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Harding EF, Russo AG, Yan GJH, Waters PD, White PA. Ancient viral integrations in marsupials: a potential antiviral defence. Virus Evol 2021; 7:veab076. [PMID: 34548931 PMCID: PMC8449507 DOI: 10.1093/ve/veab076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 08/05/2021] [Accepted: 08/31/2021] [Indexed: 12/28/2022] Open
Abstract
Marsupial viruses are understudied compared to their eutherian mammal counterparts, although they may pose severe threats to vulnerable marsupial populations. Genomic viral integrations, termed 'endogenous viral elements' (EVEs), could protect the host from infection. It is widely known past viral infections and EVEs play an active role in antiviral defence in invertebrates and plants. This study aimed to characterise actively transcribed EVEs in Australian marsupial species, because they may play an integral role in cellular defence against viruses. This study screened publicly available RNA sequencing data sets (n = 35) and characterised 200 viral transcripts from thirteen Australian marsupial species. Of the 200 transcripts, 188 originated from either Bornaviridae, Filoviridae, or Parvoviridae EVEs. The other twelve transcripts were from putative active infections from members of the Herpesviridae and Anelloviridae, and Hepadnaviridae. EVE transcripts (n = 188) were mapped to marsupial genomes (where available, n = 5/13) to identify the genomic insertion sites. Of the 188 transcripts, 117 mapped to 39 EVEs within the koala, bare-nosed wombat, tammar wallaby, brushtail possum, and Tasmanian devil genomes. The remaining eight animals had no available genome (transcripts n = 71). Every marsupial has Bornaviridae, Filoviridae, and Parvoviridae EVEs, a trend widely observed in eutherian mammals. Whilst eutherian bornavirus EVEs are predominantly nucleoprotein-derived, marsupial bornavirus EVEs demonstrate a surprising replicase gene bias. We predicted these widely distributed EVEs were conserved within marsupials from ancient germline integrations, as many were over 65 million years old. One bornavirus replicase EVE, present in six marsupial genomes, was estimated to be 160 million years old, predating the American-Australian marsupial split. We considered transcription of these EVEs through small non-coding RNA as an ancient viral defence. Consistent with this, in koala small RNA sequence data sets, we detected Bornaviridae replicase and Filoviridae nucleoprotein produced small RNA. These were enriched in testis tissue, suggesting they could protect marsupials from vertically transmitted viral integrations.
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Affiliation(s)
| | - Alice G Russo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Grace J H Yan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Paul D Waters
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, UNSW Sydney, Sydney, NSW 2052, Australia
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Porter AF, Pettersson JHO, Chang WS, Harvey E, Rose K, Shi M, Eden JS, Buchmann J, Moritz C, Holmes EC. Novel hepaci- and pegi-like viruses in native Australian wildlife and non-human primates. Virus Evol 2020; 6:veaa064. [PMID: 33240526 PMCID: PMC7673076 DOI: 10.1093/ve/veaa064] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Flaviviridae family of positive-sense RNA viruses contains important pathogens of humans and other animals, including Zika virus, dengue virus, and hepatitis C virus. The Flaviviridae are currently divided into four genera-Hepacivirus, Pegivirus, Pestivirus, and Flavivirus-each with a diverse host range. Members of the genus Hepacivirus are associated with an array of animal species, including humans, non-human primates, other mammalian species, as well as birds and fish, while the closely related pegiviruses have been identified in a variety of mammalian taxa, also including humans. Using a combination of total RNA and whole-genome sequencing we identified four novel hepaci-like viruses and one novel variant of a known hepacivirus in five species of Australian wildlife. The hosts infected comprised native Australian marsupials and birds, as well as a native gecko (Gehyra lauta). From these data we identified a distinct marsupial clade of hepaci-like viruses that also included an engorged Ixodes holocyclus tick collected while feeding on Australian long-nosed bandicoots (Perameles nasuta). Distinct lineages of hepaci-like viruses associated with geckos and birds were also identified. By mining the SRA database we similarly identified three new hepaci-like viruses from avian and primate hosts, as well as two novel pegi-like viruses associated with primates. The phylogenetic history of the hepaci- and pegi-like viruses as a whole, combined with co-phylogenetic analysis, provided support for virus-host co-divergence over the course of vertebrate evolution, although with frequent cross-species virus transmission. Overall, our work highlights the diversity of the Hepacivirus and Pegivirus genera as well as the uncertain phylogenetic distinction between.
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Affiliation(s)
- Ashleigh F Porter
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - John H-O Pettersson
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Wei-Shan Chang
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Erin Harvey
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Karrie Rose
- Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman 2088, Australia
| | - Mang Shi
- School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - John-Sebastian Eden
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Jan Buchmann
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
| | - Craig Moritz
- Research School of Biology, Centre for Biodiversity Analysis, Australian National University, Acton, ACT, Australia
| | - Edward C Holmes
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney 2006, Australia
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Etebari K, Shelomi M, Furlong MJ. Identification of a Novel Picorna-like Virus in Coconut Rhinoceros Beetles (Oryctes rhinoceros). Virus Res 2020; 287:198100. [PMID: 32739236 DOI: 10.1016/j.virusres.2020.198100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022]
Abstract
A novel Picorna-like virus, tentatively named Oryctes rhinoceros Picorna-like virus 1 (OrPV1), was identified in coconut rhinoceros beetle (Oryctes rhinoceros) larvae in Taiwan. The complete genome sequence consisted of 9,665 nucleotides with a polyA tail and included one open reading frame. Conserved structural domains such as Picornavirus capsid protein, RNA helicase, Peptidase and RNA-dependent RNA polymerase (RdRp) were identified through Pfam domain searches. The genome shares approximately 27-28% identity with other unclassified Picornavirales that infect honey bees (Darwin bee virus 2, Bundaberg bee virus 5, and Sacbrood virus) and a recently reported virus from Asian lady beetle (Harmonia axyridis virus 1). We did not detect this virus in any other geographical populations of O. rhinoceros collected from the South Pacific Islands and the Philippines. Analysis of the deduced RdRp amino acid sequences showed that the virus clustered with other Picorna-like viruses and separated from other members of family Dicistroviridae and Iflaviridae.
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Affiliation(s)
- Kayvan Etebari
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia.
| | - Matan Shelomi
- Department of Entomology, National Taiwan University, No 27 Lane 113 Sec 4 Roosevelt Rd, Taipei 10617, Taiwan.
| | - Michael J Furlong
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia.
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