Spatio-temporal dynamics of Hendra virus in Pteropus bats in Australia reveals high evolutionary diversity linked with spillover

Hendra virus (HeV) was first discovered in 1994 in Australia, following an outbreak of respiratory and neurological disease in horses and humans. Limited genomic data on HeV has hindered a comprehensive understanding of HeV’s evolutionary dynamics. We conducted extensive spatiotemporal sampling and whole-genome sequencing of HeV-positive samples from bats and horses and genomic analyses revealed four distinct clades and additional cryptic clades. Each clade extended over a large spatial area, with strains from different clades co-occurring within a single roost on the same day and over multiple consecutive years. This absence of spatiotemporal genotypic structuring suggests that viral shedding events are not driven by the introduction of a single lineage into a susceptible population and then strain evolution through population level immune pressure. These findings provide crucial insights into how bats generate and maintain their extraordinary viral diversity, with direct implications for zoonotic disease emergence and pandemic threats.