{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T00:44:42Z","timestamp":1759970682661,"version":"build-2065373602"},"reference-count":60,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2025,1,26]],"date-time":"2025-01-26T00:00:00Z","timestamp":1737849600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The platypus (Ornithorhynchus anatinus), a unique monotreme, represents a pivotal point in mammalian evolution with its distinctive traits, such as electroreception and venom production. Despite its evolutionary significance, the viral diversity within platypuses remains poorly understood. This study employed next-generation sequencing to investigate the virome of the dead platypuses, uncovering a range of novel and divergent viruses. Among the identified viruses were four complete genomes of papillomaviruses (OaPV1\u20134) exhibiting substantial divergence from known strains, suggesting a novel genus within the subfamily Secondpapillomavirinae. Additionally, five novel parvoviruses were detected, including two with complete genomes, highlighting the complex viral ecosystem of the platypus. Phylogenetic analysis placed these viruses in unique evolutionary branches, further demonstrating the platypus\u2019s evolutionary significance. A circular DNA virus, a tombus-like virus, and a nodamuvirus were also identified, expanding the understanding of viral diversity in monotremes. These findings offer crucial insights into viral evolution in one of the most unique mammalian lineages, emphasising the need for further exploration to assess ecological and pathological impacts on platypus populations.<\/jats:p>","DOI":"10.3390\/v17020176","type":"journal-article","created":{"date-parts":[[2025,1,27]],"date-time":"2025-01-27T04:59:10Z","timestamp":1737953950000},"page":"176","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["The Spleen Virome of Australia\u2019s Endemic Platypus Is Dominated by Highly Diverse Papillomaviruses"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2685-8377","authenticated-orcid":false,"given":"Subir","family":"Sarker","sequence":"first","affiliation":[{"name":"Biomedical Sciences & Molecular Biology, College of Medicine and Dentistry, James Cook University, Townsville, QLD 4811, Australia"},{"name":"Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia"},{"name":"Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Saranika","family":"Talukder","sequence":"additional","affiliation":[{"name":"College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ajani","family":"Athukorala","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pam L.","family":"Whiteley","sequence":"additional","affiliation":[{"name":"Melbourne Veterinary School, The University of Melbourne, Werribee, VIC 3030, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,1,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1038\/nature06936","article-title":"Genome analysis of the platypus reveals unique signatures of evolution","volume":"453","author":"Warren","year":"2008","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/jmammal\/gyz058","article-title":"The platypus: Evolutionary history, biology, and an uncertain future","volume":"100","author":"Bino","year":"2019","journal-title":"J. Mammal."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"756","DOI":"10.1038\/s41586-020-03039-0","article-title":"Platypus and echidna genomes reveal mammalian biology and evolution","volume":"592","author":"Zhou","year":"2021","journal-title":"Nature"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2603","DOI":"10.1038\/s41396-019-0458-0","article-title":"Virome heterogeneity and connectivity in waterfowl and shorebird communities","volume":"13","author":"Wille","year":"2019","journal-title":"ISME J."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/j.vetmic.2019.07.012","article-title":"Disease surveillance in wild Victorian cacatuids reveals co-infection with multiple agents and detection of novel avian viruses","volume":"235","author":"Sutherland","year":"2019","journal-title":"Vet. Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"5263","DOI":"10.1111\/mec.14918","article-title":"Virus-virus interactions and host ecology are associated with RNA virome structure in wild birds","volume":"27","author":"Wille","year":"2018","journal-title":"Mol. Ecol."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Vibin, J., Chamings, A., Klaassen, M., Bhatta, T.R., and Alexandersen, S. (2020). Metagenomic characterisation of avian parvoviruses and picornaviruses from Australian wild ducks. Sci. Rep., 10.","DOI":"10.1038\/s41598-020-69557-z"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Vibin, J., Chamings, A., Collier, F., Klaassen, M., Nelson, T.M., and Alexandersen, S. (2018). Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds. Sci. Rep., 8.","DOI":"10.1038\/s41598-018-26851-1"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/nature20167","article-title":"Redefining the invertebrate RNA virosphere","volume":"540","author":"Shi","year":"2016","journal-title":"Nature"},{"key":"ref_10","first-page":"001101","article-title":"A discovery down under: Decoding the draft genome sequence of Pantoea stewartii from Australia\u2019s critically endangered western ground parrot\/kyloring (Pezoporus flaviventris)","volume":"9","author":"White","year":"2023","journal-title":"Microb. Genom."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"White, R.T., Jelocnik, M., Klukowski, N., Haque, M.H., and Sarker, S. (2023). The first genomic insight into Chlamydia psittaci sequence type (ST)24 from a healthy captive psittacine host in Australia demonstrates evolutionary proximity with strains from psittacine, human, and equine hosts. Vet. Microbiol., 280.","DOI":"10.1016\/j.vetmic.2023.109704"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e03052-23","DOI":"10.1128\/spectrum.03052-23","article-title":"Virome of Australia\u2019s most endangered parrot in captivity evidenced of harboring hitherto unknown viruses","volume":"12","author":"Klukowski","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Sarker, S., Talukder, S., Anwar, A., Van, T.T., and Petrovski, S. (2022). Unravelling Bile Viromes of free-range laying chickens clinically diagnosed with spotty liver disease: Emergence of many novel chaphamaparvoviruses into multiple lineages. Viruses, 14.","DOI":"10.21203\/rs.3.rs-1675136\/v1"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Sarker, S. (2021). Molecular and phylogenetic characterisation of a highly divergent novel parvovirus (psittaciform chaphamaparvovirus 2) in australian neophema parrots. Pathogens, 10.","DOI":"10.3390\/pathogens10121559"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Sarker, S. (2021). Metagenomic detection and characterisation of multiple viruses in apparently healthy Australian Neophema birds. Sci. Rep., 11.","DOI":"10.1038\/s41598-021-00440-1"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Geoghegan, J.L., Duch\u00eane, S., and Holmes, E.C. (2017). Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families. PLoS Pathog., 13.","DOI":"10.1371\/journal.ppat.1006215"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2500","DOI":"10.1128\/JVI.01946-08","article-title":"Discovery of a novel single-stranded DNA virus from a sea turtle fibropapilloma by using viral metagenomics","volume":"83","author":"Ng","year":"2009","journal-title":"J. Virol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"e51971","DOI":"10.7554\/eLife.51971","article-title":"Discovery of several thousand highly diverse circular DNA viruses","volume":"9","author":"Tisza","year":"2020","journal-title":"Elife"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"2488","DOI":"10.1038\/s41467-023-38202-4","article-title":"Virus diversity, wildlife-domestic animal circulation and potential zoonotic viruses of small mammals, pangolins and zoo animals","volume":"14","author":"Cui","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Frias-De-Diego, A., Jara, M., and Escobar, L.E. (2019). Papillomavirus in Wildlife. Front. Ecol. Evol., 7.","DOI":"10.3389\/fevo.2019.00406"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/j.virol.2013.05.007","article-title":"Animal papillomaviruses","volume":"445","author":"Rector","year":"2013","journal-title":"Virology"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1038\/s44298-024-00020-w","article-title":"A novel papillomavirus in a New Zealand fur seal (Arctocephalus forsteri) with oral lesions","volume":"2","author":"Mifsud","year":"2024","journal-title":"Npj Viruses"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/S0001-706X(00)00179-0","article-title":"Anthropogenic environmental change and the emergence of infectious diseases in wildlife","volume":"78","author":"Daszak","year":"2001","journal-title":"Acta Trop."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.virusres.2017.10.016","article-title":"Meta-transcriptomics and the evolutionary biology of RNA viruses","volume":"243","author":"Shi","year":"2018","journal-title":"Virus Res."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Athukorala, A., Phalen, D.N., Das, A., Helbig, K.J., Forwood, J.K., and Sarker, S. (2021). Genomic characterisation of a highly divergent siadenovirus (psittacine siadenovirus f) from the critically endangered orange-bellied parrot (Neophema chrysogaster). Viruses, 13.","DOI":"10.3390\/v13091714"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Sarker, S., Das, S., Lavers, J.L., Hutton, I., Helbig, K., Imbery, J., Upton, C., and Raidal, S.R. (2017). Genomic characterization of two novel pathogenic avipoxviruses isolated from pacific shearwaters (Ardenna spp.). BMC Genom., 18.","DOI":"10.1186\/s12864-017-3680-z"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Sarker, S., Isberg, R.S., Moran, L.J., Araujo, D.R., Elliott, N., Melville, L., Beddoe, T., and Helbig, J.K. (2019). Crocodilepox Virus evolutionary genomics supports observed poxvirus infection dynamics on saltwater crocodile (Crocodylus porosus). Viruses, 11.","DOI":"10.3390\/v11121116"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol. J. Comput. Mol. Cell Biol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"D36","DOI":"10.1093\/nar\/gks1195","article-title":"GenBank","volume":"41","author":"Benson","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/2042-5783-1-2","article-title":"Base-By-Base version 2: Single nucleotide-level analysis of whole viral genome alignments","volume":"1","author":"Hillary","year":"2011","journal-title":"Microb. Inform. Exp."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1099\/jgv.0.001072","article-title":"ICTV Virus Taxonomy Profile: Papillomaviridae","volume":"99","author":"Chen","year":"2018","journal-title":"J. Gen. Virol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1099\/jgv.0.001212","article-title":"ICTV Virus Taxonomy Profile: Parvoviridae","volume":"100","author":"Cotmore","year":"2019","journal-title":"J. Gen. Virol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1016\/j.meegid.2016.02.011","article-title":"Diverse circular replication-associated protein encoding viruses circulating in invertebrates within a lake ecosystem","volume":"39","author":"Dayaram","year":"2016","journal-title":"Infect. Genet. Evol."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Remnant, E.J., Baty, J.W., Bulgarella, M., Dobelmann, J., Quinn, O., Gruber, M.A.M., and Lester, P.J. (2021). A diverse viral community from predatory wasps in their native and invaded range, with a new virus infectious to honey bees. Viruses, 13.","DOI":"10.3390\/v13081431"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1352","DOI":"10.1099\/vir.0.064436-0","article-title":"A novel papillomavirus in Ad\u00e9lie penguin (Pygoscelis adeliae) faeces sampled at the Cape Crozier colony, Antarctica","volume":"95","author":"Varsani","year":"2014","journal-title":"J. Gen. Virol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/S0165-2427(99)00165-8","article-title":"The immunology of animal papillomaviruses","volume":"73","author":"Nicholls","year":"2000","journal-title":"Vet. Immunol. Immunopathol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1046\/j.1476-5829.2003.00001.x","article-title":"Papillomavirus and disease in humans and animals","volume":"1","author":"Campo","year":"2003","journal-title":"Vet. Comp. Oncol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/j.virol.2013.06.007","article-title":"Diseases associated with human papillomavirus infection","volume":"445","author":"Cubie","year":"2013","journal-title":"Virology"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Canuti, M., Munro, H.J., Robertson, G.J., Kroyer, A.N.K., Roul, S., Ojkic, D., Whitney, H.G., and Lang, A.S. (2019). New insight into avian papillomavirus ecology and evolution from characterization of novel wild bird papillomaviruses. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.00701"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1007\/s00705-024-06006-6","article-title":"New duck papillomavirus type identified in a mallard in Missouri, USA","volume":"169","author":"Olivo","year":"2024","journal-title":"Arch. Virol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.virol.2013.05.012","article-title":"Evolution of the Papillomaviridae","volume":"445","year":"2013","journal-title":"Virology"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.virol.2004.03.033","article-title":"Classification of papillomaviruses","volume":"324","author":"Fauquet","year":"2004","journal-title":"Virology"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"3195","DOI":"10.1099\/vir.0.82195-0","article-title":"Papillomavirus in healthy skin of Australian animals","volume":"87","author":"Antonsson","year":"2006","journal-title":"J. Gen. Virol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1362","DOI":"10.1099\/vir.0.041483-0","article-title":"Evidence for an endogenous papillomavirus-like element in the platypus genome","volume":"93","author":"Cui","year":"2012","journal-title":"J. Gen. Virol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"2133","DOI":"10.1007\/s00705-020-04632-4","article-title":"Reorganizing the family Parvoviridae: A revised taxonomy independent of the canonical approach based on host association","volume":"165","author":"Canuti","year":"2020","journal-title":"Arch. Virol."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Shan, T., Yang, S., Wang, H., Wang, H., Zhang, J., Gong, G., Xiao, Y., Yang, J., Wang, X., and Lu, J. (2022). Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses. Microbiome, 10.","DOI":"10.1186\/s40168-022-01246-7"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"110081","DOI":"10.1016\/j.virol.2024.110081","article-title":"Opportunistic sampling of yellow canary (Crithagra flaviventris) has revealed a high genetic diversity of detected parvoviral sequences","volume":"595","author":"Zhang","year":"2024","journal-title":"Virology"},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Sarker, S., Athukorala, A., and Phalen, D.N. (2022). Characterization of a near-complete genome sequence of a chaphamaparvovirus from an australian boobook owl (Ninox boobook). Microbiol. Resour. Announc., 11.","DOI":"10.1128\/mra.00249-22"},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Sarker, S. (2022). Characterization of a novel complete-genome sequence of a galliform chaphamaparvovirus from a free-range laying chicken clinically diagnosed with spotty liver disease. Microbiol. Resour. Announc., 11.","DOI":"10.1128\/mra.01017-22"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1016\/j.meegid.2014.12.022","article-title":"Recombination in viruses: Mechanisms, methods of study, and evolutionary consequences","volume":"30","author":"Arenas","year":"2015","journal-title":"Infect. Genet. Evol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1997","DOI":"10.1099\/jgv.0.000871","article-title":"ICTV Virus Taxonomy Profile: Circoviridae","volume":"98","author":"Breitbart","year":"2017","journal-title":"J. Gen. Virol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"13014","DOI":"10.1038\/ncomms13014","article-title":"Structural insights into the assembly and regulation of distinct viral capsid complexes","volume":"7","author":"Sarker","year":"2016","journal-title":"Nat. Commun."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"e5761","DOI":"10.7717\/peerj.5761","article-title":"Virus discovery in all three major lineages of terrestrial arthropods highlights the diversity of single-stranded DNA viruses associated with invertebrates","volume":"6","author":"Rosario","year":"2018","journal-title":"PeerJ"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"2911","DOI":"10.1007\/s00705-021-05183-y","article-title":"Family Genomoviridae: 2021 taxonomy update","volume":"166","author":"Varsani","year":"2021","journal-title":"Arch. Virol."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Zhang, Q.-Y., Ke, F., Gui, L., and Zhao, Z. (2022). Recent insights into aquatic viruses: Emerging and reemerging pathogens, molecular features, biological effects, and novel investigative approaches. Water Biol. Secur., 1.","DOI":"10.1016\/j.watbs.2022.100062"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.coviro.2015.08.007","article-title":"Insect-specific viruses and their potential impact on arbovirus transmission","volume":"15","author":"Vasilakis","year":"2015","journal-title":"Curr. Opin. Virol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.actatropica.2016.11.020","article-title":"The emergence of arthropod-borne viral diseases: A global prospective on dengue, chikungunya and zika fevers","volume":"166","author":"Mayer","year":"2017","journal-title":"Acta Trop."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Longdon, B., Brockhurst, M.A., Russell, C.A., Welch, J.J., and Jiggins, F.M. (2014). The evolution and genetics of virus host shifts. PLoS Pathog., 10.","DOI":"10.1371\/journal.ppat.1004395"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"329","DOI":"10.20506\/rst.29.2.1980","article-title":"Disease risks associated with the translocation of wildlife","volume":"29","author":"Kock","year":"2010","journal-title":"Rev. Sci. Tech. Int. Off. Epizoot."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/2\/176\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T10:36:34Z","timestamp":1759919794000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/2\/176"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,26]]},"references-count":60,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2025,2]]}},"alternative-id":["v17020176"],"URL":"https:\/\/doi.org\/10.3390\/v17020176","relation":{},"ISSN":["1999-4915"],"issn-type":[{"type":"electronic","value":"1999-4915"}],"subject":[],"published":{"date-parts":[[2025,1,26]]}}}