Faecal virome of the Australian grey-headed flying fox from urban/suburban environments contains novel coronaviruses, retroviruses and sapoviruses

Abstract

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 1,375 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.

Gammaretroviruses, novel viruses and pathogenic bacteria in Australian bats with neurological signs, pneumonia and skin lesions

“…CC-BY 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted October 21, 2022. ; https://doi.org/10.1101/2022.10.20.513122 doi: bioRxiv preprint associated with the diet (26). Notably, no mammalian viruses belonging to the Flaviviridae, as well as only one short contig matching to Astroviridae and two short contigs matching to Picornaviridae, where identified in marked contrast to the results presented here (26).…”

“…Although characterising the faecal virome of bats is important for identifying novel and potentially zoonotic viruses, especially from urban bat populations, the identification of dietary invertebrate and plant viruses is common, such that viromes may differ between faecal and tissue samples (23)(24)(25). Our previous study of the faecal virome of the grey-headed flying fox identified bat viruses belonging to the Coronaviridae and Caliciviridae, as well as a myriad of insect and plant viruses likely associated with the diet (26). Notably, no mammalian viruses belonging to the Flaviviridae, as well as only one short contig matching to Astroviridae and two short contigs matching to Picornaviridae, where identified in marked contrast to the results presented here (26).…”

“…Our previous study of the faecal virome of the grey-headed flying fox identified bat viruses belonging to the Coronaviridae and Caliciviridae , as well as a myriad of insect and plant viruses likely associated with the diet (26). Notably, no mammalian viruses belonging to the Flaviviridae , as well as only one short contig matching to Astroviridae and two short contigs matching to Picornaviridae , where identified in marked contrast to the results presented here (26).…”