Inferring epidemiological parameters under an infectious phylogeography model with visitor dynamics

During an outbreak, infectious disease can spread among populations through host movement, potentially fueling local outbreaks with their own epidemiological dynamics. However, it is difficult to know how often infections between populations are transmitted by diseased travelers infecting healthy residents when abroad, rather than by diseased residents infecting healthy travelers, who later return home with the new pathogen. In this paper, we introduce a phylogeographic model where pathogens spread through visitor dynamics, whereby hosts "visit" other populations for short trips before returning home. To do so, we used the stationary properties of an epidemiological compartment model with visitor dynamics to construct an approximation that is statistically accurate and computationally tractable for phylogenetic modeling. We applied our model to empirical infection data and travel statistics from the European SARS-CoV-2 pandemic. Inference under our model suggests that, in the early stages of the outbreak, SARS CoV-2 was more often "pulled" into new countries by returning travelers than "pushed" into new countries by visitors from the source country. Estimates of host movement-related parameter values under our visitor model suggest that competing migration models, with trips of indefinite length, may underestimate the magnitude of outbreaks caused by visitors. This study emphasizes the importance of carefully incorporating host movement dynamics into such models. Significance StatementViral infections can spread among distinct locations by human travel. Being able to identify the source of a local outbreak - whether triggered by infected visitors or individuals returning home - is crucial. Here, we designed a phylogenetic model for modeling infectious disease transmission in spatially structured populations, explicitly accounting for realistic host movement. By accounting for "short trips", our model can help inform travelrelated strategies for containing outbreaks.