Tomato spotted wilt virus (TSWV) is a thrips-transmitted tripartite RNA virus with a broad panel of host plants including several Solanaceae, one of the most economically important plant families and the most valuable in terms of vegetable crops. TSWV is one of the major causes of crop losses in tomato and several other vegetables worldwide. The study of the interaction between plant and viruses, in a context that can occur in nature, will provide the knowledge to evolve new defence strategy in agriculture. In this work plant-virus interactions have been investigates with different approaches. Starting from a wide comparison on the gene expression profile on leaves and roots, the level of the main plant hormones involved in defence was measured and discussed. The interference in gene expression originated by the concurrent presence of TSWV and a fungal symbiont on the same host plant was also analyzed. This work should be useful for who is working on applicative development of crop defence strategy based on genetic, or who is interested to highlight the plant response to infection in a complex multi-organism context.