ViPer is a multidisciplinary research project designed to address major regulatory, agronomic, and disease management challenges caused by viral infections in grapevine and fruit trees. The project consists of two work packages: one focused on grapevine fanleaf virus (GFLV) due to its prevalence and impact on Swiss vineyards, and the other on cherry rosette virus (CRV), reflecting its quarantine status and significance for Swiss fruit production. ViPer applies advanced molecular diagnostics, including high-throughput sequencing and traditional methods, to map infections, study genetic diversity, and develop sustainable management strategies. The project includes vigilant assessment of sample material for other, potentially new or uncharacterized viruses to ensure rapid detection and appropriate response. This research aims to provide actionable knowledge for growers, regulators, and scientists, enhancing plant health policy and viral disease management in perennial crops.