Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves

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.

Metadata

Item Type:	Article
Authors/Creators:	Lindsey, BB https://orcid.org/0000-0003-4227-2592 Villabona-Arenas, CJ Campbell, F Keeley, AJ https://orcid.org/0000-0001-9386-1157 Parker, MD Shah, DR Parsons, H Zhang, P Kakkar, N Gallis, M Foulkes, BH Wolverson, P Louka, SF Christou, S State, A Johnson, K Raza, M Hsu, S Jombart, T Cori, A Shah, DR Johnson, K Hsu, S de Silva, TI Cope, A Ali, N Raghei, R Heffer, J Smith, N Whiteley, M Pohare, M Hansford, SE Green, LR Wang, D Anckorn, M Angyal, A Brown, R Hornsby, H Yavuz, M Groves, DC Parsons, PJ Tucker, RM Dabrowska, MB Saville, T Schutter, J Wyles, MD Evans, C Davies, NG Pearson, CAB Quaife, M Tully, DC Abbott, S Evans, CM Partridge, DG https://orcid.org/0000-0002-0417-2016 Atkins, KE Hué, S de Silva, TI https://orcid.org/0000-0002-6498-9212
Copyright, Publisher and Additional Information:	© 2022 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
Dates:	Published: 3 February 2022 Published (online): 3 February 2022 Accepted: 17 January 2022
Institution:	The University of Sheffield
Academic Units:	The University of Sheffield > Sheffield Teaching Hospitals The University of Sheffield > Faculty of Medicine, Dentistry and Health (Sheffield)
Funding Information:	Funder Grant number National Institute for Health Research NIHRDH-IS-BRC-1215-20017 The Wellcome Trust 110058/A/15/Z
Depositing User:	Symplectic Sheffield
Date Deposited:	18 Feb 2022 08:48
Last Modified:	24 Feb 2022 19:29
Status:	Published
Publisher:	Springer Nature
Refereed:	Yes
Identification Number:	10.1038/s41467-022-28291-y
Related URLs:	PubMed URL Erratum/Corrigendum
Open Archives Initiative ID (OAI ID):	oai:eprints.whiterose.ac.uk:183765

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Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves

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