  Viral kinetics have been extensively studied in the past through the use of
spatially well-mixed ordinary differential equations describing the time
evolution of the diseased state. However, emerging spatial structures such as
localized populations of dead cells might adversely affect the spread of
infection, similar to the manner in which a counter-fire can stop a forest fire
from spreading. In a previous publication (Beauchemin et al., 2005), a simple
2-D cellular automaton model was introduced and shown to be accurate enough to
model an uncomplicated infection with influenza A. Here, this model is used to
investigate the effects of relaxing the well-mixed assumption. Particularly,
the effects of the initial distribution of infected cells, the regeneration
rule for dead epithelial cells, and the proliferation rule for immune cells are
explored and shown to have an important impact on the development and outcome
of the viral infection in our model.
