Evolution and spillover dynamics of yellow fever at the urban-forest interface

Abstract Ten years after the onset of the largest yellow fever epidemic in the Americas, its transmission dynamics in neotropical primate hosts remain unclear. Using ground- and canopy-level entomology, systematic primate carcass surveillance, and metagenomics, we reconstructed a sylvatic YFV outbreak in a 186-ha Atlantic Forest remnant embedded within São Paulo metropolis. We found that, despite evidence of multiple introductions, transmission was dominated by a single genetic cluster that was introduced during the peak of abundance of Haemagogus leucocelaenus mosquitoes. Phylogenetic-informed modelling incorporating vector and host incubation periods and carcass-detection delays yielded a basic reproduction number, R0, of 8.2 (95% CI 5.1–12.2). Untargeted sequencing also uncovered a near-complete hepatitis A virus genome in a co-infected howler monkey (A. guariba), revealing bidirectional pathogen flow across the forest–urban interface. Integrating metagenomics, multi-source surveillance and climate-driven forecasting could provide cost-effective early warnings to guide pre-emptive vaccination and conservation efforts.