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 ORCID: 0000-0002-3122-7502, Holmes, Nadine ORCID: 0000-0001-7470-3786 et al (show 4 more authors) (2022) The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks. The Journal of infectious diseases, 225 (1). pp. 10-18.

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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.

Item Type: Article
Uncontrolled Keywords: COVID-19 Genomics UK (COG-UK) consortium, Humans, Cross Infection, Reverse Transcriptase Polymerase Chain Reaction, Disease Outbreaks, Phylogeny, Health Personnel, Delivery of Health Care, Asymptomatic Infections, Personal Protective Equipment, Whole Genome Sequencing, COVID-19, SARS-CoV-2
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences
Depositing User: Symplectic Admin
Date Deposited: 10 Jan 2023 16:03
Last Modified: 16 Dec 2023 03:36
DOI: 10.1093/infdis/jiab483
Open Access URL: https://doi.org/10.1093/infdis/jiab483
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3166983
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