Europe is a recognized hotspot for emerging infectious diseases (EIDs). A total of 72% of zoonotic EID events have a wildlife origin. Those countries that conduct disease surveillance of their wild animal populations are therefore more likely to detect potential EID events at an early stage and to swiftly implement countermeasures. Detecting viruses in wildlife samples is currently done using serology, immunohistochemistry (IHC), or PCR among others. Although these techniques have their merits, they also have significant disadvantages: they either have a low specificity or require logistics that are not feasible or at best are difficult to apply in wildlife sampling. Although the proposed novel technique of in situ hybridization (ISH) has some shortcomings that have to be taken into account, it does not have these disadvantages. It provides an opportunity to profile multiple messenger RNA transcripts at a single cell level, and enables the detection of single-copy genes. As compared to PCR, ISH produces clinically relevant information regarding cellular and tissue context. Importantly, ISH can be applied to formalin-fixed, paraffin-embedded (FFPE) tissue sections, which easily can be transported and stored without biohazard or cold-chain constraints; this is a major advantage in wildlife disease surveillance. The objectives of this research are, first, to set up specific ISH techniques for the detection of viruses in FFPE tissues, including members of the families Asfarviridae, Bunyaviridae, Coronaviridae, Flaviviridae, Rhabdoviridae, Orthomyxoviridae, and Paramyxoviridae. This list is open-ended in case new viruses emerge in Europe. Second, to validate and use the ISH in a selected group of viruses and in real disease surveillance settings in the southern and eastern European borders and in EU surrounding countries. In summary, the proposed research will be of importance for the EU to help better protect itself against the incursion of emerging pathogens.