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This thesis presents the major viruses affecting three cultivars in Colombia and how experimental approaches in serology, molecular biology, and bioinformatics can be adapted to create a protocol that could be applied for physalis, passionfruit, ornamental rose, and eventually other crops. Selection of farms was carried out based on size and economic importance. Initial visual plant symptom appraisal led collection of 370 samples from 20 farms. Literature review guided the selection of antibodies of known viruses for initial ELISA testing. Thereafter NGS was carried out to discover further known and novel viruses in the cultivars. Various experiments were carried out on different samples including biotest inoculation, ELISA, RT-PCR, and NGS. Reliable and practical diagnostic tools like these could be developed for the most important viruses leading to a national agricultural certification program that could be established in a common project between German and Colombian universities, the Colombian Agricultural Institute (ICA), the Colombian Corporation of Agricultural Investigation (AGROSAVIA), and the International Center for Tropical Agriculture (CIAT).