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

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  • Additional Information
    • Corporate Authors:
      COVID-19 Genomics UK (COG-UK) consortium
    • Source:
      Publisher: Oxford University Press Country of Publication: United States NLM ID: 0413675 Publication Model: Print Cited Medium: Internet ISSN: 1537-6613 (Electronic) Linking ISSN: 00221899 NLM ISO Abbreviation: J Infect Dis Subsets: MEDLINE
    • Publication Information:
      Publication: Jan. 2011- : Oxford : Oxford University Press
      Original Publication: 1904-2010 : Chicago, IL : University of Chicago Press
    • Subject Terms:
      COVID-19* ; Cross Infection*/epidemiology ; Whole Genome Sequencing*; Disease Outbreaks/*prevention & control ; Reverse Transcriptase Polymerase Chain Reaction/*methods; Asymptomatic Infections ; Delivery of Health Care ; Health Personnel ; Humans ; Personal Protective Equipment ; Phylogeny ; SARS-CoV-2
    • 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.
      (© The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America.)
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    • Grant Information:
      MC_PC_19027 National Institute for Health Research; UK Research and Innovation; MC_PC_20027 United Kingdom MRC_ Medical Research Council; MR/S009434/1 United Kingdom MRC_ Medical Research Council; MR/R010307/1 United Kingdom MRC_ Medical Research Council; MC_PC_19027 United Kingdom MRC_ Medical Research Council
    • Contributed Indexing:
      Keywords: SARS-CoV-2; cluster; genetic epidemiology; infection control; nosocomial transmission; outbreak; virus; whole-genome sequencing: COVID-19
    • Publication Date:
      Date Created: 20210923 Date Completed: 20220111 Latest Revision: 20230315
    • Publication Date:
      20231215
    • Accession Number:
      PMC8522425
    • Accession Number:
      10.1093/infdis/jiab483
    • Accession Number:
      34555152