Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study
- University College London, United Kingdom
- Imperial College Healthcare NHS Trust, United Kingdom
- Manchester University NHS Foundation Trust, United Kingdom
- University College London Hospitals NHS Foundation Trust, United Kingdom
- Royal Free London NHS Foundation Trust, United Kingdom
- University Hospital Southampton NHS Foundation Trust, United Kingdom
- Sandwell & West Birmingham Hospitals NHS Trust, United Kingdom
- Newcastle-upon-Tyne Hospitals NHS Foundation Trust, United Kingdom
- Nottingham University Hospitals NHS Trust, United Kingdom
- St George's University Hospitals NHS Foundation Trust, United Kingdom
- Liverpool University Hospitals NHS Foundation Trust, United Kingdom
- Barts Health NHS Trust, United Kingdom
- University of Liverpool, United Kingdom
- University of Glasgow, United Kingdom
- Guy's and St Thomas' Hospital NHS Foundation Trust, United Kingdom
- University of Portsmouth, United Kingdom
- Northumbria University, United Kingdom
- St George's, University of London, United Kingdom
- London School of Hygiene & Tropical Medicine, United Kingdom
- Health Data Research UK, United Kingdom
- University of Cambridge, United Kingdom
- Guy's and St Thomas' NHS Foundation Trust, United Kingdom
- Sheffield Teaching Hospitals NHS Foundation Trust, United Kingdom
- University of Sheffield, United Kingdom
- NHS Greater Glasgow and Clyde, United Kingdom
- University of Strathclyde, United Kingdom
Abstract
Background: Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings.
Methods: We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-collection period, followed by intervention periods comprising 8 weeks of 'rapid' (<48h) and 4 weeks of 'longer-turnaround' (5-10 day) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital onset COVID-19 infections (HOCIs; detected ≥48h from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on incidence of probable/definite hospital-acquired infections (HAIs) was evaluated.
Results: A total of 2170 HOCI cases were recorded from October 2020-April 2021, corresponding to a period of extreme strain on the health service, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (incidence rate ratio 1.60, 95%CI 0.85-3.01; P=0.14) or rapid (0.85, 0.48-1.50; P=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8% and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2% and 11.6% of cases where the report was returned. In a 'per-protocol' sensitivity analysis there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Capacity to respond effectively to insights from sequencing was breached in most sites by the volume of cases and limited resources.
Conclusion: While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days.
Funding: COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) [grant code: MC_PC_19027], and Genome Research Limited, operating as the Wellcome Sanger Institute.
Clinical trial number: ClinicalTrials.gov Identifier: NCT04405934.
Data availability
A fully anonymised version of the dataset generated and analysed for this study is available on the UCL Research Data Repository (https://doi.org/10.5522/04/20769637.v1).
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COG-UK hospital-onset COVID-19 infection study datasetUCL Research Data Repository, doi.org/10.5522/04/20769637.v1.
Article and author information
Author details
Funding
Medical Research Council
- Judith Breuer
National Institute for Health and Care Research (MC_PC_19027)
- Judith Breuer
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Marc J Bonten, University Medical Center Utrecht, Netherlands
Ethics
Human subjects: Ethical approval for the study was granted by NHS HRA (REC 20/EE/0118). The need for consent from individual participants was waived because the study involved a hospital-level intervention that did not directly affect the clinical management of individual participants once diagnosed with a SARS-COV-2 infection.
Version history
- Preprint posted: February 13, 2022 (view preprint)
- Received: March 11, 2022
- Accepted: August 25, 2022
- Accepted Manuscript published: September 13, 2022 (version 1)
- Version of Record published: October 25, 2022 (version 2)
Copyright
© 2022, Stirrup 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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Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study
eLife 11:e78427.
https://doi.org/10.7554/eLife.78427
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