{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T17:08:52Z","timestamp":1790615332128,"version":"4.1.0"},"reference-count":38,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2021,3,31]],"date-time":"2021-03-31T00:00:00Z","timestamp":1617148800000},"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>Rubella virus (RuV) is the causative agent of rubella (\u201cGerman measles\u201d) and remains a global health concern. Until recently, RuV was the only known member of the genus Rubivirus and the only virus species classified within the Matonaviridae family of positive-sense RNA viruses. Recently, two new rubella-like matonaviruses, Rustrela virus and Ruhugu virus, have been identified in several mammalian species, along with more divergent viruses in fish and reptiles. To screen for the presence of additional novel rubella-like viruses, we mined published transcriptome data using genome sequences from Rubella, Rustrela, and Ruhugu viruses as baits. From this, we identified a novel rubella-like virus in a transcriptome of Tetronarce californica\u2014order Torpediniformes (Pacific electric ray)\u2014that is more closely related to mammalian Rustrela virus than to the divergent fish matonavirus and indicative of a complex pattern of cross-species virus transmission. Analysis of host reads confirmed that the sample analysed was indeed from a Pacific electric ray, and two other viruses identified in this animal, from the Arenaviridae and Reoviridae, grouped with other fish viruses. These findings indicate that the evolutionary history of the Matonaviridae is more complex than previously thought and highlights the vast number of viruses that remain undiscovered.<\/jats:p>","DOI":"10.3390\/v13040585","type":"journal-article","created":{"date-parts":[[2021,3,31]],"date-time":"2021-03-31T00:13:10Z","timestamp":1617149590000},"page":"585","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["A Novel Rubi-Like Virus in the Pacific Electric Ray (Tetronarce californica) Reveals the Complex Evolutionary History of the Matonaviridae"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7529-9823","authenticated-orcid":false,"given":"Rebecca M.","family":"Grimwood","sequence":"first","affiliation":[{"name":"Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9596-3552","authenticated-orcid":false,"given":"Edward C.","family":"Holmes","sequence":"additional","affiliation":[{"name":"Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0970-0153","authenticated-orcid":false,"given":"Jemma L.","family":"Geoghegan","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand"},{"name":"Institute of Environmental Science and Research, Wellington 5018, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,3,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/S0065-3527(08)60328-0","article-title":"Molecular biology of rubella virus","volume":"44","author":"Frey","year":"1994","journal-title":"Adv. Virus Res."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2297","DOI":"10.1016\/S0140-6736(14)60539-0","article-title":"Rubella","volume":"385","author":"Lambert","year":"2015","journal-title":"Lancet"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"iii","DOI":"10.1017\/S0950268800048627","article-title":"Congenital cataract following German measles in the mother","volume":"107","author":"Gregg","year":"1991","journal-title":"Epidemiol. Infect"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1275","DOI":"10.1056\/NEJM196412172712501","article-title":"Virologic and Serologic Studies on Human Products of Conception after Maternal Rubella","volume":"271","author":"Alford","year":"1964","journal-title":"N. Engl. J. Med."},{"key":"ref_5","first-page":"1408","article-title":"Clinical evaluation of a new measles-mumps-rubella trivalent vaccine","volume":"129","author":"Schwarz","year":"1975","journal-title":"Am. J. Dis. Child"},{"key":"ref_6","unstructured":"Oliv\u00e9, J.M. (2000). Historical review and summary of meeting objectives. Report of a Meeting on Preventing Congenital Rubella Syndrome: Immunization Strategies, Surveillance Needs, WHO."},{"key":"ref_7","first-page":"55","article-title":"Control of rubella and congenital rubella syndrome (CRS) in developing countries, Part 1: Burden of disease from CRS","volume":"75","author":"Cutts","year":"1997","journal-title":"Bull. World Health Organ."},{"key":"ref_8","first-page":"149","article-title":"Some Account of a Rash Liable to be Mistaken for Scarlatina","volume":"5","author":"Maton","year":"1815","journal-title":"Med. Trans. Coll. Physicians"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1016\/B978-012374410-4.00628-2","article-title":"Togaviruses: Molecular Biology","volume":"3","author":"Ryman","year":"2008","journal-title":"Encycl. Virol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1038\/s41586-018-0012-7","article-title":"The evolutionary history of vertebrate RNA viruses","volume":"556","author":"Shi","year":"2018","journal-title":"Nature"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"veab005","DOI":"10.1093\/ve\/veab005","article-title":"Host evolutionary history and ecology shape virome composition in fishes","volume":"7","author":"Geoghegan","year":"2021","journal-title":"Virus Evol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1038\/s41586-020-2812-9","article-title":"Relatives of rubella virus in diverse mammals","volume":"586","author":"Bennett","year":"2020","journal-title":"Nature"},{"key":"ref_13","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_14","doi-asserted-by":"crossref","unstructured":"Turnbull, O.M.H., Ortiz-Baez, A.S., Eden, J.S., Shi, M., Williamson, J.E., Gaston, T.F., Zhang, Y.Z., Holmes, E.C., and Geoghegan, J.L. (2020). Meta-Transcriptomic Identification of Divergent Amnoonviridae in Fish. Viruses, 12.","DOI":"10.1101\/2020.10.06.329003"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Li, B., and Dewey, C.N. (2011). RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-323"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"ref_21","unstructured":"(2020, February 04). Geneious Prime. Available online: https:\/\/www.geneious.com."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"Gabaldon","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: Fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1093\/molbev\/msx281","article-title":"UFBoot2: Improving the ultrafast bootstrap approximation","volume":"35","author":"Hoang","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_26","unstructured":"Rambaut, A. (2021, February 01). FigTree. Available online: http:\/\/tree.bio.ed.ac.uk\/software\/figtree\/."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Stavrianakou, M., Perez, R., Wu, C., Sachs, M.S., Aramayo, R., and Harlow, M. (2017). Draft de novo transcriptome assembly and proteome characterization of the electric lobe of Tetronarce californica: A molecular tool for the study of cholinergic neurotransmission in the electric organ. BMC Genom., 18.","DOI":"10.1186\/s12864-017-3890-4"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/j.jviromet.2016.08.004","article-title":"Validation of RPS13 as a reference gene for absolute quantification of SIV RNA in tissue of rhesus macaques","volume":"236","author":"Robichaux","year":"2016","journal-title":"J. Virol. Methods"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1006\/viro.1996.0028","article-title":"Orbivirus structure and assembly","volume":"216","author":"Roy","year":"1996","journal-title":"Virology"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Tomazatos, A., Marschang, R.E., Maranda, I., Baum, H., Bialonski, A., Spinu, M., Luhken, R., Schmidt-Chanasit, J., and Cadar, D. (2020). Letea Virus: Comparative Genomics and Phylogenetic Analysis of a Novel Reassortant Orbivirus Discovered in Grass Snakes (Natrix natrix). Viruses, 12.","DOI":"10.3390\/v12020243"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/nature11741","article-title":"Functional and evolutionary insight from the crystal structure of rubella virus protein E1","volume":"493","author":"DuBois","year":"2013","journal-title":"Nature"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1128\/jvi.67.2.673-681.1993","article-title":"Immunodominant T-cell epitopes of rubella virus structural proteins defined by synthetic peptides","volume":"67","author":"McCarthy","year":"1993","journal-title":"J. Virol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1006\/viro.2001.0939","article-title":"Mutations in the GDD motif of rubella virus putative RNA-dependent RNA polymerase affect virus replication","volume":"285","author":"Wang","year":"2001","journal-title":"Virology"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"7920","DOI":"10.1128\/JVI.00832-16","article-title":"Distinct Viral Lineages from Fish and Amphibians Reveal the Complex Evolutionary History of Hepadnaviruses","volume":"90","author":"Dill","year":"2016","journal-title":"J. Virol."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Geoghegan, J.L., Duchene, 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_36","doi-asserted-by":"crossref","first-page":"315","DOI":"10.20506\/rst.34.2.2359","article-title":"African horse sickness","volume":"34","author":"Zientara","year":"2015","journal-title":"Rev. Sci. Technol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2007","DOI":"10.1099\/0022-1317-70-8-2007","article-title":"The characterization of equine encephalosis virus and the development of genomic probes","volume":"70","author":"Viljoen","year":"1989","journal-title":"J. Gen. Virol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.coviro.2018.11.001","article-title":"Arenavirus genomics: Novel insights into viral diversity, origin, and evolution","volume":"34","author":"Pontremoli","year":"2019","journal-title":"Curr. Opin. Virol."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/13\/4\/585\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,13]],"date-time":"2025-10-13T14:10:34Z","timestamp":1760364634000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/13\/4\/585"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,3,31]]},"references-count":38,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2021,4]]}},"alternative-id":["v13040585"],"URL":"https:\/\/doi.org\/10.3390\/v13040585","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.02.08.430315","asserted-by":"object"}]},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,3,31]]}}}