Genomic epidemiology of COVID-19 in care homes in the east of England
William L. Hamilton, Gerry Tonkin‐Hill, Darren Smith, Dinesh Aggarwal, Charlotte J. Houldcroft, Ben Warne, Luke W. Meredith, Myra Hosmillo, Aminu S. Jahun, Martin D. Curran, Surendra Parmar, Laura Caller, Sarah Caddy, Fahad Khokhar, Anna Yakovleva, Grant Hall, Theresa Feltwell, Malte L. Pinckert, Iliana Georgana, Yasmin Chaudhry, Colin Brown, Sónia 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 Goodfellow, M. Estée Török
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.