High-Resolution Screening of Viral Communities and Identification of New Pathogens in Fish Using Next-Generation Sequencing.

Discovery of viral genomes in fish has historically been based on viral enrichment, random priming, cloning, and Sanger sequencing. However, the development of next-generation sequencing has enabled the possibility to sequence the entire virome of a tissue sample. This has led to an enormous increase in discovery of new viruses. In this chapter, we describe a simple and rapid method for viral discovery in fish. The method is based on Illumina sequencing of total RNA from diseased tissue or cell culture and in silico removal of host RNA.