Genomic epidemiology of covid-19 in care homes in the east of England

COVID-19 Genomics Consortium UK

doi:10.7554/eLife.64618

Genomic epidemiology of covid-19 in care homes in the east of England

COVID-19 Genomics Consortium UK

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

16 Citations (Scopus)

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.

Original language	English
Article number	64618
Number of pages	31
Journal	eLife
Volume	10
DOIs	https://doi.org/10.7554/eLife.64618
Publication status	Published - 2 Mar 2021

Bibliographical note

Funding Information:
M Estee Torok: I have received grant support from the Academy of Medical Sciences, the Health Foundation, and the NIHR Biomedical Research Centre. I have also received book royalties from Oxford University Press and honoraria from the Wellcome Sanger Institute. The other authors declare that no competing interests exist.

Funding Information:
Medical Research Council COG-UK MC-PC-19027 Sharon J Peacock National Institute for Health Research COG-UK MC-PC-19027 Sharon J Peacock Wellcome Trust COG-UK MC-PC-19027 Sharon J Peacock Wellcome Trust Senior Fellowship 097997/Z/ 11/Z Ian G Goodfellow Academy of Medical Sciences Clinician Scientist Fellowship M Estee Torok Health Foundation Clinician Scientist Fellowship M Estee Torok National Institute for Health Research William L Hamilton Emily R Smith Ben Warne M Estee Torok Wellcome Trust Collabrative grant 204870/ Z/16/Z Charlotte J Houldcroft.

Publisher Copyright:
© Hamilton et al.

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10.7554/eLife.64618

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@article{583f186c8bdc4a9e988ba51c5153a11a,

title = "Genomic epidemiology of covid-19 in care homes in the east of England",

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.",

author = "{COVID-19 Genomics Consortium UK} and Hamilton, {William L.} and Gerry Tonkin-Hill and Smith, {Emily R.} and Dinesh Aggarwal and Houldcroft, {Charlotte J.} and Ben Warne and Meredith, {Luke W.} and Myra Hosmillo and Jahun, {Aminu S.} and Martin Curran and Surendra Parmar and Caller, {Laura G.} and Caddy, {Sarah L.} and Khokhar, {Fahad A.} and Anna Yakovleva and Grant Hall and Theresa Feltwell and Pinckert, {Malte L.} and Iliana Georgana and Yasmin Chaudhry and Brown, {Colin S.} and Sonia Gon{\c c}alves and Roberto Amato and Harrison, {Ewan M.} and Nicholas Brown and Beale, {Mathew A.} and Chapman, {Michael Spencer} and Jackson, {David K.} and Ian Johnston and Alex Alderton and John Sillitoe and Cordelia Langford and Gordon Dougan and Sharon Peacock and Kwiatowski, {Dominic P.} and Goodfellow, {Ian G.} and {Estee Torok}, M.",

note = "Funding Information: M Estee Torok: I have received grant support from the Academy of Medical Sciences, the Health Foundation, and the NIHR Biomedical Research Centre. I have also received book royalties from Oxford University Press and honoraria from the Wellcome Sanger Institute. The other authors declare that no competing interests exist. Funding Information: Medical Research Council COG-UK MC-PC-19027 Sharon J Peacock National Institute for Health Research COG-UK MC-PC-19027 Sharon J Peacock Wellcome Trust COG-UK MC-PC-19027 Sharon J Peacock Wellcome Trust Senior Fellowship 097997/Z/ 11/Z Ian G Goodfellow Academy of Medical Sciences Clinician Scientist Fellowship M Estee Torok Health Foundation Clinician Scientist Fellowship M Estee Torok National Institute for Health Research William L Hamilton Emily R Smith Ben Warne M Estee Torok Wellcome Trust Collabrative grant 204870/ Z/16/Z Charlotte J Houldcroft. Publisher Copyright: {\textcopyright} Hamilton et al.",

year = "2021",

month = mar,

day = "2",

doi = "10.7554/eLife.64618",

language = "English",

volume = "10",

journal = "eLife",

issn = "2050-084X",

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T1 - Genomic epidemiology of covid-19 in care homes in the east of England

AU - COVID-19 Genomics Consortium UK

AU - Hamilton, William L.

AU - Tonkin-Hill, Gerry

AU - Smith, Emily R.

AU - Aggarwal, Dinesh

AU - Houldcroft, Charlotte J.

AU - Warne, Ben

AU - Meredith, Luke W.

AU - Hosmillo, Myra

AU - Jahun, Aminu S.

AU - Curran, Martin

AU - Parmar, Surendra

AU - Caller, Laura G.

AU - Caddy, Sarah L.

AU - Khokhar, Fahad A.

AU - Yakovleva, Anna

AU - Hall, Grant

AU - Feltwell, Theresa

AU - Pinckert, Malte L.

AU - Georgana, Iliana

AU - Chaudhry, Yasmin

AU - Brown, Colin S.

AU - Gonçalves, Sonia

AU - Amato, Roberto

AU - Harrison, Ewan M.

AU - Brown, Nicholas

AU - Beale, Mathew A.

AU - Chapman, Michael Spencer

AU - Jackson, David K.

AU - Johnston, Ian

AU - Alderton, Alex

AU - Sillitoe, John

AU - Langford, Cordelia

AU - Dougan, Gordon

AU - Peacock, Sharon

AU - Kwiatowski, Dominic P.

AU - Goodfellow, Ian G.

AU - Estee Torok, M.

N1 - Funding Information: M Estee Torok: I have received grant support from the Academy of Medical Sciences, the Health Foundation, and the NIHR Biomedical Research Centre. I have also received book royalties from Oxford University Press and honoraria from the Wellcome Sanger Institute. The other authors declare that no competing interests exist. Funding Information: Medical Research Council COG-UK MC-PC-19027 Sharon J Peacock National Institute for Health Research COG-UK MC-PC-19027 Sharon J Peacock Wellcome Trust COG-UK MC-PC-19027 Sharon J Peacock Wellcome Trust Senior Fellowship 097997/Z/ 11/Z Ian G Goodfellow Academy of Medical Sciences Clinician Scientist Fellowship M Estee Torok Health Foundation Clinician Scientist Fellowship M Estee Torok National Institute for Health Research William L Hamilton Emily R Smith Ben Warne M Estee Torok Wellcome Trust Collabrative grant 204870/ Z/16/Z Charlotte J Houldcroft. Publisher Copyright: © Hamilton et al.

PY - 2021/3/2

Y1 - 2021/3/2

N2 - 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.

AB - 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.

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DO - 10.7554/eLife.64618

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SN - 2050-084X

VL - 10

JO - eLife

JF - eLife

M1 - 64618

ER -

Genomic epidemiology of covid-19 in care homes in the east of England

Abstract

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