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Metagenomic and Molecular Detection of Novel Fecal Viruses in Free-Ranging Agile Wallabies

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Abstract

The agile wallaby (Notamacropus agilis) is one of the most abundant marsupial species in northern Queensland and a competent host for the zoonotic Ross River virus. Despite their increased proximity and interactions with humans, little is known about the viruses carried by these animals, and whether any are of conservation or zoonotic importance. Metagenomics and molecular techniques were used in a complementary manner to identify and characterize novel viruses in the fecal samples of free-ranging agile wallabies. We detected a variety of novel marsupial-related viral species including agile wallaby atadenovirus 1, agile wallaby chaphamaparvovirus 1–2, agile wallaby polyomavirus 1–2, agile wallaby associated picobirnavirus 1–9, and a known macropod gammaherpesvirus 3. Phylogenetic analyses indicate that most of these novel viruses would have co-evolved with their hosts (agile wallabies). Additionally, non-marsupial viruses that infect bacteria (phages), plants, insects, and other eukaryotes were identified. This study highlighted the utility of non-invasive sampling as well as the integration of broad-based molecular assays (consensus PCR and next generation sequencing) for monitoring the emergence of potential pathogenic viruses in wildlife species. Furthermore, the novel marsupial viruses identified in this study will enrich the diversity of knowledge about marsupial viruses, and may be useful for developing diagnostics and vaccines.

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Data availability

The generated raw sequence reads from this study are available in NCBI SRA database under BioProject number PRJNA907146. The novel marsupial-associated viral sequences are available in GenBank under Accession Numbers OQ030229 to OQ030244 (Supplementary file 2).

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Acknowledgements

The authors would like to acknowledge and thank Dr. Cadhla Firth (James Cook University) and Dr. Ira Cooke (James Cook University) for their expert advice during the conceptualization phase of this research.

Funding

This study was funded by Australian Wildlife Society University Student Grant and JCU Higher Degree Research Enhancement Scheme Grant.

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  1. College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia

    God’spower Richard Okoh, Ellen Ariel, David Whitmore & Paul F. Horwood

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  1. God’spower Richard Okoh
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  2. Ellen Ariel
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Correspondence to God’spower Richard Okoh or Paul F. Horwood.

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Okoh, G.R., Ariel, E., Whitmore, D. et al. Metagenomic and Molecular Detection of Novel Fecal Viruses in Free-Ranging Agile Wallabies. EcoHealth 20, 427–440 (2023). https://doi.org/10.1007/s10393-023-01659-2

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