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

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)
9 Downloads (Pure)


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 languageEnglish
Article numbere64618
Pages (from-to)1-31
Number of pages31
Early online date26 Mar 2021
Publication statusPublished - 2 Sept 2021


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