Stochastic model of virus and defective interfering particle spread   across mammalian cells with immune response
  Much of the work on modeling the spread of viral infections utilized partial differential equa- tions. Traveling-wave solutions to these PDEs are typically concentrated on velocities and their dependence on the various parameters. Most of the investigations into the dynamical interaction of virus and defective interfering particles (DIP), which are incomplete forms of the virus that replicate through co-infection, have followed the same lines. In this work we present an agent based model of viral infection with consideration of DIP and the negative feedback loop introduced by interferon production as part of the host innate immune response. The model is based high resolution microscopic images of plaques of dead cells we took from mammalian cells infected with Sendai virus with low and high DIP. In order to investigate the effects of the discrete stochastic microscopic mechanisms, which are responsible for virus spreading, have on the macroscopic growth of viral plaques, we generate an agent-based model of viral infection. The two main aims of this work are to (i) investigate the effects of discrete microscopic randomness on the macroscopic growth of viral plaques; and (ii) examine the dynamic interactions between the full length virus, DIP and interferon, and interpret what may be the function of DIP. We find that we can explain the qualitative differences between our stochastic model and deterministic models in terms of the fractal geometry of the resulting plaques, and that DIP have a delaying effect while the interaction between interferon and DIP has a slowing effect on the growth of viral plaques, potentially contributing to viral latency. 
Neil R. Clark, Karla A. Tapia, Aditi Dandapani, Benjamin D. MacArthur,   Carolina Lopez, Avi Ma`ayan
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