Anticipating how epidemics will spread across landscapes requires understanding host dispersal events that are notoriously difficult to measure. Here, we contrast host and virus genetic signatures to resolve the spatiotemporal dynamics underlying geographic expansions of vampire bat rabies virus (VBRV) in Peru. Phylogenetic analysis revealed recent viral spread between populations that, according to extreme geographic structure in maternally inherited host mitochondrial DNA, appeared completely isolated. In contrast, greater population connectivity in biparentally inherited nuclear microsatellites explained the historical limits of invasions, suggesting that dispersing male bats spread VBRV between genetically isolated female populations. Host nuclear DNA further indicated unanticipated gene flow through the Andes mountains connecting the VBRV-free Pacific coast to the VBRV-endemic Amazon rainforest. By combining Bayesian phylogeography with landscape resistance models, we projected invasion routes through northern Peru that were validated by real-time livestock rabies mortality data. The first outbreaks of VBRV on the Pacific coast of South America could occur by June 2020, which would have serious implications for agriculture, wildlife conservation, and human health. Our results show that combining host and pathogen genetic data can identify sex biases in pathogen spatial spread, which may be a widespread but underappreciated phenomenon, and demonstrate that genetic forecasting can aid preparedness for impending viral invasions.

Association for the Conservation and Development of Natural Resources Lima 41 Peru;

Association for the Conservation and Development of Natural Resources Lima 41 Peru; National Service of Agrarian Health SENASA Peru Lima 12 Peru

Institute of Biodiversity Animal Health and Comparative Medicine University of Glasgow Glasgow G12 8QQ Scotland; Medical Research Council University of Glasgow Centre for Virus Research Glasgow G61 1QH Scotland; Odum School of Ecology University of Georgia Athens GA 30602;

Instituto Nacional de Salud Ministry of Health of Peru Lima 11 Peru;

Medical Research Council University of Glasgow Centre for Virus Research Glasgow G61 1QH Scotland;

Odum School of Ecology University of Georgia Athens GA 30602;

Odum School of Ecology University of Georgia Athens GA 30602; Institute of Vertebrate Biology Czech Academy of Sciences 603 65 Brno Czech Republic; Department of Evolutionary Ecology Max Planck Institute for Evolutionary Biology 24306 Ploen Germany;

Poxvirus and Rabies Branch Division of High Consequence Pathogen and Pathology Centers for Disease Control and Prevention Atlanta GA 30329;

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