Pathosim: A Multi-Pathogen Agent-Based Model 

Overview

Existing modeling tools either fail to capture pathogen-pathogen interactions and the spread of arbitrary pathogens, or have significant limitations. To address this, we expanded upon the foundation set by Covasim, an agent-based model (ABM) developed solely for SARS-CoV-2 outbreak simulations and its mitigation strategies [1]. Our software package is capable of modeling multiple co-circulating pathogens including outbreaks of arbitrary fully parameterizable pathogens as well as surveillance and mitigation strategies.

Features

Below is a list of all the features that have been implemented in the current Pathosim Software.
Some features that were already present in Covasim are not mentioned.
  • Run simulations with multiple co-circulating pathogens where interaction parameters are fully customizable (changes in susceptibility, transmission and disease progression).
  • Configure a fully arbitrary pathogen with the ability to customize the pathogen’s variants, transmission parameters, prognoses, disease progression parameters, etc.
  • Create pathogens using an alternative framework for tracking an individual’s immunity against an arbitrary pathogen.
  • A flexible stratification system which allows users to pick the characteristics they’re interested in (e.g. age, gender, location, whether someone has a smartwatch, etc.), set conditions upon those characteristics (e.g. age between 25 and 50), and obtain simulation results only for people who match those conditions.
  • Plot various simulation data and multi-pathogen spread results such as co-infections.
  • Incorporate basic intervention strategies for arbitrary pathogens in multi-pathogen simulations such as custom vaccines, testing, etc.
  • Active surveillance and serosurveillance programs. 
Contributors: Philippe Teichmann, Nathan Duarte, Alina Shimizu-Jozi, ​Ritchie Yu,​ Caroline E. Wagner, Jing Yuan Luo 

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