Bats are known reservoirs of a wide variety of viruses that rarely result in overt clinical disease in the bat host. However, anthropogenic influences on the landscape and climate can change species assemblages and interactions, as well as undermine host-resilience. The cumulative result is a disturbance of bat–pathogen dynamics, which facilitate spillover events to sympatric species, and may threaten bat communities already facing synergistic stressors through ecological change. Therefore, characterisation of viral pathogens in bat communities provides important basal information to monitor and predict the emergence of diseases relevant to conservation and public health. This study used targeted molecular techniques, serological assays and next generation sequencing to characterise adenoviruses, coronaviruses and paramyxoviruses from 11 species of insectivorous bats within the South West Botanical Province of Western Australia. Phylogenetic analysis indicated complex ecological interactions including virus–host associations, cross-species infections, and multiple viral strains circulating concurrently within selected bat populations. Additionally, we describe the entire coding sequences for five alphacoronaviruses (representing four putative new species), and one novel adenovirus. Results indicate that viral burden (both prevalence and richness) is not homogeneous among species, with Chalinolobus gouldii identified as a key epidemiological element within the studied communities.

Australian bat lyssavirus (ABLV) is a known causative agent of neurological disease in bats, humans and horses. It has been isolated from four species of pteropid bats and a single microbat species (Saccolaimus flaviventris). To date, ABLV surveillance has primarily been passive, with active surveillance concentrating on eastern and northern Australian bat populations. As a result, there is scant regional ABLV information for large areas of the country. To better inform the local public health risks associated with human-bat interactions, this study describes the lyssavirus prevalence in microbat communities in the South West Botanical Province of Western Australia. We used targeted real-time PCR assays to detect viral RNA shedding in 839 oral swabs representing 12 species of microbats, which were sampled over two consecutive summers spanning 2016–2018. Additionally, we tested 649 serum samples via Luminex^® assay for reactivity to lyssavirus antigens. Active lyssavirus infection was not detected in any of the samples. Lyssavirus antibodies were detected in 19 individuals across six species, with a crude prevalence of 2.9% (95% CI: 1.8–4.5%) over the two years. In addition, we present the first records of lyssavirus exposure in two Nyctophilus species, and Falsistrellus mackenziei.

Bat species are expected to exhibit low genetic structuring due to their high mobility. Thus, habitat connectivity is important to maintain gene flow and genetic diversity to retain evolutionary potential. The ghost bat (Macroderma gigas) is a large carnivorous bat endemic to Australia. Listed as Vulnerable, the species has a disjunct distribution across northern Australia and is patchily distributed at local scales due to limited roost habitat availability and anthropogenic impacts. Here, we survey the genetic diversity and structure of M. gigas in the isolated, arid Pilbara bioregion in Western Australia, primarily using noninvasively collected fecal DNA samples obtained from roosts. Fecal and tissue samples, representing 399 individuals, were genotyped using an optimized autosomal marker panel, with a subset also being sequenced at the mitochondrial D-loop region to investigate historical gene flow. Spatially explicit Bayesian clustering analyses of autosomal markers revealed low genetic structure and high levels of gene flow amongst the two Pilbara subregions, with some further structuring evident within the Hamersley Ranges. Mitochondrial DNA sequencing showed strong geographic structuring of haplotypes between the subpopulations, with only a small number of shared haplotypes indicating low levels of maternal gene flow. Such patterns across the two marker types are consistent with maternal philopatry and male-mediated gene flow that has previously been described for this species. Conservation actions for the ghost bat in the Pilbara should therefore recognize maintenance of connectivity between roosts and subregions is important to maintain gene flow for this threatened species in the face of anthropogenic threats.