A Novel Cogu-like Virus Identified in Wine Grapes

A new negative-strand RNA virus was identified in grapevines from a 38-year-old 'Chardonnay' block in Idaho through high-throughput sequencing (HTS) of total RNA. This virus was tentatively named grapevine-associated cogu-like Idaho virus (GaCLIdV). GaCLIdV has three negative-sense, single-stranded RNA genome segments of ca. 7 kb, 1.9 kb, and 1.3 kb, encoding L protein (RNA-dependent RNA polymerase, RdRP), a movement protein (MP), and a nucleocapsid protein (NC), respectively, identified based on pair-wise comparisons with other cogu- and cogu-like viruses. In phylogenetic analysis based on the RdRP, GaCLIdV grouped within the family <i>Phenuiviridae</i> and was placed in a lineage of plant-infecting phenuiviruses as a sister clade of the genus <i>Laulavirus</i>, clustering most closely with switchgrass phenui-like virus 1 (SgPLV-1) and more distantly related to grapevine-associated cogu-like viruses from the <i>Laulavirus</i> and <i>Coguvirus</i> clades. Both GaCLIdV and SgPhLV-1 are proposed to form a new genus, Switvirus, within the family <i>Phenuiviridae</i>. The presence of GaCLIdV in the original 'Chardonnay' samples was confirmed by RT-PCR amplification and Sanger sequencing. This new virus was found in five wine grape cultivars and in six vineyards sampled in Idaho and in Oregon during the 2020-2024 seasons. GaCLIdV may have contributed to the decline observed in the old 'Chardonnay' block, although the role of the virus in symptom development awaits further investigation.