eLife (Mar 2021)
Genomic epidemiology of COVID-19 in care homes in the east of England
- William L Hamilton,
- Gerry Tonkin-Hill,
- Emily R Smith,
- Dinesh Aggarwal,
- Charlotte J Houldcroft,
- Ben Warne,
- Luke W Meredith,
- Myra Hosmillo,
- Aminu S Jahun,
- Martin D Curran,
- Surendra Parmar,
- Laura G Caller,
- Sarah L Caddy,
- Fahad A Khokhar,
- Anna Yakovleva,
- Grant Hall,
- Theresa Feltwell,
- Malte L Pinckert,
- Iliana Georgana,
- Yasmin Chaudhry,
- Colin S Brown,
- Sonia Gonçalves,
- Roberto Amato,
- Ewan M Harrison,
- Nicholas M Brown,
- Mathew A Beale,
- Michael Spencer Chapman,
- David K Jackson,
- Ian Johnston,
- Alex Alderton,
- John Sillitoe,
- Cordelia Langford,
- Gordon Dougan,
- Sharon J Peacock,
- Dominic P Kwiatowski,
- Ian G Goodfellow,
- M Estee Torok,
- COVID-19 Genomics Consortium UK
Affiliations
- William L Hamilton
- ORCiD
- Cambridge University Hospitals NHS Foundation Trust, Departments of Infectious Diseases and Microbiology, Cambridge, United Kingdom; University of Cambridge, Department of Medicine, Cambridge, United Kingdom
- Gerry Tonkin-Hill
- ORCiD
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Emily R Smith
- Cambridgeshire County Council, Cambridge, United Kingdom
- Dinesh Aggarwal
- ORCiD
- University of Cambridge, Department of Medicine, Cambridge, United Kingdom; Public Health England, Colindale, United Kingdom
- Charlotte J Houldcroft
- ORCiD
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
- Ben Warne
- Cambridge University Hospitals NHS Foundation Trust, Departments of Infectious Diseases and Microbiology, Cambridge, United Kingdom; University of Cambridge, Department of Medicine, Cambridge, United Kingdom
- Luke W Meredith
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
- Myra Hosmillo
- ORCiD
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
- Aminu S Jahun
- ORCiD
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
- Martin D Curran
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge, United Kingdom
- Surendra Parmar
- Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge, United Kingdom
- Laura G Caller
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom; The Francis Crick Institute, London, United Kingdom
- Sarah L Caddy
- ORCiD
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
- Fahad A Khokhar
- University of Cambridge, Department of Medicine, Cambridge, United Kingdom
- Anna Yakovleva
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
- Grant Hall
- ORCiD
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
- Theresa Feltwell
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
- Malte L Pinckert
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
- Iliana Georgana
- ORCiD
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
- Yasmin Chaudhry
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
- Colin S Brown
- Public Health England, Colindale, United Kingdom
- Sonia Gonçalves
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Roberto Amato
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Ewan M Harrison
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Nicholas M Brown
- ORCiD
- Cambridge University Hospitals NHS Foundation Trust, Departments of Infectious Diseases and Microbiology, Cambridge, United Kingdom; Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge, United Kingdom
- Mathew A Beale
- ORCiD
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Michael Spencer Chapman
- ORCiD
- Wellcome Sanger Institute, Hinxton, United Kingdom; Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, United Kingdom
- David K Jackson
- ORCiD
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Ian Johnston
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Alex Alderton
- Wellcome Sanger Institute, Hinxton, United Kingdom
- John Sillitoe
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Cordelia Langford
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Gordon Dougan
- University of Cambridge, Department of Medicine, Cambridge, United Kingdom
- Sharon J Peacock
- ORCiD
- University of Cambridge, Department of Medicine, Cambridge, United Kingdom
- Dominic P Kwiatowski
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Ian G Goodfellow
- ORCiD
- University of Cambridge, Department of Pathology, Division of Virology, Cambridge, United Kingdom
- M Estee Torok
- ORCiD
- Cambridge University Hospitals NHS Foundation Trust, Departments of Infectious Diseases and Microbiology, Cambridge, United Kingdom; University of Cambridge, Department of Medicine, Cambridge, United Kingdom
- COVID-19 Genomics Consortium UK
- DOI
- https://doi.org/10.7554/eLife.64618
- Journal volume & issue
-
Vol. 10
Abstract
COVID-19 poses a major challenge to care homes, as SARS-CoV-2 is readily transmitted and causes disproportionately severe disease in older people. Here, 1167 residents from 337 care homes were identified from a dataset of 6600 COVID-19 cases from the East of England. Older age and being a care home resident were associated with increased mortality. SARS-CoV-2 genomes were available for 700 residents from 292 care homes. By integrating genomic and temporal data, 409 viral clusters within the 292 homes were identified, indicating two different patterns – outbreaks among care home residents and independent introductions with limited onward transmission. Approximately 70% of residents in the genomic analysis were admitted to hospital during the study, providing extensive opportunities for transmission between care homes and hospitals. Limiting viral transmission within care homes should be a key target for infection control to reduce COVID-19 mortality in this population.
Keywords
