Grapevine virus P: a novel vitivirus found through virome analysis of bulk grape genetic resources in Japan

Abstract

Abstract To understand the potential risks posed by viruses and viroids to viticulture in Japan, virome analysis was performed on 174 grape genetic resources from the National Agriculture and Food Research Organization. A total of 20 bulk samples were prepared by grouping the vines into batches of 6–10. Each of the bulk samples was analyzed using next-generation sequencing, which detected 26 viruses and 5 viroids. One contig initially categorized into grapevine virus A (GVA) in the genus Vitivirus with a maximum nucleotide sequence identity of only 58% with GVA variants was further analyzed. The determined genome was 7,461 nucleotides in length and encoded five open reading frames showing the typical genomic structure of vitiviruses. Phylogenetic trees of vitiviruses placed it at a distinct position nearest to GVA or grapevine virus F (GVF) in genomes and amino acids of deduced replication-associated protein (RAP) and coat protein (CP). The amino acid sequence identities of RAP and CP with GVA, GVF, and other vitiviruses were a maximum of 53% and 73%, respectively, which were significantly below the species demarcation threshold of 80% in the genus. The low identity and phylogenetic analyses indicate the discovery of a novel vitivirus species provisionally named grapevine virus P.