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

Getz, Michael; Wang, Yafei; An, Gary; Becker, Andrew; Cockrell, Chase; Collier, Nicholson; Craig, Morgan; Davis, Courtney L.; Faeder, James; Versypt, Ashlee N. Ford; Gianlupi, Juliano F.; Glazier, James A.; Hamis, Sara; Heiland, Randy; Hillen, Thomas; Hou, Dennis; Islam, Mohammad Aminul; Jenner, Adrianne; Kurtoglu, Furkan; Liu, Bing; Macfarlane, Fiona; Maygrundter, Pablo; Morel, Penelope A; Narayanan, Aarthi; Ozik, Jonathan; Pienaar, Elsje; Rangamani, Padmini; Shoemaker, Jason Edward; Smith, Amber M.; Macklin, Paul

The 2019 novel coronavirus, SARS-CoV-2, is an emerging pathogen of critical significance to international public health. Knowledge of the interplay between molecular-scale virus-receptor interactions, single-cell viral replication, intracellular-scale viral transport, and emergent tissue-scale viral propagation is limited. Moreover, little is known about immune system-virus-tissue interactions and how these can result in low-level (asymptomatic) infections in some cases and acute respiratory distress syndrome (ARDS) in others, particularly with respect to presentation in different age groups or pre-existing inflammatory risk factors like diabetes. Given the nonlinear interactions within and among each of these processes, multiscale simulation models can shed light on the emergent dynamics that lead to divergent outcomes, identify actionable “choke points” for pharmacologic interventions, screen potential therapies, and identify potential biomarkers that differentiate patient outcomes. Given the complexity of the problem and the acute need for an actionable model to guide therapy discovery and optimization, we introduce and iteratively refine a prototype of a multiscale model of SARS-CoV-2 dynamics in lung tissue. The first prototype model was built and shared internationally as open source code and an online interactive model in under 12 hours, and community domain expertise is driving rapid refinements with a two-to-four week release cycle. In a sustained community effort, this consortium is integrating data and expertise across virology, immunology, mathematical biology, quantitative systems physiology, cloud and high performance computing, and other domains to accelerate our response to this critical threat to international health.