Nine challenges in modelling the emergence of novel pathogens

• We summarize key challenges in modeling the emergence of novel infectious agents.
• We focus on connections to data, including epidemiologic and genetic data.
• Zoonoses are emphasized, because they are the source of most new human pathogens.
• Challenges span reservoir dynamics, cross-species spillover, and outbreak dynamics.
• Estimation of fatality rates and overall risk assessment are also addressed.

Studying the emergence of novel infectious agents involves many processes spanning host species, spatial scales, and scientific disciplines. Mathematical models play an essential role in combining insights from these investigations and drawing robust inferences from field and experimental data. We describe nine challenges in modelling the emergence of novel pathogens, emphasizing the interface between models and data.