Rapid community-driven development of a SARS-CoV-2 tissue simulator

Yafei Wang; Randy Heiland; Morgan Craig; Courtney L. Davis; Ashlee N Ford Versypt; Adrianne Jenner; Jonathan Ozik; Nicholson Collier; Chase Cockrell; Andrew Becker; Gary An; James A. Glazier; Aarthi Narayanan; Amber M Smith; Paul Macklin

In this proof of concept prototype, we modeled a simplified set of biological hypotheses: The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.02.019075 doi: bioRxiv preprint 1.T.2 Virus adhesion to a cell stops its diffusion (acts as an uptake term) 1.V.1 Adhered virus undergoes endocytosis and then becomes uncoated 1.V.2 Uncoated virus (viral contents) lead to release of functioning RNA 1.V.3 RNA creates protein forever, unless it degrades 1.V.4 Protein is transformed to an assembled virus state 1.V.5 Assembled virus is released by the cell 1.VR.1 As a proxy for viral disruption of the cell, the probability of cell death increases with the total number of assembled virions 1.VR.2 Apoptosed cells lyse and release some or all of their contents (In the above, X.C.Y denotes prototype X, modeling component C, biological hypothesis Y, allowing us to easily refer to any individual hypothesis or assumption in discussion and community feedback.) In the next version of this model, we will use the design document protocols for each of these components.