AVA Conference Brisbane 2018

A number of transmission network models have recently been published that combine genomic and epidemiological data to model who infected whom in outbreaks. This research evaluates these models for their usefulness in reliably informing decision-making in future foot-and-mouth disease (FMD) outbreaks on the basis that they must be capable of producing accurate robust predictions within short timeframes based on the sparse data available early in such outbreaks. First, a formal comparison was made of the performance of several published transmission network models based on a set of simulated FMD outbreaks seeded in Victoria with the Australian Animal Disease (AADIS) hybrid model together with phylogenomic simulators. Then, the best-performing of the evaluated models were implemented on real data from the 2010 outbreak of FMD in Miyazaki Prefecture in Japan. The findings from this study point to which models might reliably be used to reconstruct future FMD outbreaks and how to interpret the outputs to inform control. Further ongoing research involves extending the models to explicitly represent a more complete range of farm-type variables and within-animal diversity so they can handle next generation sequencing data.