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

Kate F. Cook; Angela H. Beckett; Sharon Glaysher; Salman Goudarzi; Christopher Fearn; Katie F. Loveson; Scott Elliott; Sarah Wyllie; Allyson Lloyd; Kelly Bicknell; Sally Lumley; Anoop J. Chauhan; Samuel C. Robson; The COVID-19 Genomics UK (COG-UK) Consortium; 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

doi:10.3389/fcimb.2022.1066390

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

Kate F. Cook, Angela H. Beckett, Sharon Glaysher, Salman Goudarzi, Christopher Fearn, Katie F. Loveson, Scott Elliott, Sarah Wyllie, Allyson Lloyd, Kelly Bicknell, Sally Lumley, Anoop J. Chauhan, Samuel C. Robson^*, The COVID-19 Genomics UK (COG-UK) Consortium, Darren L Smith, Matthew Bashton, Gregory R Young, Clare M McCann, Andrew Nelson, Matthew R CrownJohn H Henderson, Amy Hollis, William Stanley, Wen C Yew

^*Corresponding author for this work

Applied Sciences Department

Research output: Contribution to journal › Article › peer-review

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Abstract

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.

Original language	English
Article number	1066390
Pages (from-to)	1-20
Number of pages	20
Journal	Frontiers in cellular and infection microbiology
Volume	12
DOIs	https://doi.org/10.3389/fcimb.2022.1066390
Publication status	Published - 20 Jan 2023

Keywords

COVID-19
SARS-CoV-2
nosocomial infection
hospital-acquired infection
transmission dynamics
alpha variant
Oxford Nanopore Technologies (ONT)
whole genome sequencing (WGS)

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.3389/fcimb.2022.1066390Licence: CC BY

fcimb-12-1066390Final published version, 11 MBLicence: CC BY

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Cook, K. F., Beckett, A. H., Glaysher, S., Goudarzi, S., Fearn, C., Loveson, K. F., Elliott, S., Wyllie, S., Lloyd, A., Bicknell, K., Lumley, S., Chauhan, A. J., Robson, S. C., The COVID-19 Genomics UK (COG-UK) Consortium, Smith, D. L., Bashton, M., Young, G. R., McCann, C. M., Nelson, A., ... Yew, W. C. (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, 1-20. Article 1066390. https://doi.org/10.3389/fcimb.2022.1066390

@article{d4ed050a95ea4680994444107d71ff93,

title = "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",

abstract = "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.",

keywords = "COVID-19, SARS-CoV-2, nosocomial infection, hospital-acquired infection, transmission dynamics, alpha variant, Oxford Nanopore Technologies (ONT), whole genome sequencing (WGS)",

author = "Cook, {Kate F.} and Beckett, {Angela H.} and Sharon Glaysher and Salman Goudarzi and Christopher Fearn and Loveson, {Katie F.} and Scott Elliott and Sarah Wyllie and Allyson Lloyd and Kelly Bicknell and Sally Lumley and Chauhan, {Anoop J.} and Robson, {Samuel C.} and {The COVID-19 Genomics UK (COG-UK) Consortium} and Smith, {Darren L} and Matthew Bashton and Young, {Gregory R} and McCann, {Clare M} and Andrew Nelson and Crown, {Matthew R} and Henderson, {John H} and Amy Hollis and William Stanley and Yew, {Wen C}",

note = "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'.",

year = "2023",

month = jan,

day = "20",

doi = "10.3389/fcimb.2022.1066390",

language = "English",

volume = "12",

pages = "1--20",

journal = "Frontiers in cellular and infection microbiology",

issn = "2235-2988",

publisher = "Frontiers",

}

Cook, KF, Beckett, AH, Glaysher, S, Goudarzi, S, Fearn, C, Loveson, KF, Elliott, S, Wyllie, S, Lloyd, A, Bicknell, K, Lumley, S, Chauhan, AJ, Robson, SC, The COVID-19 Genomics UK (COG-UK) Consortium, Smith, DL , Bashton, M, Young, GR, McCann, CM , Nelson, A, Crown, MR, Henderson, JH, Hollis, A, Stanley, W & Yew, WC 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, vol. 12, 1066390, pp. 1-20. https://doi.org/10.3389/fcimb.2022.1066390

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 et al.
In: Frontiers in cellular and infection microbiology, Vol. 12, 1066390, 20.01.2023, p. 1-20.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - 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

AU - Cook, Kate F.

AU - Beckett, Angela H.

AU - Glaysher, Sharon

AU - Goudarzi, Salman

AU - Fearn, Christopher

AU - Loveson, Katie F.

AU - Elliott, Scott

AU - Wyllie, Sarah

AU - Lloyd, Allyson

AU - Bicknell, Kelly

AU - Lumley, Sally

AU - Chauhan, Anoop J.

AU - Robson, Samuel C.

AU - The COVID-19 Genomics UK (COG-UK) Consortium

AU - Smith, Darren L

AU - Bashton, Matthew

AU - Young, Gregory R

AU - McCann, Clare M

AU - Nelson, Andrew

AU - Crown, Matthew R

AU - Henderson, John H

AU - Hollis, Amy

AU - Stanley, William

AU - Yew, Wen C

N1 - 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’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'.

PY - 2023/1/20

Y1 - 2023/1/20

N2 - 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.

AB - 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.

KW - COVID-19

KW - SARS-CoV-2

KW - nosocomial infection

KW - hospital-acquired infection

KW - transmission dynamics

KW - alpha variant

KW - Oxford Nanopore Technologies (ONT)

KW - whole genome sequencing (WGS)

U2 - 10.3389/fcimb.2022.1066390

DO - 10.3389/fcimb.2022.1066390

M3 - Article

C2 - 36741977

SN - 2235-2988

VL - 12

SP - 1

EP - 20

JO - Frontiers in cellular and infection microbiology

JF - Frontiers in cellular and infection microbiology

M1 - 1066390

ER -

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

Abstract

Keywords

UN SDGs

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