COVID 19 Related Simulation

Note: Some of these features are currently in the c19-updates branch.

Synthea provides simulation of SARS-CoV-2 infection, progression to COVID-19 and vaccination. Given the recency of the COVID-19 pandemic, Synthea is able to leverage real-world data to simulate infection and vaccinate rates.

SARS-CoV-2 Infection Rate

The infection rate for SARS-CoV-2 is driven by data obtained from the Our World In Data GitHub Repository (OWID). The OWID data set provides daily COVID-19 case counts as well as the rate of cases per 100K. While the dataset provided by OWID is for the entire world, Synthea currently uses data for the US. The probability of an unvaccinated individual contracting a SARS-CoV-2 infection on a given day in the simulation is the US national case rate per 100K divided by 100K.

Infections happen in the Synthea COVID-19 Module. This module uses a CSV look up table, covid19_prob.csv, for infection rates.

Individuals who are vaccinated in the simulation are 100 times less likely to be infected. This figure was arbitrarily chosen by the Synthea team and may be updated as data on vaccine prevention of infection is made available and agreed upon by the scientific community.

Updating Infection Rate Data

The Synthea project provides a method for updating case count data. Users can run the update_case_counts.js script, contained in src/main/javascript. This script will fetch the case count data from GitHub and update covid19_prob.csv. The script requires node.js (the script was tested with version 16.5.0) and curl to be installed.