Multiple pathways of SARS-CoV-2 nosocomial transmission uncovered by integrated genomic and epidemiological analyses during the second wave of the COVID-19 pandemic in the UK

Cook, Kate F,, Beckett, Angela H., Glaysher, Sharon, Goudarzi, Salman, Fearn, Christopher, Loveson, Katie F., Elliott, Scott, Wyllie, Sarah, Lloyd, Allyson, Bicknell, Kelly, Lumley, Sally, Chauhan, Anoop J., Robson, Samuel C., The COVID-19 Genomics UK (COG-UK) Consortium, , Smith, Darren, Bashton, Matthew, Young, Greg, McCann, Clare, Nelson, Andrew, Crown, Matthew, Henderson, John, Hollis, Amy, Stanley, William and Yew, Wen Chyin (2023) Multiple pathways of SARS-CoV-2 nosocomial transmission uncovered by integrated genomic and epidemiological analyses during the second wave of the COVID-19 pandemic in the UK. Frontiers in Cellular and Infection Microbiology, 12. p. 1066390. ISSN 2235-2988

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INTRODUCTION: Throughout the global COVID-19 pandemic, nosocomial transmission has represented a major concern for healthcare settings and has accounted for many infections diagnosed within hospitals. As restrictions ease and novel variants continue to spread, it is important to uncover the specific pathways by which nosocomial outbreaks occur to understand the most suitable transmission control strategies for the future.

METHODS: In this investigation, SARS-CoV-2 genome sequences obtained from 694 healthcare workers and 1,181 patients were analyzed at a large acute NHS hospital in the UK between September 2020 and May 2021. These viral genomic data were combined with epidemiological data to uncover transmission routes within the hospital. We also investigated the effects of the introduction of the highly transmissible variant of concern (VOC), Alpha, over this period, as well as the effects of the national vaccination program on SARS-CoV-2 infection in the hospital.

RESULTS: Our results show that infections of all variants within the hospital increased as community prevalence of Alpha increased, resulting in several outbreaks and super-spreader events. Nosocomial infections were enriched amongst older and more vulnerable patients more likely to be in hospital for longer periods but had no impact on disease severity. Infections appeared to be transmitted most regularly from patient to patient and from patients to HCWs. In contrast, infections from HCWs to patients appeared rare, highlighting the benefits of PPE in infection control. The introduction of the vaccine at this time also reduced infections amongst HCWs by over four-times.

DISCUSSION: These analyses have highlighted the importance of control measures such as regular testing, rapid lateral flow testing alongside polymerase chain reaction (PCR) testing, isolation of positive patients in the emergency department (where possible), and physical distancing of patient beds on hospital wards to minimize nosocomial transmission of infectious diseases such as COVID-19.

Item Type: Article
Additional Information: Funding information: This work was primarily funded by the COVID-19 Genomics UK (COG-UK) consortium. COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) grant code: MC_PC_19027, and Genome Research Limited, operating as the Wellcome Sanger Institute. The authors acknowledge use of data generated through the COVID-19 Genomics Program funded by the Department of Health and Social Care. Additional funding came from the University of Portsmouth Faculty of Science and Health, and the Wessex Academic Health Sciences Centre (AHSC). In addition, SR and AB are funded by Research England{\textquoteright}s Expanding Excellence in England (E3) Fund. 'Darren L Smith, Matthew Bashton, Gregory R Young, Clare M McCann, Andrew Nelson, Matthew R Crown, John H Henderson, Amy Hollis, William Stanley, Wen C Yew are members of The COVID-19 Genomics UK (COG-UK) Consortium'.
Uncontrolled Keywords: COVID-19, SARS-CoV-2, nosocomial infection, hospital-acquired infection, transmission dynamics, alpha variant, Oxford Nanopore Technologies (ONT), whole genome sequencing (WGS)
Subjects: C100 Biology
C400 Genetics
Department: Faculties > Health and Life Sciences > Applied Sciences
Depositing User: John Coen
Date Deposited: 22 Feb 2023 11:23
Last Modified: 22 Feb 2023 11:30

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