Competition among viruses at the within- and between-host scales

Many infectious pathogens, and in particular viruses, have an extremely high rate of mutation. This can lead to rapid evolution driven by selection pressures operating at the withinand betweenhost levels, as strains compete for resources within their host while also competing to effectively transmit to new hosts. In the case of chronic viral infections, such as those caused by HIV or hepatitis C, substantial viral evolution may take place within a single infected individual. The fitness of a pathogen has been studied at the epidemic scale and at the within-host level, but linking the two levels of selection pressure has yet to be satisfactorily resolved. We modify a simple model describing the within-host dynamics of HIV infection by including N different pathogen strains and allowing these strains to mutate. Within the host we observe different strategies for pathogen success during different stages of infection. We embed the within-host model into a simple epidemic model first analytically, resulting in a largest-eigenvalue problem for a particular integral operator, and into a Monte Carlo simulation. We show that co-existence of strains is possible and we explore the factors leading to pathogen success.