The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study - 12/12/21

Doi : 10.1016/j.jinf.2021.09.022

Florencia A.T. Boshier ^a,^{^{1
These authors contributed equally to this work.}}, Cristina Venturini ^a,^{^{1
These authors contributed equally to this work.}}, Oliver Stirrup ^b, José Afonso Guerra-Assunção ^a,^c, Adela Alcolea-Medina ^d,^e, Angela H. Becket ^f,^g, Matthew Byott ^h,ⁱ, Themoula Charalampous ^d, Ana da Silva Filipe ^j, Dan Frampton ^h,^k, Sharon Glaysher ^l, Tabassum Khan ^m, Raghavendran Kulasegara-Shylini ^m, Beatrix Kele ^m, Irene M. Monahan ⁿ, Guy Mollett ^j, Matthew Parker ^o,^p,^q, Emanuela Pelosi ^r, Paul Randell ^s, Sunando Roy ^a, Joshua F. Taylor ^t, Sophie J. Weller ^u, Eleri Wilson-Davies ^r, Phillip Wade ^v,^w, Rachel Williams ^c, Andrew J. Copas ^b, Teresa Cutino-Moguel ^m, Nick Freemantle ^y, Andrew C. Hayward ^z, Alison Holmes ^aa,^ab, Joseph Hughes ^j, Tabitha W. Mahungu ^u, Gaia Nebbia ^d,^ac, Eleni Nastouli ^ad,^ae,^af,ⁱ, David G. Partridge ^v,^w, Cassie F. Pope ^n,^ag, James R. Price ^ah, Samuel C. Robson ^f,^g,^ai, Kordo Saeed ^aj,^ak, Gee Yen Shin ^af, Thushan I. de Silva ^v,^w, Luke B. Snell ^d,^ac, Emma C. Thomson ^j, Adam A. Witney ⁿ, Judith Breuer ^a,^al,^⁎
COG-UK HOCI Variant Substudy consortium*, The COVID-19 Genomics UK (COG-UK) consortium^{^†}
Full list of consortium member's names and affiliations can be found in the appendix.
, ^x
^a Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
^b Institute for Global Health, University College London, London, United Kingdom
^c Department of Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
^d Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
^e Infection Sciences, Viapath, London, United Kingdom
^f Centre for Enzyme Innovation, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom
^g School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
^h Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, United Kingdom
ⁱ The Francis Crick Institute, London, United Kingdom
^j MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
^k Division of Infection and Immunity, University College London, London, United Kingdom
^l Portsmouth Hospitals University NHS Trust, Queen Alexandra Hospital, Portsmouth PO6 3LY, United Kingdom
^m Division of Infection, The Royal London Hospital, Barts Health, United Kingdom
ⁿ Institute for Infection and Immunity, St George's University of London, Cranmer Terrace, London SW17 0RE, United Kingdom
^o Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, United Kingdom
^p Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, United Kingdom
^q Sheffield Biomedical Research Centre, The University of Sheffield, Sheffield, United Kingdom
^r Southampton Specialist Virology Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
^s Department of Infection and Immunity, North West London Pathology, London, United Kingdom
^t Department of Microbiology, South West London Pathology, Jenner Wing, St. George's Hospital, Blackshaw Road, London SW17 0QT, United Kingdom
^u Department of Virology, Royal Free London NHS Foundation Trust, London, United Kingdom
^v Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
^w The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
^x https://www.cogconsortium.uk, United Kingdom
^y Institute for Clinical Trials and Methodology, University College London, London, United Kingdom
^z Institute of Epidemiology and Health Care, University College London, London, United Kingdom
^aa Department of Infectious Disease, Faculty of Medicine, Imperial College London, United Kingdom
^ab Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, United Kingdom
^ac Department of Infectious Diseases, Guy's and St Thomas’ Hospital NHS Foundation Trust, London, United Kingdom
^ad Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
^ae Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, United Kingdom
^af Department of Clinical Virology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
^ag Infection Care Group, St George's University Hospitals NHS Foundation Trust, Blackshaw Road, London SW17 0QT, United Kingdom
^ah Imperial College Healthcare NHS Trust, London, United Kingdom
^ai School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, United Kingdom
^aj Department of Infection, University Hospital Southampton NHS Foundation Trust, Tremona Road, Southampton, United Kingdom
^ak Faculty of Medicine, Clinical and Experimental Sciences, University of Southampton, Tremona Road, Southampton, United Kingdom
^al Department of Microbiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom

^⁎Corresponding author at: Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United KingdomDepartment of InfectionImmunity and InflammationUCL Great Ormond Street Institute of Child HealthUniversity College LondonLondonUnited Kingdom

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Summary

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.

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Keywords : COVID-19, Transmissibility, Nosocomial outbreaks, Lineage B.1.1.7, Alpha variant, SARS-CoV-2, Variants of concern

Plan

Introduction

Methods

Sequence and patient meta-data

SARS-CoV-2 sequencing

Prevalence in community testing (Pillar 2) from COG-UK

Statistical analysis

Results

Study dataset

Prevalence of the Alpha variant

Pairwise distance in HCAI

Outbreaks

Discussion

Funding

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Vol 83 - N° 6

P. 693-700 - décembre 2021 Retour au numéro

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The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study - 12/12/21

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Results

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