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.
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.
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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Background:
Biological aging exhibits heterogeneity across multi-organ systems. However, it remains unclear how is lifestyle associated with overall and organ-specific aging and which factors contribute most in Southwest China.
Methods:
This study involved 8396 participants who completed two surveys from the China Multi-Ethnic Cohort (CMEC) study. The healthy lifestyle index (HLI) was developed using five lifestyle factors: smoking, alcohol, diet, exercise, and sleep. The comprehensive and organ-specific biological ages (BAs) were calculated using the Klemera–Doubal method based on longitudinal clinical laboratory measurements, and validation were conducted to select BA reflecting related diseases. Fixed effects model was used to examine the associations between HLI or its components and the acceleration of validated BAs. We further evaluated the relative contribution of lifestyle components to comprehension and organ systems BAs using quantile G-computation.
Results:
About two-thirds of participants changed HLI scores between surveys. After validation, three organ-specific BAs (the cardiopulmonary, metabolic, and liver BAs) were identified as reflective of specific diseases and included in further analyses with the comprehensive BA. The health alterations in HLI showed a protective association with the acceleration of all BAs, with a mean shift of –0.19 (95% CI −0.34, –0.03) in the comprehensive BA acceleration. Diet and smoking were the major contributors to overall negative associations of five lifestyle factors, with the comprehensive BA and metabolic BA accounting for 24% and 55% respectively.
Conclusions:
Healthy lifestyle changes were inversely related to comprehensive and organ-specific biological aging in Southwest China, with diet and smoking contributing most to comprehensive and metabolic BA separately. Our findings highlight the potential of lifestyle interventions to decelerate aging and identify intervention targets to limit organ-specific aging in less-developed regions.
Funding:
This work was primarily supported by the National Natural Science Foundation of China (Grant No. 82273740) and Sichuan Science and Technology Program (Natural Science Foundation of Sichuan Province, Grant No. 2024NSFSC0552). The CMEC study was funded by the National Key Research and Development Program of China (Grant No. 2017YFC0907305, 2017YFC0907300). The sponsors had no role in the design, analysis, interpretation, or writing of this article.
