Covid-19 infection and attributable mortality in UK long term care facilities: Cohort study using active surveillance and electronic records (March-June 2020)
This repository contains computer scripts for the pre-print manuscript available from medRxiv (DOI: 10.1101/2020.07.14.20152629).
Background: Rates of Covid-19 infection have declined in many countries, but outbreaks persist in residents of long-term care facilities (LTCFs) who are at high risk of severe outcomes. Epidemiological data from LTCFs are scarce. We used population-level active surveillance to estimate incidence of, and risk factors for Covid-19, and attributable mortality in elderly residents of LTCFs.
Methods: Cohort study using individual-level electronic health records from 8,713 residents and daily counts of infection for 9,339 residents and 11,604 staff across 179 UK LTCFs. We modelled risk factors for infection and mortality using Cox proportional hazards and estimated attributable fractions.
Findings: 2,075/9,339 residents developed Covid-19 symptoms (22.2% [95% confidence interval: 21.4%; 23.1%]), while 951 residents (10.2% [9.6%; 10.8%]) and 585 staff (5.0% [4.7%; 5.5%]) had laboratory confirmed infections. Confirmed infection incidence in residents and staff respectively was 152.6 [143.1; 162.6] and 62.3 [57.3; 67.5] per 100,000 person-days. 121/179 (67.6%) LTCFs had at least one Covid-19 infection or death. Lower staffing ratios and higher occupancy rates were independent risk factors for infection. 1,694 all-cause deaths occurred in 8,713 (19.4% [18.6%; 20.3%]) residents. 217 deaths occurred in 607 residents with confirmed infection (case-fatality rate: 35.7% [31.9%; 39.7%]). 567/1694 (33.5%) of all-cause deaths were attributable to Covid-19, 28.0% of which occurred in residents with laboratory-confirmed infection. The remainder of excess deaths occurred in asymptomatic or symptomatic residents in the context of limited testing for infection, suggesting substantial under-ascertainment.
Interpretation: 1 in 5 residents had symptoms of infection during the pandemic, but many cases were not tested. Higher occupancy and lower staffing levels increase infection risk. Disease control measures should integrate active surveillance and testing with fundamental changes in staffing and care home occupancy to protect staff and residents from infection.
Funding: This work was supported by the Economic and Social Research Council (grant reference ES/V003887/1).