Task 1b: Contribution of between-host variability in shedding to pathogen spread in a herd: application to Coxiella burnetii (Cb) and Mycobacterium avium subsp. paratuberculosis (Map) in cattle

First, we will study in a theoretical framework how predictions of epidemiological models change with the definition of host infection statuses. We will compare two assumptions: (1) host infectiousness varies within a host over the infection period and among infected hosts; (2) host infectiousness is constant for a given host for the entire infection duration, but varies among hosts in a discrete way (i.e. by distinguishing several classes of animals), assuming the existence of super-shedders.

We then will describe the shedding patterns of infected hosts for two entities for which observed data are currently available: Cb and Map. We will identify if a continuous level of shedding can be observed for an animal over time in order to choose between the two previously studied assumptions.

More generally, the individual and genetic variability among hosts will be investigated to complement the two forms of between-host heterogeneity based on age and risk-structure that are studied most widely in the literature. We will study the impact of individual-level heterogeneity by allowing the susceptibility, infectiousness and infection duration to be specific for each individual. We therefore will study how the integration of such individual characteristics will modify the predicted epidemic patterns and how these patterns differ from conventional model predictions.