Unveiling Viral and Phytoplasma Threats in Belgian Viticulture: A first step toward Virome Analysis

Belgian viticulture has expanded rapidly, growing from 72 hectares in 2006 to 891 hectares by 2023. Despite the absence of a deep-rooted winemaking tradition, this rapid development has led to the establishment of novel agro-ecosystems where diverse grape varieties and cultivation techniques are being explored. However, this expansion is accompanied by increased vulnerability to viral, viroid, and phytoplasma pathogens, raising critical questions: Which pathogens threaten Belgian vineyards and to what extent are they already present and distributed? How do they spread, and what strategies are in place to manage outbreaks?

To address these pressing concerns, a twofold study was conducted. First, 88 vine growers were surveyed using questionnaires and interviews to assess vineyard structure, cultivar diversity, planting material origin, cultural practices, and awareness of viral and phytoplasma threats. This qualitative data was complemented by a nationwide virome study: over 7,000 plants, symptomatic and asymptomatic, representing 50 grape varieties were sampled across 86 vineyards. For asymptomatic samples, double-stranded RNA (dsRNA) was extracted from pools of 10 plants per plot, while symptomatic leaves were subjected to total RNA extraction. Subsequent sequencing and RT-PCR validation identified a diverse range of viral pathogens. In addition to HTS analyses phytoplasmas were also analysed through DNA extractions and specific molecular assays.

Preliminary results reveal a rich diversity viral pathogens, including grapevine leafroll-associated virus -1, -2 and -3, and grapevine fanleaf virus, detected for the first time in Belgium and independently confirmed by RT-PCR. Genome based analyses of these viruses are ongoing, while phytoplasma diagnostics are still in progress. This research highlights the diversity and distribution of pathogens in Belgian vineyards. In the future, the focus will be on developing rapid, reliable detection protocols, tracing the origin of pathogens, and conducting risk assessments to guide effective management strategies. By advancing preparedness for viral and phytoplasma threats, this study supports the sustainable development of Belgium’s growing viticulture sector.