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03 17, 2021;10

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

Jamie M Ellingford, Ryan George, John H McDermott, Shazaad Ahmad, Jonathan J Edgerley, David Gokhale, William G Newman, Stephen Ball, Nicholas Machin, Graeme Cm Black
Author Information
  1. Jamie M Ellingford: Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom. ORCID
  2. Ryan George: Department of Infection Prevention & Control, Manchester University NHS Foundation Trust, Manchester, United Kingdom.
  3. John H McDermott: Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom.
  4. Shazaad Ahmad: Department of Virology, Manchester Medical Microbiology Partnership, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, United Kingdom.
  5. Jonathan J Edgerley: Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom.
  6. David Gokhale: Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom.
  7. William G Newman: Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom.
  8. Stephen Ball: Division of Diabetes, Endocrinology & Gastroenterology, School of Medical Sciences, University of Manchester, Manchester, United Kingdom.
  9. Nicholas Machin: Department of Virology, Manchester Medical Microbiology Partnership, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, United Kingdom.
  10. Graeme Cm Black: Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom.
PMID: 33729154 DOI: 10.7554/eLife.65453

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.

Keywords

SARS-CoV-2 genetics genome genomics healthcare worker healthcare-associated human infectious disease microbiology nosocomial sequencing virus

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Grants

  1. IS-BRC-1215-20007/Manchester NIHR Biomedical Research Centre

MeSH Term

Aged
COVID-19
Contact Tracing
Cross Infection
Female
Health Personnel
Humans
Infectious Disease Transmission, Patient-to-Professional
Infectious Disease Transmission, Professional-to-Patient
Male
SARS-CoV-2
Whole Genome Sequencing
Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 60

Word Cloud

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