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A new flavi-like virus identified in populations of wild carrots

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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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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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Correspondence to Thierry Candresse.

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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

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