Complete genome coding sequence of freesia sneak virus from Freesia refracta necrotic leaves

Authors: ROTUNNO, SILVIA - National Research Council - Italy; MARRA, MONICA - National Research Council - Italy; FRASCATI, FULCO - National Research Council - Italy; PIERRO, ROBERTO - National Research Council - Italy; RESTUCCIA, PASQUALE - Sanremo Floriculture Cooperative; Hammond, John; MIOZZI, LAURA - National Research Council - Italy; VAIRA, ANNA MARIA - National Research Council - Italy

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/16/2024
Publication Date: 8/6/2024
Citation: Rotunno, S., Marra, M., Frascati, F., Pierro, R., Restuccia, P., Hammond, J., Miozzi, L., Vaira, A. 2024. Complete genome coding sequence of freesia sneak virus from Freesia refracta necrotic leaves. Archives of Virology. https://doi.org/10.1007/s42161-024-01712-1.
DOI: https://doi.org/10.1007/s42161-024-01712-1

Interpretive Summary: Virus infection of ornamental plants often reduces the visual appeal of the plants, affecting quality in addition to losses of productivity. A necrotic streaking disease of freesia foliage causing considerable economic losses has been recognized for more than 50 years in Europe, and has since been reported in other regions of the world where freesia are grown for cut flowers or as garden plants. Freesia sneak virus was associated with the necrosis in 2006, but could not be detected in all plants with necrotic streak symptoms; however, this virus remained incompletely characterized. In the current work the almost complete genome sequence of an Italian isolate of freesia sneak virus was determined, and revealed for the first time the presence of a fourth genome segment not previously detected, and previously known for only three of seven related viruses. Freesia sneak virus was detected in 32 of 39 freesia plants collected in 2014 and 2022, further demonstrating the high but not absolute correlation of freesia sneak virus with the observed necrosis. These results will be on value to freesia breeders and producers working to improve the health and productivity of the crop, and to virologists studying the group of viruses to which freesia sneak virus belongs.

Technical Abstract: The necrotic disorder of freesia (Freesia refracta hyb., family Iridaceae) was first described in the Netherlands more than 50 years ago and reported in Germany and England soon afterwards. Typical symptoms are interveinal chlorotic spots and streaks at the leaf tips that expand downwards and turn necrotic, and may vary according to cultivar and climate. These symptoms have been widely linked to the presence of an ophiovirus named freesia sneak virus (Ophiovirus freesiae) FreSV, belonging to the family Aspiviridae, which is soil-transmitted by Olpidium sp. and has up to now been detected in freesia in several temperate world regions. However, while the correlation between the presence of symptoms and FreSV detection is high, there may also be alternative agents involved in the syndrome. Here we report for the first time the near-complete genome of an isolate of FreSV, including the first identification of RNA4, previously reported for only three of seven recognized ophiovirus species. FreSV RNA4 encodes a 38.6 kDa protein most closely related to the homologous protein of ranunculus white mottle virus, and a putative smaller protein lacking significant similarity to any known proteins. The presence of FreSV was confirmed in 32 of 39 freesia plants collected in 2014 and 2022, further demonstrating the high but not absolute correlation of FreSV with the observed necrosis.