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

Abstract

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.

Citation

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. https://doi.org/10.1093/infdis/jiab483

• 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
• DOI: https://doi.org/10.1093/infdis/jiab483
• Keywords: Infectious Diseases; Immunology and Allergy
• Public URL: https://nottingham-repository.worktribe.com/output/6916753
• Publisher URL: https://academic.oup.com/jid/article/225/1/10/6374543
• Additional Information: Authors on behalf of the COVID-19 Genomics UK (COG-UK) consortium.