{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T13:11:56Z","timestamp":1788873116327,"version":"build-2803163510"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2023,11,2]],"date-time":"2023-11-02T00:00:00Z","timestamp":1698883200000},"content-version":"vor","delay-in-days":124,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Friedrich-Loeffler-Institut","award":["FLI-IVD-XX-2021-83"],"award-info":[{"award-number":["FLI-IVD-XX-2021-83"]}]},{"name":"Friedrich-Loeffler-Institut","award":["FLI-IVD-XX-2021-83"],"award-info":[{"award-number":["FLI-IVD-XX-2021-83"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Recently, we discovered two novel orthobornaviruses in colubrid and viperid snakes using an in silico data-mining approach. Here, we present the results of a screening of more than 100,000 nucleic acid sequence datasets of fish samples from the Sequence Read Archive (SRA) for potential bornaviral sequences. We discovered the potentially complete genomes of seven bornavirids in datasets from osteichthyans and chondrichthyans. Four of these are likely to represent novel species within the genus Cultervirus, and we propose that one genome represents a novel genus within the family of Bornaviridae. Specifically, we identified sequences of W\u01d4h\u00e0n sharpbelly bornavirus in sequence data from the widely used grass carp liver and kidney cell lines L8824 and CIK, respectively. A complete genome of Murray\u2013Darling carp bornavirus was identified in sequence data from a goldfish (Carassius auratus). The newly discovered little skate bornavirus, identified in the little skate (Leucoraja erinacea) dataset, contained a novel and unusual genomic architecture (N-Vp1-Vp2-X-P-G-M-L), as compared to other bornavirids. Its genome is thought to encode two additional open reading frames (tentatively named Vp1 and Vp2), which appear to represent ancient duplications of the gene encoding the viral glycoprotein (G). The datasets also provided insights into the possible transcriptional gradients of these bornavirids and revealed previously unknown splicing mechanisms.<\/jats:p>","DOI":"10.1093\/ve\/vead062","type":"journal-article","created":{"date-parts":[[2023,10,17]],"date-time":"2023-10-17T08:56:15Z","timestamp":1697532975000},"source":"Crossref","is-referenced-by-count":10,"title":["Diving deep into fish bornaviruses: Uncovering hidden diversity and\u00a0transcriptional strategies through comprehensive data mining"],"prefix":"10.1093","volume":"9","author":[{"given":"Mirette I Y","family":"Eshak","sequence":"first","affiliation":[{"name":"Friedrich-Loeffler-Institut, Institute of Diagnostic Virology , S\u00fcdufer 10, Greifswald\u2014Insel Riems 17493, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dennis","family":"Rubbenstroth","sequence":"additional","affiliation":[{"name":"Friedrich-Loeffler-Institut, Institute of Diagnostic Virology , S\u00fcdufer 10, Greifswald\u2014Insel Riems 17493, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Beer","sequence":"additional","affiliation":[{"name":"Friedrich-Loeffler-Institut, Institute of Diagnostic Virology , S\u00fcdufer 10, Greifswald\u2014Insel Riems 17493, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0178-6183","authenticated-orcid":false,"given":"Florian","family":"Pfaff","sequence":"additional","affiliation":[{"name":"Friedrich-Loeffler-Institut, Institute of Diagnostic Virology , S\u00fcdufer 10, Greifswald\u2014Insel Riems 17493, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,11,2]]},"reference":[{"key":"2023111418024565700_R1","doi-asserted-by":"crossref","first-page":"3293","DOI":"10.1007\/s00705-014-2197-x","article-title":"Improvements to Pairwise Sequence Comparison (PASC): A Genome-based Web Tool for\u00a0Virus Classification","volume":"159","author":"Bao","year":"2014","journal-title":"Archives of Virology"},{"key":"2023111418024565700_R2","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1016\/B978-012374410-4.00710-X","volume-title":"Encyclopedia of Virology","author":"Bao","year":"2008"},{"key":"2023111418024565700_R3","doi-asserted-by":"crossref","first-page":"11486","DOI":"10.1073\/pnas.89.23.11486","article-title":"Borna Disease Virus, a Negative-strand RNA Virus, Transcribes in\u00a0the Nucleus of\u00a0Infected Cells.","volume":"89","author":"Briese","year":"1992","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"2023111418024565700_R4","doi-asserted-by":"crossref","first-page":"4362","DOI":"10.1073\/pnas.91.10.4362","article-title":"Genomic Organization of\u00a0Borna Disease Virus","volume":"91","author":"Briese","year":"1994","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"2023111418024565700_R5","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","article-title":"Sensitive Protein Alignments at Tree-of-life Scale Using DIAMOND","volume":"18","author":"Buchfink","year":"2021","journal-title":"Nature Methods"},{"key":"2023111418024565700_R6","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giz100","article-title":"rnaSPAdes: A de Novo Transcriptome Assembler and\u00a0Its Application to RNA-Seq Data","volume":"8","author":"Bushmanova","year":"2019","journal-title":"Gigascience"},{"key":"2023111418024565700_R7","first-page":"34","volume-title":"Winfield, Nelson (Hg.) 1991 \u2013 Cyprinid Fishes","author":"Cavender","year":"1991"},{"key":"2023111418024565700_R8","article-title":"Transcriptomics Sequencing Provides Insights into Understanding the Mechanism of\u00a0Grass Carp Reovirus Infection","volume":"19","author":"Chen","year":"2018","journal-title":"International Journal of Molecular Sciences"},{"key":"2023111418024565700_R9","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1093\/sysbio\/syw037","article-title":"Terrace Aware Data Structure for\u00a0Phylogenomic Inference from Supermatrices","volume":"65","author":"Chernomor","year":"2016","journal-title":"Systematic Biology"},{"key":"2023111418024565700_R10","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/veab034","article-title":"Metagenomic Sequencing Reveals a Lack of\u00a0Virus Exchange between Native and\u00a0Invasive Freshwater Fish across the Murray-Darling Basin, Australia","volume":"7","author":"Costa","year":"2021","journal-title":"Virus Evolution"},{"key":"2023111418024565700_R11","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-017-14930-8","article-title":"Secretoneurin A Regulates Neurogenic and\u00a0Inflammatory Transcriptional Networks in\u00a0Goldfish (Carassius Auratus) Radial Glia","volume":"7","author":"Da Fonte","year":"2017","journal-title":"Scientific Reports"},{"key":"2023111418024565700_R12","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1093\/protein\/gzh013","article-title":"Prediction of\u00a0Proprotein Convertase Cleavage Sites","volume":"17","author":"Duckert","year":"2004","journal-title":"Protein Engineering, Design & Selection: PEDS"},{"key":"2023111418024565700_R13","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1038\/s41586-021-04332-2","article-title":"Petabase-scale Sequence Alignment Catalyses Viral Discovery","volume":"602","author":"Edgar","year":"2022","journal-title":"Nature"},{"key":"2023111418024565700_R14","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: Multiple Sequence Alignment with High Accuracy and\u00a0High Throughput","volume":"32","author":"Edgar RC","year":"2004","journal-title":"Nucleic Acids Research"},{"key":"2023111418024565700_R15","volume-title":"FAO Yearbook: Fishery and Aquaculture Statistics 2019\/FAO Annuaire. Statistiques Des P\u00eaches Et de L\u2019aquaculture 2019\/FAO Anuario. Estad\u00edsticas de Pesca Y Acuicultura 2019","author":"FAO","year":"2021"},{"key":"2023111418024565700_R16","doi-asserted-by":"crossref","first-page":"1522","DOI":"10.1126\/science.1254432","article-title":"Nonhuman Genetics. Genomic Basis for\u00a0the Convergent Evolution of\u00a0Electric Organs","volume":"344","author":"Gallant","year":"2014","journal-title":"Science"},{"key":"2023111418024565700_R17","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btac667","article-title":"Metadata Retrieval from Sequence Databases with Ffq","volume":"39","author":"G\u00e1lvez-Merch\u00e1n","year":"2023","journal-title":"Bioinformatics"},{"key":"2023111418024565700_R18","doi-asserted-by":"crossref","first-page":"968","DOI":"10.1128\/jvi.57.3.968-975.1986","article-title":"The Soluble Glycoprotein of\u00a0Vesicular Stomatitis Virus Is Formed during or Shortly after the Translation Process","volume":"57","author":"Graeve","year":"1986","journal-title":"Journal of Virology"},{"key":"2023111418024565700_R19","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.virol.2008.03.004","article-title":"Genomic Characterisation of\u00a0Wongabel Virus Reveals Novel Genes within the Rhabdoviridae","volume":"376","author":"Gubala","year":"2008","journal-title":"Virology"},{"key":"2023111418024565700_R20","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.virol.2009.12.013","article-title":"Ngaingan Virus, a Macropod-associated Rhabdovirus, Contains a Second Glycoprotein Gene and\u00a0Seven Novel Open Reading Frames","volume":"399","author":"Gubala","year":"2010","journal-title":"Virology"},{"key":"2023111418024565700_R21","article-title":"DeepTMHMM Predicts Alpha and\u00a0Beta Transmembrane Proteins Using Deep Neural Networks","author":"Hallgren","year":"2022","journal-title":"BioRxiv"},{"key":"2023111418024565700_R22","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":"Molecular Biology and Evolution"},{"key":"2023111418024565700_R23","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1056\/NEJMoa1415627","article-title":"A Variegated Squirrel Bornavirus Associated with Fatal Human Encephalitis","volume":"373","author":"Hoffmann","year":"2015","journal-title":"New England Journal of Medicine"},{"key":"2023111418024565700_R24","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1006881","article-title":"Divergent Bornaviruses from Australian Carpet Pythons with Neurological Disease Date the Origin of\u00a0Extant Bornaviridae Prior to the end-Cretaceous Extinction","volume":"14","author":"Hyndman","year":"2018","journal-title":"PLoS Pathogens"},{"key":"2023111418024565700_R25","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: Fast Model Selection for\u00a0Accurate Phylogenetic Estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nature Methods"},{"key":"2023111418024565700_R26","article-title":"Trim Galore","author":"Krueger","year":"2019"},{"key":"2023111418024565700_R27","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1007\/s00705-014-2276-z","article-title":"Taxonomic Reorganization of\u00a0the Family Bornaviridae","volume":"160","author":"Kuhn","year":"2015","journal-title":"Archives of Virology"},{"key":"2023111418024565700_R28","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.1126\/science.290.5494.1151","article-title":"The Evolutionary Fate and\u00a0Consequences of\u00a0Duplicate Genes","volume":"290","author":"Lynch","year":"2000","journal-title":"Science"},{"key":"2023111418024565700_R29","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt Removes Adapter Sequences from High-throughput Sequencing Reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet J"},{"key":"2023111418024565700_R30","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models and\u00a0Efficient Methods for\u00a0Phylogenetic Inference in\u00a0the Genomic Era","volume":"37","author":"Minh","year":"2020","journal-title":"Molecular Biology and Evolution"},{"key":"2023111418024565700_R31","doi-asserted-by":"crossref","DOI":"10.12688\/f1000research.29032.2","article-title":"Sustainable Data Analysis with Snakemake","volume":"10","author":"M\u00f6lder","year":"2021","journal-title":"F1000Res"},{"key":"2023111418024565700_R32","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1016\/S1473-3099(19)30546-8","article-title":"Zoonotic Spillover Infections with Borna Disease Virus 1 Leading to Fatal Human Encephalitis, 1999-2019: An Epidemiological Investigation","volume":"20","author":"Niller","year":"2020","journal-title":"The Lancet Infectious Diseases"},{"key":"2023111418024565700_R33","article-title":"SRAminer","volume-title":"10.5281\/ZENODO.8385126","author":"Pfaff","year":"2023"},{"key":"2023111418024565700_R34","doi-asserted-by":"crossref","first-page":"2611","DOI":"10.1007\/s00705-021-05138-3","article-title":"Two Novel Bornaviruses Identified in\u00a0Colubrid and\u00a0Viperid Snakes","volume":"166","author":"Pfaff","year":"2021","journal-title":"Archives of Virology"},{"key":"2023111418024565700_R35","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Core Team","year":"2022"},{"key":"2023111418024565700_R36","doi-asserted-by":"crossref","first-page":"4528","DOI":"10.1128\/JVI.72.5.4528-4533.1998","article-title":"Processing of\u00a0the Borna Disease Virus Glycoprotein Gp94 by the Subtilisin-like Endoprotease Furin","volume":"72","author":"Richt","year":"1998","journal-title":"Journal of Virology"},{"key":"2023111418024565700_R37","doi-asserted-by":"crossref","DOI":"10.3390\/v14071513","article-title":"Avian Bornavirus Research-A Comprehensive Review","volume":"14","author":"Rubbenstroth","year":"2022","journal-title":"Viruses"},{"key":"2023111418024565700_R38","doi-asserted-by":"crossref","DOI":"10.1099\/jgv.0.001613","article-title":"ICTV Virus Taxonomy Profile: Bornaviridae","volume":"102","author":"Rubbenstroth","year":"2021","journal-title":"The Journal of General Virology"},{"key":"2023111418024565700_R39","doi-asserted-by":"crossref","first-page":"6514","DOI":"10.1128\/jvi.68.10.6514-6522.1994","article-title":"Identification of\u00a0Signal Sequences that Control Transcription of\u00a0Borna Disease Virus, a Nonsegmented, Negative-strand RNA Virus","volume":"68","author":"Schneemann","year":"1994","journal-title":"Journal of Virology"},{"key":"2023111418024565700_R40","doi-asserted-by":"crossref","first-page":"5007","DOI":"10.1128\/jvi.68.8.5007-5012.1994","article-title":"RNA Splicing in\u00a0Borna Disease Virus, a Nonsegmented, Negative-strand RNA Virus","volume":"68","author":"Schneider","year":"1994","journal-title":"Journal of Virology"},{"key":"2023111418024565700_R41","doi-asserted-by":"crossref","DOI":"10.3390\/fishes6040079","article-title":"Comparative Transcriptome Analysis of\u00a0Female and\u00a0Male Fine-Patterned Puffer: Identification of\u00a0Candidate Genes Associated with Growth and\u00a0Sex Differentiation","volume":"6","author":"Shan","year":"2021","journal-title":"Fishes"},{"key":"2023111418024565700_R42","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1038\/s41586-018-0012-7","article-title":"The Evolutionary History of\u00a0Vertebrate RNA Viruses","volume":"556","author":"Shi","year":"2018","journal-title":"Nature"},{"key":"2023111418024565700_R43","doi-asserted-by":"crossref","first-page":"1263","DOI":"10.1093\/molbev\/mst044","article-title":"Gene Duplication is Infrequent in\u00a0the Recent Evolutionary History of\u00a0RNA Viruses","volume":"30","author":"Simon-Loriere","year":"2013","journal-title":"Molecular Biology and Evolution"},{"key":"2023111418024565700_R44","doi-asserted-by":"crossref","first-page":"12788","DOI":"10.1073\/pnas.97.23.12788","article-title":"Identification of\u00a0Alternative Splicing and\u00a0Negative Splicing Activity of\u00a0a Nonsegmented Negative-strand RNA Virus, Borna Disease Virus","volume":"97","author":"Tomonaga","year":"2000","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"2023111418024565700_R45","article-title":"Parallel-Fastq-Dump","author":"Valieris","year":"2021"},{"key":"2023111418024565700_R46","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1006\/viro.1993.1423","article-title":"Adelaide River Rhabdovirus Expresses Consecutive Glycoprotein Genes as Polycistronic mRNAs: New Evidence of\u00a0Gene Duplication as an Evolutionary Process","volume":"195","author":"Wang","year":"1993","journal-title":"Virology"},{"key":"2023111418024565700_R47","first-page":"10","article-title":"A Cell Line Derived from the Kidney of\u00a0Grass Carp (Ctenopharyngodon Idellus)","volume":"10","author":"Wengong","year":"1986","journal-title":"Journal of Fisheries of China"}],"container-title":["Virus Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ve\/advance-article-pdf\/doi\/10.1093\/ve\/vead062\/52773480\/vead062.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/9\/2\/vead062\/53404059\/vead062.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/9\/2\/vead062\/53404059\/vead062.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,14]],"date-time":"2023-11-14T13:49:01Z","timestamp":1699969741000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ve\/article\/doi\/10.1093\/ve\/vead062\/7337132"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,7,1]]},"references-count":47,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2023,11,14]]}},"URL":"https:\/\/doi.org\/10.1093\/ve\/vead062","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.08.23.554433","asserted-by":"object"}]},"ISSN":["2057-1577"],"issn-type":[{"value":"2057-1577","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,7,1]]},"published":{"date-parts":[[2023,7,1]]},"article-number":"vead062"}}