocomial transmission intervention measures, including admissions ward point-of-care testing and introduction of portable HEPA14 filters. Conversely, WGS excluded nosocomial transmission in 2 instances with temporospatial linkage, conserving time and resources. In summary, WGS significantly enhanced understanding of SARS-CoV-2 clusters in a hospital setting, both identifying high-risk areas and conversely validating existing control measures in other units, maintaining clinical service overall.


Francis, R. V., Billam, H., Clarke, M., Yates, C., Tsoleridis, T., Berry, L., …McClure, C. P. (2022). The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks. Journal of Infectious Diseases, 225(1), 10-18.

Journal Article Type Article
Acceptance Date Sep 20, 2021
Online Publication Date Nov 15, 2021
Publication Date Jan 5, 2022
Deposit Date Dec 10, 2021
Publicly Available Date Nov 16, 2022
Journal The Journal of infectious diseases
Print ISSN 0022-1899
Electronic ISSN 1537-6613
Publisher Oxford University Press (OUP)
Peer Reviewed Peer Reviewed
Volume 225
Issue 1
Pages 10-18
Keywords Infectious Diseases; Immunology and Allergy
Public URL
Publisher URL
Additional Information Authors on behalf of the COVID-19 Genomics UK (COG-UK) consortium.


You might also like

Downloadable Citations