Quantifying transmissibility of SARS-CoV-2 and impact of intervention within long-term healthcare facilities
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Abstract
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.
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SciScore for 10.1101/2021.02.01.21249903: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:There are limitations to the study. The reported attack rate and modelled population size for LTHC facilities was based upon the maximum capacity for that facility, which may be larger than the total number of exposed individuals. Conversely, staff and family members may contribute to transmission in addition to facility residents. Although we allowed the maximum capacity size to vary to account for these factors, we lacked detailed …
SciScore for 10.1101/2021.02.01.21249903: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
No key resources detected.
Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:There are limitations to the study. The reported attack rate and modelled population size for LTHC facilities was based upon the maximum capacity for that facility, which may be larger than the total number of exposed individuals. Conversely, staff and family members may contribute to transmission in addition to facility residents. Although we allowed the maximum capacity size to vary to account for these factors, we lacked detailed data to inform this. Similarly, we did not consider a distinction between the behaviour of staff and residents. Although we estimated parameter ζ, the rate at which interventions brought R(t) below 1, the manner in which intervention curtailed transmission was not explicitly explored within this study, because the exact nature of interventions and their timings was not precisely known. We considered all outbreaks as originating from a single index case in a closed population. Community prevalence remained low in BC during the period of this study so this seems a fair assumption, but it is possible that some facilities had multiple introductions. We also removed all outbreaks of size 1 since one data point does not contain enough information to fit the compartmental model, but in leaving out those outbreaks we do lose some information about transmission. How much to account for this seems unclear, however, without further data on how much opportunity for transmission these single cases had. Although the fact that 30/53 LTHC outbreaks resulted in on...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from scite Reference Check: We found no unreliable references.
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