Nanopore sequencing as a revolutionizing diagnostic tool for viral enteric disease complexes in pig health management
Novel viruses have been increasingly discovered in feces of piglets, indicating the existence of viral enteric disease complexes and emphasizing the need for novel diagnostic tools. The MinION was used to detect cell culture grown porcine coronavirus and rotavirus. Next, a viral metagenomics approach was applied to investigate diarrheic feces of a 1 week old piglet. Preamplification of nucleic acids was not performed. In the first case, 6169 and 987 reads were assigned to PEDV and RVA, respectively. Complete and partial genomes were assembled with varying coverage rates, respectively. In the diarrheic sample, a kobuvirus was detected for the first time in Belgium, besides bacteriophages, an enterovirus G and an astrovirus. The kobuvirus is now being investigated on the farm using a longitudinal study. In conclusion, the MinION is a useful tool for diagnosis of enteric disease in pig medicine and can be directly applied on unamplified viral nucleic acids.