Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids).

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37941997", "kind": "science-record", "revision": 3, "content_hash": "sha256:c6c4a9381e752a259164251bd1c0437b10d6a3b43b7e0e3b9727d88cfed13eb3", "created_at": "2026-11-01T19:02:50Z", "updated_at": "2026-11-01T21:31:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids).", "doi": "10.1093/ve/vead061", "pmid": "37941997", "authors": ["Erin Harvey", "Jonathon C O Mifsud", "Edward C Holmes", "Jackie E Mahar"], "journal": "Virus evolution", "year": 2023, "abstract": "Although Australian marsupials are characterised by unique biology and geographic isolation, little is known about the viruses present in these iconic wildlife species. The Dasyuromorphia are an order of marsupial carnivores found only in Australia that include both the extinct Tasmanian tiger (thylacine) and the highly threatened Tasmanian devil. Several other members of the order are similarly under threat of extinction due to habitat loss, hunting, disease, and competition and predation by introduced species such as feral cats. We utilised publicly available RNA-seq data from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database to document the viral diversity within four Dasyuromorph species. Accordingly, we identified fifteen novel virus sequences from five DNA virus families (Adenoviridae, Anelloviridae, Gammaherpesvirinae, Papillomaviridae, and Polyomaviridae) and three RNA virus taxa: the order Jingchuvirales, the genus Hepacivirus, and the delta-like virus group. Of particular note was the identification of a marsupial-specific clade of delta-like viruses that may indicate an association of deltaviruses with marsupial species. In addition, we identified a highly divergent hepacivirus in a numbat liver transcriptome that falls outside of the larger mammalian clade. We also detect what may be the first Jingchuvirales virus in a mammalian host-a chu-like virus in Tasmanian devils-thereby expanding the host range beyond invertebrates and ectothermic vertebrates. As many of these Dasyuromorphia species are currently being used in translocation efforts to reseed populations across Australia, understanding their virome is of key importance to prevent the spread of viruses to naive populations.", "claims": [{"id": "claim-method", "statement": "Phylogenetic trees were estimated using IQ-TREE 2 (v2.2.2) (Minh et al. 2020) with the appropriate substitution model selected using ModelFinder (Kalyaanamoorthy et al. 2017). Branch support was assessed with 1,000 bootstrap replicates using ultrafast bootstrapping (Hoang et al. 2017).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37941997", "locator": "sections[5] \"Phylogenetic analysis\" paragraph 2", "quote": "Phylogenetic trees were estimated using IQ-TREE 2 (v2.2.2) (Minh et al. 2020) with the appropriate substitution model selected using ModelFinder (Kalyaanamoorthy et al. 2017). Branch support was assessed with 1,000 bootstrap replicates using ultrafast bootstrapping (Hoang et al. 2017)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All viral genomes and corresponding sequences assembled in this study and the alignments generated in this study for phylogenetic analysis are available at https://github.com/erinhunter4/dasyurid_virome. The SRA virus discovery pipeline is available at https://github.com/JonathonMifsud/BatchArtemisSRAMiner.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37941997", "locator": "sections[17] \"Data availability\" paragraph 2", "quote": "All viral genomes and corresponding sequences assembled in this study and the alignments generated in this study for phylogenetic analysis are available at https://github.com/erinhunter4/dasyurid_virome. The SRA virus discovery pipeline is available at https://github.com/JonathonMifsud/BatchArtemisSRAMiner."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified fifteen novel virus sequences from five DNA virus families and three RNA virus taxa in publicly available Dasyuromorphia transcriptomes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37941997", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Accordingly, we identified fifteen novel virus sequences from five DNA virus families (Adenoviridae, Anelloviridae, Gammaherpesvirinae, Papillomaviridae, and Polyomaviridae) and three RNA virus taxa: the order Jingchuvirales, the genus Hepacivirus, and the delta-like virus group."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study identified fifteen novel virus sequences from five DNA virus families and three RNA virus taxa in publicly available Dasyuromorphia transcriptomes.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:37941997"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_unresolved", "description": "The GEO series accession resolves and its sample accessions are listed. 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