Biological evidence and molecular modeling of a grapevine Pinot gris virus outbreak in a vineyard

Since its identification in 2003, little has been revealed about the spread of grapevine Pinot gris virus (GPGV), an emerging grapevine virus. According to studies from Italy, GPGV transmission in the vineyard can be fast but progressive over the years. To gain new insights into the spread of GPGV infections, we tested 67 grapevines in a single vineyard parcel in southern France. These vines were sampled over eight years (2013-2020) and tested for GPGV by RT-PCR using a new primer pair designed from the recently described genetic diversity of GPGV worldwide. While focusing on a portion of the samples (20), we observed a drastic increase in newly GPGV-infected vines from 2014 (5%, 1 of 20) to 2015 (80%, 16 of 20) and 2016 (90%, 18 of 20). Infected vines were scattered throughout the vineyard with no distinct pattern of distribution and some rare vines remained negative through 2020. Using all available genomic information, we performed Bayesian-based phylogeographic analyses that identified a major intra-vineyard transmission in 2014-2015. To test our model, we analyzed 47 additional grapevines and confirmed the outbreak of GPGV in 2015, validating our in-silico projection. Interestingly, some grapevines remained negative throughout the study, in spite of their close proximity to infected plants. These results raise questions on the dynamic of vector populations and environmental conditions that may be required for virus spread to occur in the vineyard.