Viral diseases limit the yield of many important crops. They are particularly problematic in vegetatively propagated crops where they are transmitted from generation to generation. Therefore, viruses are a constant concern for propagation companies from different sectors as they carry a high responsibility for the agricultural and horticultural sector, often with legal and economic consequences. The overall objective of this project is the evaluation and optimisation of a high-throughput sequencing-based strategy for the detection of viruses, in function of certification and in vitro therapy for the creation of virus-free mother plants. Hereby, an adapted HTS strategy will be offered to the different target groups to support them in obtaining virus-free starting material.