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

Kate Van Brussel, Jackie E. Mahar, Ayda Susana Ortiz-Baez, Maura Carrai, Derek Spielman, Wayne S.J. Boardman, Michelle L. Baker, Julia A. Beatty, Jemma L. Geoghegan, Vanessa R. Barrs, Edward C. Holmes*

*Corresponding author for this work

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review

14 Citations (Scopus)
40 Downloads (CityUHK Scholars)

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 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.
Original languageEnglish
Pages (from-to)42-51
JournalVirology
Volume576
Online published19 Sept 2022
DOIs
Publication statusPublished - Nov 2022

Research Keywords

  • Coronavirus
  • Faecal
  • Grey-headed flying fox
  • Mammalian
  • Retrovirus
  • Sapovirus

Publisher's Copyright Statement

  • This full text is made available under CC-BY 4.0. https://creativecommons.org/licenses/by/4.0/

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