An unprecedented cluster of Australian bat lyssavirus in Pteropus conspicillatus indicates pre-flight flying fox pups are at risk of mass infection

In November 2017, two groups of P. conspicillatus pups from separate locations in Far North Queensland presented with neurological signs consistent with Australian bat lyssavirus (ABLV) infection. These pups (n = 11) died over an 11-day period and were submitted to a government laboratory for testing where ABLV infection was confirmed. Over the next several weeks, additional ABLV cases in flying foxes in Queensland were also detected. Brain tissue from ABLV-infected flying foxes during this period, as well as archived brain tissue, was selected for next-generation sequencing. Phylogenetic analysis suggests that the two groups of pups were each infected from single sources. They were likely exposed while in crèche at night as their dams foraged. This study identifies crèche-age pups at a potentially heightened risk for mass ABLV infection