Dynamics selection and pathogenicity in avian influenza: from individual to population

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(a) Develop a family of models relating pathogen strain structure to epidemic dynamics in Equine Influenza (EI), spanning levels from within-host to population, based on experimentally quantifying: (i) within-host strain dynamics (by genotyping of longitudinal viral samples); (ii) impact of transmission founder effects on viral genetic diversity. (b) Apply the models to understand the dynamics of EIV phylogeny, notably, drift and co-circulation of strains. (c) Generalise the EI model to explore strain dynamics of other pathogens: (i) rabies; and (ii) Foot and Mouth Disease.