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; The COVID-19 Genomics UK (COG-UK) Consortium; John Allan; Matthew Bashton; Joshua Loh; Andrew Nelson; Darren L. Smith; Wen C. Yew; Gregory R. Young

doi:10.7554/eLife.64618

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 ChaudhryColin 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^*, The COVID-19 Genomics UK (COG-UK) Consortium, John Allan, Matthew Bashton, Joshua Loh, Andrew Nelson, Darren L. Smith, Wen C. Yew, Gregory R. Young

^*Corresponding author for this work

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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	e64618
Pages (from-to)	1-31
Number of pages	31
Journal	eLife
Volume	10
Early online date	26 Mar 2021
DOIs	https://doi.org/10.7554/eLife.64618
Publication status	Published - 2 Sept 2021

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elife-64618-v3Final published version, 1.55 MBLicence: CC BY

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Hamilton, W. L., Tonkin-Hill, G., Smith, E. R., Aggarwal, D., Houldcroft, C. J., Warne, B., Meredith, L. W., Hosmillo, M., Jahun, A. S., Curran, M. D., Parmar, S., Caller, L. G., Caddy, S. L., Khokhar, F. A., Yakovleva, A., Hall, G., Feltwell, T., Pinckert, M. L., Georgana, I., ... Young, G. R. (2021). Genomic epidemiology of covid-19 in care homes in the east of England. eLife, 10, 1-31. Article e64618. https://doi.org/10.7554/eLife.64618

@article{e38b11a7427a42c480d99055281dca90,

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 = "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 Curran, {Martin D.} 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 Brown, {Nicholas M.} 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 Peacock, {Sharon J.} and Kwiatowski, {Dominic P.} and Goodfellow, {Ian G.} and {Estee Torok}, M. and {The COVID-19 Genomics UK (COG-UK) Consortium} and John Allan and Matthew Bashton and Joshua Loh and Andrew Nelson and Smith, {Darren L.} and Yew, {Wen C.} and Young, {Gregory R.}",

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.",

year = "2021",

month = sep,

day = "2",

doi = "10.7554/eLife.64618",

language = "English",

volume = "10",

pages = "1--31",

journal = "eLife",

issn = "2050-084X",

publisher = "eLife Sciences Publications",

}

Hamilton, WL, Tonkin-Hill, G, Smith, ER, Aggarwal, D, Houldcroft, CJ, Warne, B, Meredith, LW, Hosmillo, M, Jahun, AS, Curran, MD, Parmar, S, Caller, LG, Caddy, SL, Khokhar, FA, Yakovleva, A, Hall, G, Feltwell, T, Pinckert, ML, Georgana, I, Chaudhry, Y, Brown, CS, Gonçalves, S, Amato, R, Harrison, EM, Brown, NM, Beale, MA, Chapman, MS, Jackson, DK, Johnston, I, Alderton, A, Sillitoe, J, Langford, C, Dougan, G, Peacock, SJ, Kwiatowski, DP, Goodfellow, IG, Estee Torok, M, The COVID-19 Genomics UK (COG-UK) Consortium, Allan, J, Bashton, M, Loh, J, Nelson, A , Smith, DL, Yew, WC & Young, GR 2021, 'Genomic epidemiology of covid-19 in care homes in the east of England', eLife, vol. 10, e64618, pp. 1-31. https://doi.org/10.7554/eLife.64618

TY - JOUR

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

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 D.

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 M.

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 J.

AU - Kwiatowski, Dominic P.

AU - Goodfellow, Ian G.

AU - Estee Torok, M.

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

AU - Allan, John

AU - Bashton, Matthew

AU - Loh, Joshua

AU - Nelson, Andrew

AU - Smith, Darren L.

AU - Yew, Wen C.

AU - Young, Gregory R.

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.

PY - 2021/9/2

Y1 - 2021/9/2

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.

UR - http://www.scopus.com/inward/record.url?scp=85103336880&partnerID=8YFLogxK

U2 - 10.7554/eLife.64618

DO - 10.7554/eLife.64618

M3 - Article

C2 - 33650490

AN - SCOPUS:85103336880

SN - 2050-084X

VL - 10

SP - 1

EP - 31

JO - eLife

JF - eLife

M1 - e64618

ER -

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

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