{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T13:19:59Z","timestamp":1788268799584,"version":"build-2803163510"},"reference-count":48,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T00:00:00Z","timestamp":1787961600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"USDA-ARS project","award":["8042-22000-324-000-D"],"award-info":[{"award-number":["8042-22000-324-000-D"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Dahlia is an economically important ornamental crop in the United States and worldwide. Dahlia is primarily propagated vegetatively through bulbs, which can result in vertical transmission of and constant accumulation of viruses. In this study, mosaic and yellowing symptoms were observed in Dahlia plants in a residential garden in California. Dahlia samples were collected and sequenced using high-throughput sequencing (HTS). HTS analysis was used to explore the Dahlia virome in the symptomatic plants, which revealed the presence of several contigs with homology to known Dahlia-infecting viruses, such as Dahlia common mosaic virus (DCMV) and tobacco streak virus (TSV), and Dahlia latent viroid. However, two contigs showed that they belong to the genera Potyvirus and Miraophiovirus with low to medium homology to previously known Potyvirus and Miraophiovirus species. Sequence identity showed that these two contigs represent two novel viruses tentatively named Dahlia potyvirus 1 (DaPoV1) and Dahlia miraophiovirus 1 (DaMV1). In addition, two other contigs showed low homology to a partitivirus and yue-like virus, indicating novelty. Mechanical inoculation of infected Dahlia tissue did not result in successful transmission onto indicator hosts. Electron microscopy of symptomatic plants showed typical potyviral-like flexuous virions. Phylogenetic analysis confirmed the placement of DaPoV1 and DaMV1 in their respective genera. This study represents a significant expansion of the known Dahlia virome and uncovers the complexity of viral infections where DCMV and TSV have been historically the primary focus in Dahlia. Widespread surveys should reveal the distribution of these viruses at commercial production sites.<\/jats:p>","DOI":"10.3390\/v18090947","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T12:41:18Z","timestamp":1788266478000},"page":"947","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Dahlia Virome Analysis Reveals Multiple Novel Viruses in Mixed Infections"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9613-2838","authenticated-orcid":false,"given":"Peter","family":"Abrahamian","sequence":"first","affiliation":[{"name":"USDA Agriculture Research Service (USDA-ARS), National Germplasm Resources Laboratory, Beltsville, MD 20705, USA"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"}]},{"given":"Crosley","family":"Kudla-Williams","sequence":"additional","affiliation":[{"name":"USDA Agriculture Research Service (USDA-ARS), National Germplasm Resources Laboratory, Beltsville, MD 20705, USA"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1708-8235","authenticated-orcid":false,"given":"Samuel","family":"Grinstead","sequence":"additional","affiliation":[{"name":"USDA Agriculture Research Service (USDA-ARS), Molecular Plant Pathology Laboratory, Beltsville, MD 20705, USA"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"}]},{"given":"Katie","family":"Posis","sequence":"additional","affiliation":[{"name":"Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832, USA"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"}]},{"given":"Nicholas","family":"Winarto","sequence":"additional","affiliation":[{"name":"Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832, USA"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"}]},{"given":"Tongyan","family":"Tian","sequence":"additional","affiliation":[{"name":"Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,29]]},"reference":[{"key":"ref_1","first-page":"103","article-title":"Research on dahlia, the national flower of Mexico","volume":"1288","year":"2020","journal-title":"Acta Hortic."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Ohno, S., and Onozaki, T. (2025). Dahlia (Dahlia variabilis L.) Flower Color and Vase Life. Breeding of Ornamental Crops: Bulbous Flowers, Springer Nature Switzerland.","DOI":"10.1007\/978-3-031-77900-8_8"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"419","DOI":"10.21273\/HORTTECH05217-23","article-title":"Comparison of Dahlia Cultivars for Cut Flower Production in the Northeastern United States","volume":"33","author":"Burnett","year":"2023","journal-title":"HortTechnology"},{"key":"ref_4","first-page":"199","article-title":"Overview of dahlia breeding","volume":"60","year":"2016","journal-title":"Sci. Pap.-Ser. B Hortic."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1094\/PD-91-0088","article-title":"Seed transmission of Dahlia mosaic virus in Dahlia pinnata","volume":"91","author":"Pahalawatta","year":"2007","journal-title":"Plant Dis."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"697","DOI":"10.21273\/HORTSCI.40.3.697","article-title":"Dahlia mosaic virus: Molecular detection and distribution in dahlia in the United States","volume":"40","author":"Pappu","year":"2005","journal-title":"HortScience"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2325","DOI":"10.1007\/s00705-022-05567-8","article-title":"Untangling the taxonomy of dahlia mosaic virus","volume":"167","author":"Geering","year":"2022","journal-title":"Arch. Virol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1007\/s00705-025-06478-0","article-title":"Genome sequence of dahlia mosaic virus revisited: Molecular characterization and genetic diversity of DMV and dahlia common mosaic virus","volume":"171","author":"Gnanasekaran","year":"2026","journal-title":"Arch. Virol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1016\/j.virol.2008.03.003","article-title":"A new and distinct species in the genus Caulimovirus exists as an endogenous plant pararetroviral sequence in its host, Dahlia variabilis","volume":"376","author":"Pahalawatta","year":"2008","journal-title":"Virology"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1138","DOI":"10.1094\/PDIS-92-7-1138B","article-title":"Dahlia mosaic virus and Tobacco streak virus in Dahlia (Dahlia variabilis) in New Zealand","volume":"92","author":"Pappu","year":"2008","journal-title":"Plant Dis."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Sastry, K.S., Mandal, B., Hammond, J., Scott, S.W., and Briddon, R.W. (2019). Dahlia spp. Encyclopedia of Plant Viruses and Viroids, Springer.","DOI":"10.1007\/978-81-322-3912-3_303"},{"key":"ref_12","first-page":"537","article-title":"First report of tomato chlorotic dwarf viroid in dahlia in China","volume":"108","author":"Wang","year":"2024","journal-title":"Plant Dis."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.virusres.2013.12.007","article-title":"Methods in virus diagnostics: From ELISA to next generation sequencing","volume":"186","author":"Boonham","year":"2014","journal-title":"Virus Res."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Jones, S., Baizan-Edge, A., MacFarlane, S., and Torrance, L. (2017). Viral diagnostics in plants using next generation sequencing: Computational analysis in practice. Front. Plant Sci., 8.","DOI":"10.3389\/fpls.2017.01770"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1489","DOI":"10.1094\/PDIS-03-17-0306-RE","article-title":"Application of next generation sequencing for diagnostic testing of tree fruit viruses and viroids","volume":"101","author":"Rott","year":"2017","journal-title":"Plant Dis."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1094\/PHYTO-07-18-0257-RVW","article-title":"High throughput sequencing for plant virus detection and discovery","volume":"109","author":"Villamor","year":"2019","journal-title":"Phytopathology"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Saldarelli, P., Giampetruzzi, A., Maree, H.J., and Al Rwahnih, M. (2017). High-throughput sequencing: Advantages beyond virus identification. Grapevine Viruses: Molecular Biology, Diagnostics and Management, Springer International Publishing.","DOI":"10.1007\/978-3-319-57706-7_30"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Wang, J., Zhou, J., Chen, M., Li, Z., and Song, S. (2023). Identification and Genome Characterization of a Dahlia Common Mosaic Virus Isolate from China. Genes, 14.","DOI":"10.3390\/genes14101833"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"3179","DOI":"10.1007\/s00705-021-05225-5","article-title":"Construction of an infectious dahlia common mosaic virus clone","volume":"166","author":"Yamamoto","year":"2021","journal-title":"Arch. Virol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.virol.2019.11.009","article-title":"Metagenomic analysis of virome cross-talk between cultivated Solanum lycopersicum and wild Solanum nigrum","volume":"540","author":"Ma","year":"2020","journal-title":"Virology"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Debat, H., and Bejerman, N. (2025). An Update on RNA Virus Discovery: Current Challenges and Future Perspectives. Viruses, 17.","DOI":"10.3390\/v17070983"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1094\/PD-65-84","article-title":"Sorghum stunt mosaic","volume":"65","author":"Mayhew","year":"1981","journal-title":"Plant Dis."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1544","DOI":"10.1094\/PDIS-09-23-1963-RE","article-title":"Genetic analysis of the emerging citrus yellow vein clearing virus reveals a divergent virus population in American isolates","volume":"108","author":"Abrahamian","year":"2024","journal-title":"Plant Dis."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Diaz-Lara, A., Navarro, B., Di Serio, F., Stevens, K., Hwang, M.S., Kohl, J., Vu, S.T., Falk, B.W., Golino, D., and Al Rwahnih, M. (2019). Two novel negative-sense RNA viruses infecting grapevine are members of a newly proposed genus within the family Phenuiviridae. Viruses, 11.","DOI":"10.3390\/v11080685"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1007\/s00705-007-1053-7","article-title":"Design and application of two novel degenerate primer pairs for the detection and complete genomic characterization of potyviruses","volume":"153","author":"Ha","year":"2008","journal-title":"Arch. Virol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_27","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."},{"key":"ref_28","unstructured":"Bushnell, B. (2014). BBMap: A Fast, Accurate, Splice-Aware Aligner."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1099\/vir.0.048751-0","article-title":"Dahlia latent viroid: A recombinant new species of the family Pospiviroidae posing intriguing questions about its origin and classification","volume":"94","author":"Verhoeven","year":"2013","journal-title":"J. Gen. Virol."},{"key":"ref_30","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_31","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1093\/molbev\/msz189","article-title":"ModelTest-NG: A new and scalable tool for the selection of DNA and protein evolutionary models","volume":"37","author":"Darriba","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"4453","DOI":"10.1093\/bioinformatics\/btz305","article-title":"RAxML-NG: A fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference","volume":"35","author":"Kozlov","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved metagenomic analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1007\/s00705-018-4065-6","article-title":"Molecular characterization and analysis of conserved potyviral motifs in bean common mosaic virus (BCMV) for RNAi-mediated protection","volume":"164","author":"Worrall","year":"2019","journal-title":"Arch. Virol."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Nigam, D., LaTourrette, K., Souza, P.F., and Garcia-Ruiz, H. (2019). Genome-wide variation in potyviruses. Front. Plant Sci., 10.","DOI":"10.3389\/fpls.2019.01439"},{"key":"ref_36","first-page":"47","article-title":"First report of the incidence of potato virus Y in some ornamental plants in Iran","volume":"42","author":"Salehzadeh","year":"2023","journal-title":"Iran. Agric. Res."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jmb.2005.12.021","article-title":"An unusual structure at one end of potato potyvirus particles","volume":"357","author":"Torrance","year":"2006","journal-title":"J. Mol. Biol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2159","DOI":"10.1007\/s007050050449","article-title":"Potyvirus aphid transmission requires helper component and homologous coat protein for maximal efficiency","volume":"143","author":"Flasinski","year":"1998","journal-title":"Arch. Virol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"3281","DOI":"10.1099\/0022-1317-80-12-3281","article-title":"Context of the coat protein DAG motif affects potyvirus transmissibility by aphids","volume":"80","author":"Wang","year":"1999","journal-title":"J. Gen. Virol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1080\/13102818.2002.10819155","article-title":"Loss of aphid transmissibility of plum pox virus isolates","volume":"16","author":"Kamenova","year":"2002","journal-title":"Biotechnol. Biotechnol. Equip."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1161","DOI":"10.1099\/jgv.0.000836","article-title":"ICTV virus taxonomy profile: Ophioviridae","volume":"98","author":"Hammond","year":"2017","journal-title":"J. Gen. Virol."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Debat, H., Garcia, M.L., and Bejerman, N. (2023). Expanding the repertoire of the plant-infecting Ophioviruses through metatranscriptomics data. Viruses, 15.","DOI":"10.1101\/2023.01.27.525910"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"001904","DOI":"10.1099\/jgv.0.001904","article-title":"ICTV Virus Taxonomy Profile: Yueviridae 2023","volume":"104","author":"Krupovic","year":"2023","journal-title":"J. Gen. Virol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1186\/s12985-026-03075-8","article-title":"The analysis of the virome associated with Freesia refracta plants with necrotic disorder sheds new light on the phylogenetic relationships in the Konkoviridae and Yueviridae families","volume":"23","author":"Marra","year":"2026","journal-title":"Virol. J."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"e00260-22","DOI":"10.1128\/jvi.00260-22","article-title":"Transcriptome mining expands knowledge of RNA viruses across the plant kingdom","volume":"96","author":"Mifsud","year":"2022","journal-title":"J. Virol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1899","DOI":"10.1098\/rstb.2010.0057","article-title":"Lifestyles of plant viruses","volume":"365","author":"Roossinck","year":"2010","journal-title":"Philos. Trans. R. Soc. B Biol. Sci."},{"key":"ref_47","first-page":"505","article-title":"Long term survival of cryptic viruses in aseptically grown in vitro propagated plants","volume":"725","author":"Szego","year":"2004","journal-title":"Acta Hortic."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1146\/annurev-phyto-021621-114618","article-title":"International trade and local effects of viral and bacterial diseases in ornamental plants","volume":"61","author":"Hammond","year":"2023","journal-title":"Annu. Rev. Phytopathol."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/9\/947\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T12:43:39Z","timestamp":1788266619000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/9\/947"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,29]]},"references-count":48,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["v18090947"],"URL":"https:\/\/doi.org\/10.3390\/v18090947","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,29]]}}}