COVID-19 Toolset

The Information is licensed as is, and the Information Provider excludes all representations, warranties, obligations, and liabilities, whether expressed or implied, to the maximum extent permitted by law.
Point-prevalence map and algorithms: Steven Horn1
Missed infections calculator: Steve Guillouzic 1, Ramzi Mirshak1, Andrew Sirjoosingh1,2
1DRDC - Centre for Operational Research and Analysis
2Directorate of Data Science, ADM Data, Innovation, Analytics
This toolset was developed at the request of the Canadian Forces Health Services. Estimates made within it are intended to be used by medical advisors, e.g. to support local risk assessment and related advice provided to commanders. This toolset IS NOT intended as a standalone decision-making product in the absence of medical advice, and IS NOT to be used in this way.
Point-prevalence map: Shows the current and predicted SARS-CoV-2 virus infections in global sub-populations.
Point prevalence is estimated by health region in Canada, and at various scales outside of Canada, using a Bayesian inference method (a statistical approach) that considers important epidemiological estimates (e.g. incubation period, infectious period, asymptomatic fraction) combined with open-source case information (e.g. cases). The method takes account of lags in reporting (e.g. between testing and reporting) and dynamically adjusts for biases in case reporting. Once the model is tuned to the case detections of the population, a prediction is provided to provide an indication of the expected future prevalence and cases.
Notes
  • Analysis of each region is updated at varying intervals. Regions with higher prevalence, or changing prevalence are updated more frequently. Each region should be updated at least once every 7 days.
  • This tool continues to be optimized. In some cases, estimates are not provided for an area, e.g., because the available data do not allow robust estimation of point prevalence. We are working to address such gaps on a continual basis.
  • All prevalence values are in percent of population infected (exposed or infectious).
Missed infection calculator: Calculate the probability of one or more individuals in a group to be infected with SARS-CoV-2 after a variable quarantine period and testing.
  • Canadian case data is provided by the COVID-19 Canada Open Data Working Group

    Berry I, Soucy J-PR, Tuite A, Fisman D. Open access epidemiologic data and an interactive dashboard to monitor the COVID-19 outbreak in Canada. CMAJ. 2020 Apr 14;192(15):E420. doi: https://doi.org/10.1503/cmaj.75262
  • Global and United States County level case data is provided by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University

    Dong E, Du H, Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Inf Dis. 20(5):533-534. doi: 10.1016/S1473-3099(20)30120-1
  • Effectiveness of PCR tests is estimated from data published by researchers from Johns Hopkins University and extrapolated to 30 days

    Kucirka LM, Lauer SA, Laeyendecker O, Boon D, Lessler J. Variation in False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction-Based SARS-CoV-2 Tests by Time Since Exposure. Ann Intern Med. 2020;173(4):262-267. doi:10.7326/M20-1495
  • For Antigen tests, the missed infection calculator uses a notional effectiveness curve adapted from one provided by a researcher from the Public Health Agency of Canada

    Champredon D, Private communication.
The following individuals have provided support or contribution to this project: David Waller, Steven Schofield, Mathew Samuel, Michael A. Salciccoli, Alasdair Grant