Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
Ryan George
Department of Infection Prevention & Control, Manchester University NHS Foundation Trust, Manchester, United Kingdom
John H McDermott
Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
Shazaad Ahmad
Department of Virology, Manchester Medical Microbiology Partnership, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
Jonathan J Edgerley
Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
David Gokhale
Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
William G Newman
Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
Stephen Ball
Division of Diabetes, Endocrinology & Gastroenterology, School of Medical Sciences, University of Manchester, Manchester, United Kingdom; Department of Clinical Endocrinology, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
Nicholas Machin
Department of Virology, Manchester Medical Microbiology Partnership, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, United Kingdom; Manchester Medical Microbiology Partnership, Public Health England and Manchester University NHS Foundation Trust, Manchester, United Kingdom
Graeme CM Black
Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
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.
