Lost and found: Rediscovery and genomic characterization of sowthistle yellow vein virus after a 30+ year hiatus

• Published in: Virus research 2020-07, Vol.284, p.197987-197987, Article 197987
• Main Authors: Stenger, Drake C., Burbank, Lindsey P., Wang, Renyuan, Stewart, Alexander A., Mathias, Caleb, Goodin, Michael M.
• Format: Article
• Language: English
• Subjects: Betanucleorhabdovirus; Nucleorhabdovirus; Plant rhabdovirus
• ISSN: 0168-1702; 1872-7492
• DOI: 10.1016/j.virusres.2020.197987

•Sowthistle yellow vein virus (SYVV) is an historically important plant rhabdovirus.•SYVV had not been observed in the environment for 30 years.•Partial genome sequence of historic SYVV was obtained from archived cDNA clones.•Complete SYVV genome sequence was obtained from a 2018 field sample.•Phylogenetic analysis places SYVV in the genus Betanucleorhabdovirus. Beginning in the 1960’s, sowthistle yellow vein virus (SYVV) was the subject of pioneering research that demonstrated propagation of a plant virus in its insect vector. Since the 1980’s there has been a paucity of research on SYVV, with historic isolates no longer maintained and no genomic sequence available. Once commonly observed infecting sowthistle (Sonchus oleraceous L.) in California, SYVV incidence declined ca. 1990, likely due to displacement of the black currant aphid (Hyperomyzus lactucae L.) by an invasive non-vector aphid. In 2018, SYVV was fortuitously rediscovered infecting sowthistle in an organic citrus grove in Kern County, CA. The SYVV genome sequence (13,719 nts) obtained from the 2018 sample (designated HWY65) encoded all six expected genes: N, P, MP, M, G, and L. Nucleotide sequence (representing ∼86 % of the genome) of the SYVV Berkeley lab isolate, used by E. S. Sylvester and colleagues for the paradigm-shifting research mentioned above, was determined from an archived library of cDNA clones constructed in 1986. The two nucleotide sequences share 98.5 % identity, confirming both represent the same virus, thereby linking biology of the historic isolate with extant SYVV rediscovered in 2018. Phylogenetic analysis of the L protein indicated SYVV is positioned within a clade containing a subset of viruses currently assigned to the genus Nucleorhabdovirus. As Nucleorhabdovirus is paraphyletic, the International Committee on the Taxonomy of Viruses has proposed abolishment of the genus and establishment of three new genera. In this revised taxonomy, the clade containing SYVV constitutes a new genus designated Betanucleorhabdovirus.