The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks. (23rd September 2021)

• Record Type: Journal Article
• Authors: 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
• Is Part Of: Journal of infectious diseases. Volume 225:Number 1(2022)
• Page Start: 10
• Page End: 18
• Publication Date: 2021-09-23
• Subjects: cluster -- genetic epidemiology -- infection control -- nosocomial transmission -- outbreak -- SARS-CoV-2 -- virus -- whole-genome sequencing: COVID-19; Communicable diseases -- Periodicals; Diseases -- Causes and theories of causation -- Periodicals; Medicine -- Periodicals; Communicable Diseases -- Periodicals; Electronic journals; 616.9
• DOI: 10.1093/infdis/jiab483
• Languages: English
• ISSNs: 0022-1899

Abstract

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. Abstract : SARS-CoV-2 whole-genome sequencing, combined with classical epidemiology, identified nosocomial transmission events, informing targeted infection prevention measures during the UK's second epidemic wave. Conversely, nosocomial transmission was excluded by sequencing in 2 instances with temporospatial linkage, conserving time and resources.