A Prototype QSP Model of the Immune Response to SARS-COV-2 for Community Development

The model mechanistically accounts for the influence of key mediators relevant to COVID-19 pathophysiology including, interactions between viral dynamics, the major host immune response mediators, and alveolar tissue damage and regeneration.

Prerequisites

MATLAB

This code was written in MATLAB 2019a

Setup

Add all files in this repository to the MATLAB working directory.

Contents

The repository should contain the following required files:

1. covid19_dxdt.m -> model file with ODEs
2. covidEventFcn.m
3. Driver.m
4. figuremods.m
5. function_run_model.m
6. function_run_model_noplots.m
7. generate_figures.m -> generates manuscript figures
8. get_data_dictionary.m
9. plot_vp.m
10. run_parameter_sweep.m
11. run_unit_test_script.m -> runs unit tests in model
12. run_VP.m
13. SolveBalances.m
14. vp_figure.m
15. Initialize.xlsx

Usage

The command listed below generates figures of all the results in the manuscript and saves them as .png files.

run generate_figures.m

Authors

Wei Dai*, Rohit Rao*, Anna Sher, Nessy Tania, CJ Musante, Richard Allen**

* Joint first authors
** Correspondence to: richard.allen@pfizer.com