Abstract
We report the discovery of a new flavi-like virus identified in wild carrots (Daucus carota subsp. carota), using a double-stranded (ds)RNA high-throughput sequencing (HTS) approach. The new virus, tentatively named “carrot flavi-like virus 1” (CtFLV-1), has a large genome of 21.8 kb that harbours a single open reading frame encoding a 7,078-aa polyprotein with conserved RNA helicase (Hel) and RNA-dependent RNA polymerase (RdRp) domains. The new virus is phylogenetically related to recently described flavi-like viruses from arthropods, but its closest relative is a plant-associated virus, gentian Kobu-sho-associated virus (GKSaV). A pairwise comparison showed that these two viruses share 38.4% amino acid (aa) sequence identity in their polyproteins and 73% and 47.8% aa sequence identity in their conserved RdRp and Hel domains, respectively. Based on their similar genome organization and phylogenetic relationship, GKSaV and CtFLV-1 could form the basis for a new genus of plant-associated viruses, possibly within the family Flaviviridae, for which the name “Koshovirus” is proposed.
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References
Marais A, Faure C, Bergey B, Candresse T (2018) Viral double-stranded RNAs (dsRNAs) from plants: alternative nucleic acid substrates for high-throughput sequencing. In: Pantaleo V, Chiumenti M (eds) Viral metagenomics. Methods in molecular biology. Humana Press, New York, pp 45–53
Kobayashi K, Atsumi G, Iwadate Y, Tomita R, Chiba K, Akasaka S, Nishihara M, Takahashi H, Yamaoka N, Nishiguchi M, Sekine KT (2013) Gentian Kobu-sho-associated virus: A tentative, novel double-stranded RNA virus that is relevant to gentian Kobu-sho syndrome. J Gen Plant Pathol 79:56–63. https://doi.org/10.1007/s10327-012-0423-5
Atsumi G, Tomita R, Kobayashi K, Sekine KT (2013) Prevalence and genetic diversity of an unusual virus associated with Kobu-sho disease of gentian in Japan. J Gen Virol 94:2360–2365. https://doi.org/10.1099/vir.0.053637-0
Shi M, Lin X-D, Vasilakis N, Tian J-H, Li C-X, Chen L-J, Eastwood G, Diao X-N, Chen M-H, Chen X, Qin X-C, Widen SG, Wood TG, Tesh RB, Xu J, Holmes EC, Zhang Y-Z (2016) Divergent viruses discovered in arthropods and vertebrates revise the evolutionary history of the Flaviviridae and related viruses. J Virol 90:659–669. https://doi.org/10.1128/jvi.02036-15
Paraskevopoulou S, Käfer S, Zirkel F, Donath A, Petersen M, Liu S, Zhou X, Drosten C, Misof B, Junglen S (2021) Viromics of extant insect orders unveil the evolution of the flavi-like superfamily. Virus Evol 7:1–16. https://doi.org/10.1093/ve/veab030
Marais A, Svanella-Dumas L, Barone M, Gentit P, Faure C, Charlot G et al (2011) Development of a polyvalent RT-PCR detection assay covering the genetic diversity of Cherry capillovirus A (CVA). Plant Pathol 61:195–204. https://doi.org/10.1111/j.1365-3059.2011.02488.x
Shaffer C, Michener DC, Vlasava NB, Botermans M, Starre J, Tzanetakis IE (2021) First report of Gentian Kobu-sho-associated virus infecting peony in the United States and the Netherlands. Plant Dis. https://doi.org/10.1094/PDIS-06-21-1316-PDN
Acknowledgements
The authors wish to thank the INRAE GenoToul Platform (Toulouse, France) for Illumina sequencing, L. Svanella-Dumas (UMR BFP, INRAE, Bordeaux) for help in collecting carrot samples, and S. Plas (Invenio), S. Dandin (Ctifl Sileban), and F. Villeneuve (Ctifl Lanxade) for arranging access to carrot crops.
Funding
This study was funded by the European Union through a Horizon 2020 Marie Skłodowska-Curie Actions Innovative Training Network (H2020 MSCA- 60 ITN) project “INEXTVIR” (GA 813542).
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Schönegger, D., Marais, A., Faure, C. et al. A new flavi-like virus identified in populations of wild carrots. Arch Virol 167, 2407–2409 (2022). https://doi.org/10.1007/s00705-022-05544-1
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DOI: https://doi.org/10.1007/s00705-022-05544-1