Exploratory Modeling and Simulation of the Evolutionary Dynamics of Single-Stranded RNA Virus Populations

Infection, replication and mutation govern the population dynamics of viruses and are the key mechanisms driving their evolution. In particular, RNA viruses (such as the causative agents of Ebola, Dengue, Zika, West Nile, and SARS) have the highest mutation rates which enable them to form highly diverse populations within a single host, evade immune responses and develop resistances to drugs. Understanding the complexity of virus evolution is crucial for developing reliable countermeasures. We present an exploratory simulation model to study the evolution of heterogeneous virus populations in heterogeneous cell environments. This is a unique model that operates at three scales and captures the core mechanisms of the evolutionary process. To the best of our knowledge, this is the first HPC-based simulation of its kind.