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

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

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.