Grapevine virus A: nucleotide sequence, genome organization, and relationship in the Trichovirus genus

The 5' terminal region of the genomic RNA of grapevine virus A (GVA), a tentative member of the Trichovirus genus, encompassing 5466 nucleotides, was sequenced. Evidence was obtained that the RNA is capped. Two putative open reading frames (ORF) were identified: ORF 1 that codes for a 194 kDa polypeptide with conserved motifs of replication-related proteins of positive-strand RNA viruses, and ORF 2 that encodes a 19 kDa polypeptide with no significant homology with protein sequences from databases. This polypeptide, however, showed 44% similarity with the product expressed by a comparable ORF present in grapevine virus B (GVB). GVA genome had the same size and structural organization as that of GVB. It also had the same size of the genome of apple chlorotic leaf spot virus (ACLSV), the type species of the Trichovirus genus, but differed substantially in the number (5 versus 3), size, and order of genes. Differences existed also in the degree of sequence homology between polymerases, which did not cluster together in phylogenetic trees. Definitive (ACLSV, PVT) and tentative (GVA, GVB) trichovirus species differ molecularly, biologically and epidemiologically to an extent that warrants the taxonomic revision of the genus.