Collecting epidemiological data on the spatial and temporal dynamics of disease in the field is expensive and difficult. Experiments are difficult to replicate and the underlying dynamics of disease are often hidden by incomplete sampling, local variation of global fluctuations in temperature or other variables.
We therefore use laboratory microcosms experiments to help us to understand the underlying principles that drive epidemics. Microcosms allow fast, highly replicated epidemics under controlled environmental conditions. For example, by using microcosms of radish or other seedlings exposed to known amounts of initial inoculum of Rhizoctonia solani, it is possible to observe and map entire epidemics within 20 d periods.
Epidemiological challenges are:
- to analyse the relative importance of primary infection (driven by resident inoculum) and secondary infection (driven by transmission from infected to susceptible individuals) on the dynamics of epidemics;
- to analyse the effects of demographic stochasticity (chance effects in transmission from infected to susceptible individuals under otherwise identical conditions) from environmental stochasticity (when transmission parameters are influenced by local or global changes in environmental variables);
- to scale from individual to population to metapopulation behaviour.