Investigation of a severe SARS-CoV-2 outbreak in a long-term care home early in the pandemic

Abstract

Background: The implementation of outbreak management measures has decreased the frequency and severity of SARS-CoV-2 outbreaks in Ontario long-term care homes. We describe the epidemiological and laboratory data from one of the first such outbreaks in Ontario to assess factors associated with its severity, and the impact of progressive interventions for infection control over the course of the outbreak.

Methods: We obtained line list and outbreak data from the public health unit to describe resident and staff cases, severity and distribution of cases over time and within the outbreak facility. Where available, we obtained data on laboratory specimens from the Public Health Ontario Laboratory and performed whole genome sequencing and phylogenetic analysis of viral specimens from the outbreak.

Results: Among 65 residents of the long-term care home, 61 (94%) contracted SARS-CoV-2, with a case fatality rate of 45% (28/61). Among 67 initial staff, 34 (51%) contracted the virus and none died. When the outbreak was declared, 12 staff, 2 visitors and 9 residents had symptoms. Resident cases were located in 3 of 4 areas of the home. Phylogenetic analysis showed tight clustering of cases, with only 1 additional strain of genetically distinct SARS-CoV-2 identified from a staff case in the third week of the outbreak. No cases were identified among 26 new staff brought into the home after full outbreak measures were implemented.

Interpretation: Rapid and undetected viral spread in a long-term care home led to high rates of infection among residents and staff. Progressive implementation of outbreak measures after the peak of cases prevented subsequent staff cases and are now part of long-term care outbreak policy in Ontario.

Figure 1:

Number of confirmed and probable cases of COVID-19 among residents, staff and visitors (n = 96) associated with an outbreak in a long-term care home, by date of symptom onset date or specimen collection (if asymptomatic) from March and April 2020. Figure excludes 1 probable case in a resident who did not have symptoms recorded before death and was not tested, but that was determined to be a probable case based on assessment by the public health unit.

Figure 2:

Maximum likelihood tree showing the phylogenetic relationship between 28 SARS-CoV-2 genomes from specimens collected from staff and residents in March and April 2020. The tree was rooted using the reference genome, Wuhan-Hu-1 (accession MN908947.3). Note: Phylogenetic analysis depicts the evolutionary relationship between sequences, with horizontal branch lengths corresponding to genetic distance (nucleotide substitutions per site). ON–PHL–20–00238 is genetically distinct, with 3 single nucleotide polymorphisms to the nearest sequence. *Staff member had travelled internationally before the outbreak.