Grapevine-associated picorna-like virus, an unusual virus identified in wine grapes (Vitis vinifera L.)

Abstract

A new picorna-like virus was identified in grapevines from a 21-year-old ‘Tempanillo’ block in eastern Oregon exhibiting leaf chlorosis and interveinal reddening, through the high-throughput sequencing (HTS) of the total RNA. This new virus was named grapevine-associated picorna-like virus (GaPLV). GaPLV has a monopartite, positive-sense, single-stranded RNA genome of 9021-nt, with a single open reading frame encoding a polyprotein that encompasses an RNA dependent RNA polymerase (RdRP), a helicase, a chymotrypsin-like protease, and three capsid proteins. The arrangement of these conserved domains in the polyprotein is so far unique among picorna-like viruses, with two structural (capsid) proteins in the N-terminal region, upstream of all other conserved domains, and one structural (capsid) domain close to the C-terminus of the polyprotein, downstream of the RdRP. In phylogenetic analysis, RdRP of GaPLV grouped inside the order Picornavirales, but outside of the known families of picorna-like viruses, at the base of the clade that includes Iflaviridae and Polycipivirdae. The presence of GaPLV in the original ‘Tempranillo’ samples was confirmed by RT-PCR amplifications and Sanger sequencing. Virus surveys conducted in 2023 and 2024 from five commercial vineyards in southwestern Idaho and eastern Oregon revealed GaPLV presence in six wine grape cultivars.