Statistical and Mathematical Modeling in Biological Applications
Abstract: Avian Influenza Viruses (AIVs) have been pivotal to the origination of human pandemic strains. Despite their scientific and public health significance, however, there remains much to be understood about the ecology and evolution of AIVs in wild birds, where major pools of genetic diversity are generated and maintained. Here, we present comparative phylodynamic analyses of human and avian influenza viruses in North America, demonstrating significantly higher standing genetic diversity and phylogenetic topology with a weaker signature of immune escape in AIVs compared with human viruses. To explain these differences, we performed statistical analyses that eliminated several potential explanations, including host diversity, differences in nucleotide substitution, and geographic structuring. In contrast, a new model shows the interaction of host demography and ecology of transmission, specifically differential persistence of subtypes in aquatic environments, to be a parsimonious explanatory mechanism. Environmental transmission---a manifestation of the ``storage effect''---highlights the potentially unpredictable impact of AIV reservoir for future human pandemics.