Nature Communications (Feb 2022)
Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves
- Benjamin B. Lindsey,
- Ch. Julián Villabona-Arenas,
- Finlay Campbell,
- Alexander J. Keeley,
- Matthew D. Parker,
- Dhruv R. Shah,
- Helena Parsons,
- Peijun Zhang,
- Nishchay Kakkar,
- Marta Gallis,
- Benjamin H. Foulkes,
- Paige Wolverson,
- Stavroula F. Louka,
- Stella Christou,
- Amy State,
- Katie Johnson,
- Mohammad Raza,
- Sharon Hsu,
- Thibaut Jombart,
- Anne Cori,
- Sheffield COVID-19 Genomics Group,
- The COVID-19 Genomics UK (COG-UK) consortium,
- CMMID COVID-19 working group,
- Cariad M. Evans,
- David G. Partridge,
- Katherine E. Atkins,
- Stéphane Hué,
- Thushan I. de Silva
Affiliations
- Benjamin B. Lindsey
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Ch. Julián Villabona-Arenas
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine
- Finlay Campbell
- Health Emergencies Programme, World Health Organization
- Alexander J. Keeley
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Matthew D. Parker
- Sheffield Biomedical Research Centre, The University of Sheffield
- Dhruv R. Shah
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Helena Parsons
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Peijun Zhang
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Nishchay Kakkar
- Sheffield Teaching Hospitals NHS Foundation Trust
- Marta Gallis
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Benjamin H. Foulkes
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Paige Wolverson
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Stavroula F. Louka
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Stella Christou
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Amy State
- Sheffield Teaching Hospitals NHS Foundation Trust
- Katie Johnson
- Sheffield Teaching Hospitals NHS Foundation Trust
- Mohammad Raza
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Sharon Hsu
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Thibaut Jombart
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine
- Anne Cori
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London
- Sheffield COVID-19 Genomics Group
- The COVID-19 Genomics UK (COG-UK) consortium
- CMMID COVID-19 working group
- Cariad M. Evans
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- David G. Partridge
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- Katherine E. Atkins
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine
- Stéphane Hué
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine
- Thushan I. de Silva
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield
- DOI
- https://doi.org/10.1038/s41467-022-28291-y
- Journal volume & issue
-
Vol. 13,
no. 1
pp. 1 – 11
Abstract
SARS-CoV-2 has resulted in multiple outbreaks in hospitals, but identifying transmission events is challenging. Here, the authors combine whole genome sequencing and epidemiological data from the first two waves of the pandemic at a UK hospital trust and characterise transmission chains.
