One main challenge is to build reliable disease transmission models that are well-suited to address the research questions at hand.
Infectious disease modeling is interdisciplinary in nature, and we collaborate with medical doctors, sociologists, mathematicians and economists. The confidence in epidemic models is based on comparison of model predictions with epidemic data, but lack of reliable data often makes parameter estimation difficult.
Besides, to make quantitative predictions, models need to incorporate assumptions about age-specific transmission patterns in the population. Social contact patterns and their relation to spread of particular infections is currently an active research area.