Characterising within-hospital SARS-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, Cariad M. Evans, David G. Partridge, Katherine E. Atkins (), Stéphane Hué () and Thushan I. Silva ()
Additional contact information
Benjamin B. Lindsey: 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: Immunity and Cardiovascular Disease, Medical School, University of Sheffield
Matthew D. Parker: Sheffield Biomedical Research Centre, The University of Sheffield
Dhruv R. Shah: Immunity and Cardiovascular Disease, Medical School, University of Sheffield
Helena Parsons: Immunity and Cardiovascular Disease, Medical School, University of Sheffield
Peijun Zhang: Immunity and Cardiovascular Disease, Medical School, University of Sheffield
Nishchay Kakkar: Sheffield Teaching Hospitals NHS Foundation Trust
Marta Gallis: Immunity and Cardiovascular Disease, Medical School, University of Sheffield
Benjamin H. Foulkes: Immunity and Cardiovascular Disease, Medical School, University of Sheffield
Paige Wolverson: Immunity and Cardiovascular Disease, Medical School, University of Sheffield
Stavroula F. Louka: Immunity and Cardiovascular Disease, Medical School, University of Sheffield
Stella Christou: 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: Immunity and Cardiovascular Disease, Medical School, University of Sheffield
Sharon Hsu: 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: School of Public Health, Imperial College London
Cariad M. Evans: Immunity and Cardiovascular Disease, Medical School, University of Sheffield
David G. Partridge: 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. Silva: Immunity and Cardiovascular Disease, Medical School, University of Sheffield

Nature Communications, 2022, vol. 13, issue 1, 1-11

Abstract: Abstract Hospital outbreaks of COVID19 result in considerable mortality and disruption to healthcare services and yet little is known about transmission within this setting. We characterise within hospital transmission by combining viral genomic and epidemiological data using Bayesian modelling amongst 2181 patients and healthcare workers from a large UK NHS Trust. Transmission events were compared between Wave 1 (1st March to 25th July 2020) and Wave 2 (30th November 2020 to 24th January 2021). We show that staff-to-staff transmissions reduced from 31.6% to 12.9% of all infections. Patient-to-patient transmissions increased from 27.1% to 52.1%. 40%-50% of hospital-onset patient cases resulted in onward transmission compared to 4% of community-acquired cases. Control measures introduced during the pandemic likely reduced transmissions between healthcare workers but were insufficient to prevent increasing numbers of patient-to-patient transmissions. As hospital-acquired cases drive most onward transmission, earlier identification of nosocomial cases will be required to break hospital transmission chains.

Date: 2022
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DOI: 10.1038/s41467-022-28291-y

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