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, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Young, Greg, McCann, Clare and Nelson, Andrew (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. ISSN 0022-1899

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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
Additional Information: Matthew Bashton, Darren L. Smith, Gregory R. Young, Clare McCann, Andrew Nelson and Wen Chyin Yew are members of the COVID-19 Genomics UK (COG-UK) Consortium. Funding information: This work was supported by the Medical Research Council, part of UK Research and Innovation; the National Institute for Health Research (grant number MC_PC_19027); and Genome Research Limited, operating as the Wellcome Sanger Institute.
Uncontrolled Keywords: cluster; genetic epidemiology; infection control; nosocomial transmission; outbreak; SARS-CoV-2; virus; wholegenome sequencing: COVID-19
Subjects: B100 Anatomy, Physiology and Pathology
C500 Microbiology
C700 Molecular Biology, Biophysics and Biochemistry
Department: Faculties > Health and Life Sciences > Applied Sciences
Depositing User: Elena Carlaw
Date Deposited: 14 Jan 2022 10:32
Last Modified: 14 Jan 2022 10:45

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