Genetic variability of Grapevine Pinot gris virus and its association with grapevine leaf mottling and deformation

The role of Grapevine Pinot gris virus (GPGV) in the etiology of grapevine leaf mottling and deformation was investigated by biological and molecular assays. A survey on different cultivars from the Trentino Region in Italy showed a widespread distribution of GPGV, which was associated with symptomatic (79%) but also with symptomless vines (21%). Symptomatic and GPGV-infected Pinot gris vines induced symptoms on grafted vines of healthy Pinot gris or Traminer, whereas GPGV-infected but symptomless vines did not. High-throughput sequencing of small RNA (sRNAs) populations of two infected Pinot gris accessions confirmed the existence of nearly overlapping viromes in vines with or without symptoms but phylogenetic analyses of the genomes of seven GPGV isolates from Italy and the Czech and Slovak Republics clearly differentiated those infecting symptomatic vines. The involvement of Grapevine rupestris vein feathering virus (GRVFV) in the disease, which was only infecting the symptomatic vine, was ruled out by RT-PCR studies. Maximum likelihood and Bayesian phylogenetic analysis of two GPGV genomic regions, encompassing part of the movement protein and coat protein gene sequences (MP/CP) and the RNA dependent RNA polymerase domain (RdRp) of the replicase gene, showed that isolates from symptomatic vines form a lineage distinct from that of symptomless vines. Moreover, the presence or lack of the MP stop codon identified in viral isolates from symptomatic or symptomless vines, respectively, is likely responsible for a six amino acids longer MP in symptomless isolates.