We analyze livestock production data from the index farm and model within-farm infection dynamics. Results suggest that repeated introduction of the virus from the wildlife reservoir into an intensively managed commercial pig population led to changes in infection dynamics in the pigs. Initial viral introduction produced a partially immune population and led to an “enhanced” epidemic upon reintroduction of the virus. Long-term within-farm persistence permitted regional spread of the virus, ultimately producing widespread human infection.

Data from the outbreaks indicate that areas at risk for bat-to-pig transmission may differ from areas at high risk for pig-to-human transmission, demonstrating that prevention strategies need to take into account the spatial heterogeneity of and interaction between flying fox ecology and domestic pig farming practices. Our analyses suggest that, within Malaysia, Perak and Johor are at highest risk of Nipah virus spillover from flying foxes and of maintaining endemic infection; however, Pulau Pinang is expected to have the most cases if the virus is allowed to spread from site of spillover.