Search

Bats are important reservoirs for viruses of public health and veterinary concern. Virus studies in Australian bats usually target the families Paramyxoviridae , Coronaviridae and Rhabdoviridae , with little known about their overall virome composition. We used metatranscriptomic sequencing to characterise the faecal virome of grey-headed flying foxes from three colonies in urban/suburban locations from two Australian states. We identified viruses from three mammalian-infecting (Coronaviridae, Caliciviridae, Retroviridae) and one possible mammalian-infecting (Birnaviridae) family. Of particular interest were a novel bat betacoronavirus (subgenus Nobecovirus) and a novel bat sapovirus (Caliciviridae), the first identified in Australian bats, as well as a potentially exogenous retrovirus. The novel betacoronavirus was detected in two sampling locations 1375 km apart and falls in a viral lineage likely with a long association with bats. This study highlights the utility of unbiased sequencing of faecal samples for identifying novel viruses and revealing broad-scale patterns of virus ecology and evolution. • First large-scale virome study of grey-headed flying foxes in Australia • Identification of novel coronaviruses, retroviruses and sapoviruses • Coronaviruses of the subgenus Nobecovirus have a long-term association with bats • Identification of likely exogenous retroviruses (genus Betaretrovirus) in bats [ABSTRACT FROM AUTHOR]

Japanese encephalitis virus (JEV) continues to cause significant numbers of human infections and fatalities despite the availability of efficacious vaccines. It is regarded as an emerging mosquito-borne pathogen with the potential of introduction into many countries. In 2022, JEV was detected in Australia on a hitherto unprecedented scale, with local transmission by indigenous mosquitoes to amplifying swine hosts and to humans. In this study, we review this recent disease activity, propose possible routes of virus movement, ecological drivers of activity, and consider possible future transmission scenarios. Measures to enhance current surveillance systems and potential strategies for health authorities to minimize future risks are discussed. [ABSTRACT FROM AUTHOR]

Despite the ongoing interest in virus discovery, little is known about the factors that shape communities of viruses within individual hosts. Here, we address how virus communities might be impacted by the age of the hosts they infect, using total RNA sequencing to reveal the RNA viromes of different age groups of Ruddy Turnstones (Arenaria interpres). From oropharyngeal and cloacal swabs we identified 14 viruses likely infecting birds, 11 of which were novel, including members of the Reoviridae , Astroviridae , and Picornaviridae. Strikingly, 12 viruses identified were from juvenile birds sampled in the first year of their life, compared to only two viruses in adult birds. Both viral abundance and alpha diversity were marginally higher in juvenile than adult birds. As well as informing studies of virus ecology, that host age might be associated with viral composition is an important consideration for the future surveillance of novel and emerging viruses. • Virus diversity and community structure in wild birds is largely unknown. • We reveal 14 viral species in Ruddy Turnstones sampled in Australia. • Virus abundance and diversity is higher in juvenile birds compared to adults. • Virus communities differ across time, suggesting the RNA virome is transient. [ABSTRACT FROM AUTHOR]

Summary: Cylindrospermopsis (Raphidiopsis) raciborskii is an invasive, filamentous, nitrogen‐fixing cyanobacterium that forms frequent blooms in freshwater habitats. While viruses play key roles in regulating the abundance, production and diversity of their hosts in aquatic ecosystems, the role(s) of viruses in the ecology of C. raciborskii is almost unexplored. Progress in this field has been hindered by the absence of a characterized virus–host system in C. raciborskii. To bridge this gap, we sequenced the genome of CrV‐01T, a previously isolated cyanosiphovirus, and its host, C. raciborskii strain Cr2010. Analyses suggest that CrV‐01T represents a distinct clade of siphoviruses infecting, and perhaps lysogenizing, filamentous cyanobacteria. Its genome contains unique features that include an intact CRISPR array and a 12 kb inverted duplication. Evidence suggests CrV‐01T recently gained the ability to infect Cr2010 and recently lost the ability to form lysogens. The cyanobacterial host contains a CRISPR‐Cas system with CRISPR spacers matching protospacers within the inverted duplication of the CrV‐01T genome. Examination of metagenomes demonstrates that viruses with high genetic identity to CrV‐01T, but lacking the inverted duplication, are present in C. raciborskii blooms in Australia. The unique genomic features of the CrV/Cr2010 system offers opportunities to investigate in more detail virus–host interactions in an ecologically important bloom‐forming cyanobacterium. [ABSTRACT FROM AUTHOR]

Alterations in transmission of vector-borne zoonoses are often linked to environmental change. However, ecological processes that determine variability in potential for transmission are generally not well understood. Ross River virus (RRV, Togoviridae: Alphavirus) is a mosquito-borne zoonosis in Australia with a significant human disease burden. The inland southwest (Wheatbelt) of Western Australia (WA) is substantially affected by an anthropogenic salinization of agricultural land (dryland salinity). Aedes camptorhynchusThomson (Diptera: Culicidae) is the dominant vector of RRV in southwest WA and is halophilic. As such, dryland salinity may influence potential for RRV transmission by influencing interactions between Ae. camptorhynchusand mammalian hosts. We surveyed areas of the Wheatbelt with varying salinity impacts and found Ae. camptorhynchuswas more abundant in saline areas, whereas sheep Ovis aries(Linnaeus 1758, Bovidae) declined with increasing salinity. We used a deterministic model to examine interactions between Ae. camptorhynchusand mammals, and we assessed potential for RRV transmission. We found variation in potential for RRV transmission was positively related to increasing salinity and abundance of Ae. camptorhynchusand negatively associated with increasing abundance of Macropus fuliginosus(Desmarest 1817, Macropodidae). Abundance of Ae. camptorhynchusdetermined more variation in potential for RRV transmission than other variables. Accordingly, dryland salinity increases the zoonotic potential for RRV transmission primarily by facilitating abundance of Ae. camptorhynchus. Human RRV notifications do not currently reflect the salinity-RRV transmission potential in the Wheatbelt but appear to be associated with RRV activity in the enzootic coastal zone. We speculate dryland salinity is a determinant of potential for RRV transmission but not activity. Dryland salinity is predicted to expand two- to four-fold by 2050. Preservation and restoration of freshwater ecosystems may ameliorate the potential for transmission of RRV and possibly incidence of human disease. [ABSTRACT FROM AUTHOR]

Conservation efforts for the orange-bellied parrot (Neophema chrysogaster), one of the world's most critically endangered bird species, have been hampered by beak and feather disease virus (BFDV) spillover infection. To understand the vulnerability of orange-bellied parrots to potential reservoirs of infection we investigated geographic versus taxonomic structure in 160 full-genome and 319 partial Rep gene BFDV sequences from captive and wild orange-bellied parrots and other wild parrot species in Australia. We found that Australian BFDV populations are structured by host taxonomy. By identifying genetic stratification of BFDV in reservoir hosts we characterized three separate recent incursions of BFDV into orange-bellied parrots from other wild parrots, which demonstrates the susceptibility of critically endangered species to multiple threats of pathogen re-emergence. Our study highlighted how loss of endemic circulating BFDV in orange-bellied parrots precipitated repeated spillover into an immunologically naïve population, causing significant disease., (© Wildlife Disease Association 2020.)