Quantifying transmissibility of SARS-CoV-2 and impact of intervention within long-term healthcare facilities

Estimates of the basic reproduction number (R ₀) for COVID-19 are particularly variable in the context of transmission within locations such as long-term healthcare (LTHC) facilities. We sought to characterize the heterogeneity of R ₀ across known outbreaks within these facilities. We used a unique comprehensive dataset of all outbreaks that occurred within LTHC facilities in British Columbia, Canada as of 21 September 2020. We estimated R ₀ in 18 LTHC outbreaks with a novel Bayesian hierarchical dynamic model of susceptible, exposed, infected and recovered individuals, incorporating heterogeneity of R ₀ between facilities. We further compared these estimates to those obtained with standard methods that use the exponential growth rate and maximum likelihood. The total size of outbreaks varied dramatically, with range of attack rates 2%-86%. The Bayesian analysis provided an overall estimate of R ₀ = 2.51 (90% credible interval 0.47-9.0), with individual facility estimates ranging between 0.56 and 9.17. Uncertainty in these estimates was more constrained than standard methods, particularly for smaller outbreaks informed by the population-level model. We further estimated that intervention led to 61% (52%-69%) of all potential cases being averted within the LTHC facilities, or 75% (68%-79%) when using a model with multi-level intervention effect. Understanding of transmission risks and impact of intervention are essential in planning during the ongoing global pandemic, particularly in high-risk environments such as LTHC facilities.