Today, the diagnosis of disease outbreaks is facing new challenges. As a result of increased mobility, global trade and global warming, disease outbreaks caused by “exotic”, “new” and re-emerging viruses such as bluetongue, Schmallenberg and African swine fever are increasing. Emerging pathogens are often not part of the diagnostic spectrum or there are no diagnostic tools available all together. Valuable time (and money) may be lost until a virus is identified due to having to screen with an array of different specific tests sequentially. In contrast, the so-called virome analysis using next generation sequencing (NGS) enables the unspecific identification of all viruses present in a sample without requiring knowledge of the virus and independent of the existence of specific diagnostic tools. The obvious advantages of this method regarding the identification of new, rare or mutated viruses make it particularly suitable for the early recognition of (re-)emerging viruses. With constantly decreasing sequencing costs, NGS analyses are becoming increasingly attractive also for the veterinary diagnostic field and – according to a ‘white paper’ commissioned by the OIE (World Organisation for Animal Health) – will substantially gain on importance in the coming years (Belak et al., 2013).
Therefore, the aim of this project is the development of a diagnostically applicable NGS method that can be implemented if routine diagnostic tools fail. Being tailored to the veterinary diagnostic requirements, this method should enable the fast, comprehensive, species-independent but also cost-efficient identification of the viral pathogen(s) present in a disease outbreak. For the technical development, already available and well characterised nasal and faecal samples of pigs will be used. In addition, manure from single bays and chew rope fluid (saliva) representing easy to gain collective samples will be included. In addition to using the virome method for diagnosis of novel viruses such as the porcine delta coronavirus (PDCoV) or the influenza C-like virus, NGS may clarify cases of diagnostic cross-reactivity (e.g. between different pestiviruses) and enables immediate genotyping of the identified viruses. Furthermore, the analysis of porcine field samples as part of the project will offer the chance to gain first indications on the spectrum of viruses detectable by NGS and enables more detailed characterisation of the circulating influenza viruses.
