Detailed analysis of in-hospital transmission of SARS-CoV-2 using whole genome sequencing

L. O'Connell*, H. Asad, G. Hall, T. Jones, J. Walters, L. Manchipp-Taylor, J. Barry, D. Keighan, H. Jones, C. Williams, M. Cronin, H. Hughes, M. Morgan, T. R. Connor, B. Healy

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Background: Hospital transmission of SARS-CoV-2 has proved difficult to control, with healthcare-associated infections troublesome throughout. Aim: To understand factors contributing to hospital transmission of infections, which is necessary for containing spread. Methods: An outbreak of 56 staff and patient cases of COVID-19 over a 31-day period in a tertiary referral unit is presented, with at least a further 29 cases identified outside of the unit and the hospital by whole genome sequencing (WGS). Findings: Transmission is documented from staff to staff, staff to patients, and patients to staff, showing disruption of a tertiary referral service, despite implementation of nationally recommended control measures, superior ventilation, and use of personal protective equipment. There was extensive spread from the index case, despite this patient spending only 10 h bed bound on the ward in strict cubicle isolation and with an initial single target low level (CT = 32) polymerase chain reaction test. Conclusion: This investigation highlights how effectively and rapidly SARS-CoV-2 can spread in certain circumstances. It raises questions about infection control measures in place at the time and calls into question the premise that transmissibility can be reliably detected by using lower sensitivity rapid antigen lateral flow tests. We also highlight the value of early intervention in reducing impact as well as the value of WGS in understanding outbreaks.

Original languageEnglish
Pages (from-to)23-33
Number of pages11
JournalJournal of Hospital Infection
Volume131
DOIs
Publication statusPublished - Jan 2023
Externally publishedYes

Bibliographical note

Funding Information:
In conclusion, the outbreak demonstrates how the healthcare environment may be very conducive to spread. We recommend reducing transmission risk through constant reinforcement of IPC guidance, developing a culture that endorses compliance, improving the design of healthcare settings (better spacing, ventilation, reduction in shared facilities for staff and patients, reduced patient movement), and adequate staffing levels (with some redundancy to support compliance in times of system stress).T.R.C. acknowledges support from the MRC, which funded computational resources used by the project (grant reference MR/L015080/1). T.R.C. acknowledges support from Supercomputing Wales, which is partially funded by the European Regional Development Fund via Welsh Government. The project was also supported by specific funding from the Welsh Government, which provided funds for the sequencing and analysis of a subset of the Welsh samples used in this study, via Genomics Partnership Wales. The sequencing of samples was funded by COG-UK, and this analysis used software provided by members of the COG-UK consortium. COG-UK is funded by the Medical Research Council part of UK Research & Innovation, the National Institute of Health Research, and Genome Research Limited, operating as the Wellcome Sanger Institute.

Funding Information:
T.R.C. acknowledges support from the MRC , which funded computational resources used by the project (grant reference MR/L015080/1). T.R.C. acknowledges support from Supercomputing Wales, which is partially funded by the European Regional Development Fund via Welsh Government . The project was also supported by specific funding from the Welsh Government , which provided funds for the sequencing and analysis of a subset of the Welsh samples used in this study, via Genomics Partnership Wales. The sequencing of samples was funded by COG- UK , and this analysis used software provided by members of the COG- UK consortium. COG- UK is funded by the Medical Research Council part of UK Research & Innovation, the National Institute of Health Research , and Genome Research Limited, operating as the Wellcome Sanger Institute.

Publisher Copyright:
© 2022 The Healthcare Infection Society

Keywords

  • COVID-19
  • Hospital outbreak
  • Personal protective equipment
  • Super-spreader event
  • Whole genome sequencing

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