The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study

COG-UK-HOCI Variant Substudy Consortium; COVID-19 Genomics UK (COG-UK) Consortium; Samuel C. Robson

doi:10.1016/j.jinf.2021.09.022

The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study

COG-UK-HOCI Variant Substudy Consortium, COVID-19 Genomics UK (COG-UK) Consortium, Samuel C. Robson

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

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Abstract

Objectives - Recently emerging SARS-CoV-2 variants have been associated with an increased rate of transmission within the community. We sought to determine whether this also resulted in increased transmission within hospitals.

Methods - We collected viral sequences and epidemiological data of patients with community and healthcare associated SARS-CoV-2 infections, sampled from 16th November 2020 to 10th January 2021, from nine hospitals participating in the COG-UK HOCI study. Outbreaks were identified using ward information, lineage and pairwise genetic differences between viral sequences.

Results - Mixed effects logistic regression analysis of 4184 sequences showed healthcare-acquired infections were no more likely to be identified as the Alpha variant than community acquired infections. Nosocomial outbreaks were investigated based on overlapping ward stay and SARS-CoV-2 genome sequence similarity. There was no significant difference in the number of patients involved in outbreaks caused by the Alpha variant compared to outbreaks caused by other lineages.

Conclusions - We find no evidence to support it causing more nosocomial transmission than previous lineages. This suggests that the stringent infection prevention measures already in place in UK hospitals contained the spread of the Alpha variant as effectively as other less transmissible lineages, providing reassurance of their efficacy against emerging variants of concern.

Original language	English
Pages (from-to)	693-700
Journal	Journal of Infection
Volume	83
Issue number	6
Early online date	2 Oct 2021
DOIs	https://doi.org/10.1016/j.jinf.2021.09.022
Publication status	Published - 1 Dec 2021

Keywords

COVID-19
Transmissibility
Nosocomial outbreaks
Lineage B.1.1.7
Alpha variant
SARS-CoV-2
Variants of concern
UKRI
MRC

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10.1016/j.jinf.2021.09.022Licence: CC BY

The Alpha variant was not associated FINALFinal published version, 951 KBLicence: CC BY

Dataset: GISAID EpiCov SARS-CoV-2 Whole Genome Sequencing Database
Robson, S. (Creator), GISAID, 18 Nov 2020
https://www.epicov.org/epi3/frontend#3bd481
Dataset
COVID-19 Genomics UK (COG-UK) consortium
Robson, S. (Creator), NCBI, 29 Apr 2020
https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB37886
Dataset

HOCI: COG-UK Project Hospital Onset COVID-19 Infections study
Robson, S., Beckett, A., Cook, K., Goudarzi, S., Fearn, C. & Glaysher, S.
University College London
15/10/20 → 31/07/21
Project: Research
STOP COVID-19: Sequencing and Tracking Of Phylogeny in COVID-19
Robson, S., Scarlett, G., Bourgeois, Y., Beckett, A., Loveson, K., Glaysher, S., Chauhan, A., Goudarzi, S., Cook, K., Fearn, C., Paul, H. & Dent, H.
COG-UK, UK Health Security Agency
1/04/20 → 31/03/23
Project: Research

Cite this

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title = "The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study",

abstract = "Objectives - Recently emerging SARS-CoV-2 variants have been associated with an increased rate of transmission within the community. We sought to determine whether this also resulted in increased transmission within hospitals.Methods - We collected viral sequences and epidemiological data of patients with community and healthcare associated SARS-CoV-2 infections, sampled from 16th November 2020 to 10th January 2021, from nine hospitals participating in the COG-UK HOCI study. Outbreaks were identified using ward information, lineage and pairwise genetic differences between viral sequences.Results - Mixed effects logistic regression analysis of 4184 sequences showed healthcare-acquired infections were no more likely to be identified as the Alpha variant than community acquired infections. Nosocomial outbreaks were investigated based on overlapping ward stay and SARS-CoV-2 genome sequence similarity. There was no significant difference in the number of patients involved in outbreaks caused by the Alpha variant compared to outbreaks caused by other lineages.Conclusions - We find no evidence to support it causing more nosocomial transmission than previous lineages. This suggests that the stringent infection prevention measures already in place in UK hospitals contained the spread of the Alpha variant as effectively as other less transmissible lineages, providing reassurance of their efficacy against emerging variants of concern.",

keywords = "COVID-19, Transmissibility, Nosocomial outbreaks, Lineage B.1.1.7, Alpha variant, SARS-CoV-2, Variants of concern, UKRI, MRC",

author = "{COG-UK-HOCI Variant Substudy Consortium} and {COVID-19 Genomics UK (COG-UK) Consortium} and Boshier, {Florencia A.T.} and Cristina Venturini and Oliver Stirrup and Guerra-Assun{\c c}{\~a}o, {Jos{\'e} Afonso} and Adela Alcolea-Medina and Becket, {Angela H.} and Matthew Byott and Themoula Charalampous and Filipe, {Ana Da Silva} and Dan Frampton and Sharon Glaysher and Tabassum Khan and Raghavendran Kulasegara-Shylini and Beatrix Kele and Monahan, {Irene M.} and Guy Mollett and Matthew Parker and Emanuela Pelosi and Paul Randell and Sunando Roy and Taylor, {Joshua F.} and Weller, {Sophie J.} and Eleri Wilson-Davies and Phillip Wade and Rachel Williams and Copas, {Andrew J.} and Teresa Cutino-Moguel and Nick Freemantle and Hayward, {Andrew C.} and Alison Holmes and Joseph Hughes and Mahungu, {Tabitha W.} and Gaia Nebbia and Eleni Nastouli and Partridge, {David G.} and Pope, {Cassie F.} and Price, {James R.} and Robson, {Samuel C.} and Kordo Saeed and Shin, {Gee Yen} and {De Silva}, {Thushan I.} and Snell, {Luke B.} and Thomson, {Emma C.} and Witney, {Adam A.} and Judith Breuer",

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doi = "10.1016/j.jinf.2021.09.022",

language = "English",

volume = "83",

pages = "693--700",

journal = "Journal of Infection",

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number = "6",

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TY - JOUR

T1 - The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study

AU - COG-UK-HOCI Variant Substudy Consortium

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

AU - Boshier, Florencia A.T.

AU - Venturini, Cristina

AU - Stirrup, Oliver

AU - Guerra-Assunção, José Afonso

AU - Alcolea-Medina, Adela

AU - Becket, Angela H.

AU - Byott, Matthew

AU - Charalampous, Themoula

AU - Filipe, Ana Da Silva

AU - Frampton, Dan

AU - Glaysher, Sharon

AU - Khan, Tabassum

AU - Kulasegara-Shylini, Raghavendran

AU - Kele, Beatrix

AU - Monahan, Irene M.

AU - Mollett, Guy

AU - Parker, Matthew

AU - Pelosi, Emanuela

AU - Randell, Paul

AU - Roy, Sunando

AU - Taylor, Joshua F.

AU - Weller, Sophie J.

AU - Wilson-Davies, Eleri

AU - Wade, Phillip

AU - Williams, Rachel

AU - Copas, Andrew J.

AU - Cutino-Moguel, Teresa

AU - Freemantle, Nick

AU - Hayward, Andrew C.

AU - Holmes, Alison

AU - Hughes, Joseph

AU - Mahungu, Tabitha W.

AU - Nebbia, Gaia

AU - Nastouli, Eleni

AU - Partridge, David G.

AU - Pope, Cassie F.

AU - Price, James R.

AU - Robson, Samuel C.

AU - Saeed, Kordo

AU - Shin, Gee Yen

AU - De Silva, Thushan I.

AU - Snell, Luke B.

AU - Thomson, Emma C.

AU - Witney, Adam A.

AU - Breuer, Judith

PY - 2021/12/1

Y1 - 2021/12/1

N2 - Objectives - Recently emerging SARS-CoV-2 variants have been associated with an increased rate of transmission within the community. We sought to determine whether this also resulted in increased transmission within hospitals.Methods - We collected viral sequences and epidemiological data of patients with community and healthcare associated SARS-CoV-2 infections, sampled from 16th November 2020 to 10th January 2021, from nine hospitals participating in the COG-UK HOCI study. Outbreaks were identified using ward information, lineage and pairwise genetic differences between viral sequences.Results - Mixed effects logistic regression analysis of 4184 sequences showed healthcare-acquired infections were no more likely to be identified as the Alpha variant than community acquired infections. Nosocomial outbreaks were investigated based on overlapping ward stay and SARS-CoV-2 genome sequence similarity. There was no significant difference in the number of patients involved in outbreaks caused by the Alpha variant compared to outbreaks caused by other lineages.Conclusions - We find no evidence to support it causing more nosocomial transmission than previous lineages. This suggests that the stringent infection prevention measures already in place in UK hospitals contained the spread of the Alpha variant as effectively as other less transmissible lineages, providing reassurance of their efficacy against emerging variants of concern.

AB - Objectives - Recently emerging SARS-CoV-2 variants have been associated with an increased rate of transmission within the community. We sought to determine whether this also resulted in increased transmission within hospitals.Methods - We collected viral sequences and epidemiological data of patients with community and healthcare associated SARS-CoV-2 infections, sampled from 16th November 2020 to 10th January 2021, from nine hospitals participating in the COG-UK HOCI study. Outbreaks were identified using ward information, lineage and pairwise genetic differences between viral sequences.Results - Mixed effects logistic regression analysis of 4184 sequences showed healthcare-acquired infections were no more likely to be identified as the Alpha variant than community acquired infections. Nosocomial outbreaks were investigated based on overlapping ward stay and SARS-CoV-2 genome sequence similarity. There was no significant difference in the number of patients involved in outbreaks caused by the Alpha variant compared to outbreaks caused by other lineages.Conclusions - We find no evidence to support it causing more nosocomial transmission than previous lineages. This suggests that the stringent infection prevention measures already in place in UK hospitals contained the spread of the Alpha variant as effectively as other less transmissible lineages, providing reassurance of their efficacy against emerging variants of concern.

KW - COVID-19

KW - Transmissibility

KW - Nosocomial outbreaks

KW - Lineage B.1.1.7

KW - Alpha variant

KW - SARS-CoV-2

KW - Variants of concern

KW - UKRI

KW - MRC

U2 - 10.1016/j.jinf.2021.09.022

DO - 10.1016/j.jinf.2021.09.022

M3 - Article

SN - 0163-4453

VL - 83

SP - 693

EP - 700

JO - Journal of Infection

JF - Journal of Infection

IS - 6

ER -

The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study

Abstract

Keywords

Access to Document

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Datasets

Dataset: GISAID EpiCov SARS-CoV-2 Whole Genome Sequencing Database

COVID-19 Genomics UK (COG-UK) consortium

Projects

HOCI: COG-UK Project Hospital Onset COVID-19 Infections study

STOP COVID-19: Sequencing and Tracking Of Phylogeny in COVID-19

Cite this