Genomic and healthcare dynamics of nosocomial SARS-CoV-2 transmission

  1. Jamie M Ellingford  Is a corresponding author
  2. Ryan George
  3. John H McDermott
  4. Shazaad Ahmad
  5. Jonathan J Edgerley
  6. David Gokhale
  7. William G Newman
  8. Stephen Ball
  9. Nicholas Machin
  10. Graeme CM Black  Is a corresponding author
  1. University of Manchester, United Kingdom
  2. Manchester University NHS Foundation Trust, United Kingdom
  3. Manchester Centre for Genomic Medicine, United Kingdom

Abstract

Understanding the effectiveness of infection control methods in reducing and preventing SARS-CoV-2 transmission in healthcare settings is of high importance. We sequenced SARS-CoV-2 genomes for patients and healthcare workers (HCWs) across multiple geographically distinct UK hospitals, obtaining 173 high-quality SARS-CoV-2 genomes. We integrated patient movement and staff location data into the analysis of viral genome data to understand spatial and temporal dynamics of SARS-CoV-2 transmission. We identified eight patient contact clusters (PCC) with significantly increased similarity in genomic variants compared to non-clustered samples. Incorporation of HCW location further increased the number of individuals within PCCs and identified additional links in SARS-CoV-2 transmission pathways. Patients within PCCs carried viruses more genetically identical to HCWs in the same ward location. SARS-CoV-2 genome sequencing integrated with patient and HCW movement data increases identification of outbreak clusters. This dynamic approach can support infection control management strategies within the healthcare setting.

Data availability

All genome sequencing datasets have been shared with COG-UK.

The following previously published data sets were used

Article and author information

Author details

  1. Jamie M Ellingford

    Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
    For correspondence
    jamie.ellingford@manchester.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1137-9768
  2. Ryan George

    Department of Infection Prevention & Control, Manchester University NHS Foundation Trust, Manchester, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  3. John H McDermott

    Manchester Centre for Genomic Medicine, Manchester, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Shazaad Ahmad

    Department of Virology, Manchester University NHS Foundation Trust, Manchester, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Jonathan J Edgerley

    Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  6. David Gokhale

    Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  7. William G Newman

    School of Medicine, University of Manchester, Manchester, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  8. Stephen Ball

    Division of Diabetes, Endocrinology & Gastroenterology, University of Manchester, Manchester, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  9. Nicholas Machin

    Department of Clinical Endocrinology, Manchester University NHS Foundation Trust, Manchester, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  10. Graeme CM Black

    Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
    For correspondence
    graeme.black@manchester.ac.uk
    Competing interests
    The authors declare that no competing interests exist.

Funding

Health Education England

  • Jamie M Ellingford

Manchester Biomedical Research Centre

  • William G Newman

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Niel Hens, Hasselt University & University of Antwerp, Belgium

Ethics

Human subjects: The study was conducted to investigate hospital outbreak investigation/surveillance; individual patient consent or ethical approvals were not required. The study protocol was approved by the Manchester Biomedical Research Centre COVID-19 rapid response group and the Manchester University NHS Foundation Trust Executive Committee. All samples and data collected were part of routine care or hospital operational policy. No patient-identifiable/individual identifiable data are presented.

Version history

  1. Received: December 4, 2020
  2. Accepted: March 16, 2021
  3. Accepted Manuscript published: March 17, 2021 (version 1)
  4. Version of Record published: March 29, 2021 (version 2)

Copyright

© 2021, Ellingford et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Jamie M Ellingford
  2. Ryan George
  3. John H McDermott
  4. Shazaad Ahmad
  5. Jonathan J Edgerley
  6. David Gokhale
  7. William G Newman
  8. Stephen Ball
  9. Nicholas Machin
  10. Graeme CM Black
(2021)
Genomic and healthcare dynamics of nosocomial SARS-CoV-2 transmission
eLife 10:e65453.
https://doi.org/10.7554/eLife.65453

Share this article

https://doi.org/10.7554/eLife.65453

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