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.
All genome sequencing datasets have been shared with COG-UK.
- Jamie M Ellingford
- William G Newman
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
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.
- Niel Hens, Hasselt University & University of Antwerp, Belgium
© 2021, Ellingford et al.
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