Grapevine deformation virus: Completion of the sequence and evidence on its origin from recombination events between Grapevine fanleaf virus and Arabis mosaic virus

The complete nucleotide (nt) sequence of Grapevine deformation virus (GDefV) RNA-1 has been determined. It consists of 7386 nt, excluding the poly(A) tail, and contains a single open reading frame (ORF) encoding a polyprotein (p1) of 252 kDa. P1 comprises the 1APro-cof proteinase cofactor, the 1BHel NTP-binding protein, the 1CVPg viral protein genome-linked, the 1DProt proteinase and the 1EPol RNA-dependent RNA polymerase, all of which are conserved domains in polyproteins of different members of the order Picornavirales. The amino acid (aa) sequence of GDefV RNA1 p1 has the highest identity with the homologous products of Grapevine fanleaf virus (GFLV, 86–88%) and Arabis mosaic virus (ArMV, 73–74%), two nepoviruses of subgroup A. Four cleavage sites for proteins processing were predicted (C/A, C/S, G/E and R/G) and found similar to those of GFLV RNA1. Phylogenetic trees constructed with the complete aa sequences of protein p1 and the RNA2-encoded protein p2 of GDeFV, GFLV and ArMV, showed an incongruent allocation of GDefV in these trees. Pairwise alignment and prediction of recombination sites of both RNA segments showed that GDefV RNA2 has a mosaic structure resulting from recombination events between GFLV and ArMV at the level of the 2AHP (homing protein), 2BMP (movement protein), 2CCP (capsid protein) and the 3′NCR (non coding region). This strongly suggests that GDefV originated from the interspecific recombination between isolates of GFLV and ArMV.