Investigation of SARS-CoV-2 outbreaks in six care homes in London, April 2020

Abstract

Background: Care homes are experiencing large outbreaks of COVID-19 associated with high case-fatality rates. We conducted detailed investigations in six London care homes reporting suspected COVID-19 outbreaks during April 2020.

Methods: Residents and staff had nasal swabs for SARS CoV-2 testing using RT-PCR and were followed-up for 14 days. They were categorized as symptomatic, post-symptomatic or pre-symptomatic if they had symptoms at the time of testing, in the two weeks before or two weeks after testing, respectively, or asymptomatic throughout. Virus isolation and whole genome sequencing (WGS) was also performed.

Findings: Across the six care homes, 105/264 (39.8%) residents were SARS CoV-2 positive, including 28 (26.7%) symptomatic, 10 (9.5%) post-symptomatic, 21 (20.0%) pre-symptomatic and 46 (43.8%) who remained asymptomatic. Case-fatality at 14-day follow-up was highest among symptomatic SARS-CoV-2 positive residents (10/28, 35.7%) compared to asymptomatic (2/46, 4.3%), post-symptomatic (2/10, 20.0%) or pre-symptomatic (3/21,14.3%) residents. Among staff, 53/254 (20.9%) were SARS-CoV-2 positive and 26/53 (49.1%) remained asymptomatic. RT-PCR cycle-thresholds and live-virus recovery were similar between symptomatic/asymptomatic residents/staff. Higher RT-PCR cycle threshold values (lower virus load) samples were associated with exponentially decreasing ability to recover infectious virus (P<0.001). WGS identified multiple (up to 9) separate introductions of different SARS-CoV-2 strains into individual care homes.

Interpretation: A high prevalence of SARS-CoV-2 positivity was found in care homes residents and staff, half of whom were asymptomatic and potential reservoirs for on-going transmission. A third of symptomatic SARS-CoV-2 residents died within 14 days. Symptom-based screening alone is not sufficient for outbreak control.

Funding: None.

Keywords: Care homes; Case-fatality rate; Covid-19; Symptoms.

Fig. 1

SARS-CoV-2 positivity, symptoms, live virus isolation and deaths in residents and staff across six London care homes experiencing a COVID-19 outbreak during April 2020. In SARS-CoV-2 positive residents, live virus was isolated from 5/17 (29.4%) of symptomatic and 14/33 (42.4%) of asymptomatic residents at the time of testing (P = 0.37) and 14/40 (35.0%) survivors compared with 5/10 (50.0%) of fatal cases (P = 0.38).

Fig. 2

a. Boxplot showing median Cycle Threshold (Ct) values with interquartile ranges (Boxes) along with minimum (Q1–1.5*IQR) and maximum (Q3+1.5*IQR) values (whiskers) and outlier values (blue circles) for asymptomatic, post-symptomatic, pre-symptomatic and symptomatic residents and staff. 2b. Live virus isolation by RT-PCR Cycle threshold (t) range in residents and staff of care homes. The data points include live virus isolation by number of strains tested.

Fig. 3

Maximum Likelihood phylogeny of 99 SARS-CoV-2 genomes from individuals within six care homes. Coloured branches are used to indicate the care home, staff are annotated on the tree with (S), genomes from patients who died after testing positive for covid-19 are shown with (X). Unannotated tips in the phylogeny represent genomes from care home residents.