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Article

Novel Picornavirus Detected in Wild Deer: Identification, Genomic Characterisation, and Prevalence in Australia

1
Department of Physiology, Anatomy, and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC 3086, Australia
2
Department of Environment, Land, Water, and Planning, Arthur Rylah Institute for Environmental Research, Heidelberg, VIC 3084, Australia
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Environmental and Conservation Sciences, School of Veterinary and Life Sciences, Murdoch University, South Street, Murdoch, WA 6150, Australia
4
South East Local Land Services, Bega, NSW 2550, Australia
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Vertebrate Pest Research Unit, Department of Primary Industries, Orange Agricultural Institute, Orange, NSW 2800, Australia
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Department of Agriculture and Fisheries, Invasive Plants & Animals Research, Biosecurity Queensland, Ecosciences Precinct, Brisbane, QLD 4102, Australia
*
Author to whom correspondence should be addressed.
Academic Editor: Regina Hofmann-Lehmann
Viruses 2021, 13(12), 2412; https://doi.org/10.3390/v13122412
Received: 4 November 2021 / Revised: 24 November 2021 / Accepted: 30 November 2021 / Published: 2 December 2021
(This article belongs to the Section Animal Viruses)
The use of high-throughput sequencing has facilitated virus discovery in wild animals and helped determine their potential threat to humans and other animals. We report the complete genome sequence of a novel picornavirus identified by next-generation sequencing in faeces from Australian fallow deer. Genomic analysis revealed that this virus possesses a typical picornavirus-like genomic organisation of 7554 nt with a single open reading frame (ORF) encoding a polyprotein of 2225 amino acids. Based on the amino acid identity comparison and phylogenetic analysis of the P1, 2C, 3CD, and VP1 regions, this novel picornavirus was closely related to but distinct from known bopiviruses detected to date. This finding suggests that deer/bopivirus could belong to a novel species within the genus Bopivirus, tentatively designated as “Bopivirus C”. Epidemiological investigation of 91 deer (71 fallow, 14 sambar and 6 red deer) and 23 cattle faecal samples showed that six fallow deer and one red deer (overall prevalence 7.7%, 95% confidence interval [CI] 3.8–15.0%) tested positive, but deer/bopivirus was undetectable in sambar deer and cattle. In addition, phylogenetic and sequence analyses indicate that the same genotype is circulating in south-eastern Australia. To our knowledge, this study reports for the first time a deer-origin bopivirus and the presence of a member of genus Bopivirus in Australia. Further epidemiological and molecular studies are needed to investigate the geographic distribution and pathogenic potential of this novel Bopivirus species in other domestic and wild animal species. View Full-Text
Keywords: Bopivirus; complete genome; viral metagenomics; viral isolation; phylogenetics; deer Bopivirus; complete genome; viral metagenomics; viral isolation; phylogenetics; deer
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MDPI and ACS Style

Huaman, J.L.; Pacioni, C.; Sarker, S.; Doyle, M.; Forsyth, D.M.; Pople, A.; Carvalho, T.G.; Helbig, K.J. Novel Picornavirus Detected in Wild Deer: Identification, Genomic Characterisation, and Prevalence in Australia. Viruses 2021, 13, 2412. https://doi.org/10.3390/v13122412

AMA Style

Huaman JL, Pacioni C, Sarker S, Doyle M, Forsyth DM, Pople A, Carvalho TG, Helbig KJ. Novel Picornavirus Detected in Wild Deer: Identification, Genomic Characterisation, and Prevalence in Australia. Viruses. 2021; 13(12):2412. https://doi.org/10.3390/v13122412

Chicago/Turabian Style

Huaman, Jose L., Carlo Pacioni, Subir Sarker, Mark Doyle, David M. Forsyth, Anthony Pople, Teresa G. Carvalho, and Karla J. Helbig. 2021. "Novel Picornavirus Detected in Wild Deer: Identification, Genomic Characterisation, and Prevalence in Australia" Viruses 13, no. 12: 2412. https://doi.org/10.3390/v13122412

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