The introduction of new sequencing technologies is revolutionizing virus discovery and providing a new means to demonstrate the safety of vaccines. Since these methods do not depend on prior assumptions of the types of viruses that may be present, they have detected viruses missed by other methods like degenerate or, family specific, PCRs. We have used massively parallel sequencing (MP-Seq) to detect new viruses in bovine serum and in the faeces of animals. When applied to sequencing the transcriptome, MP-Seq can reveal latent or silent infections. While the sequencing technology is impressive, it is bioinformatics that is the key to its successful application.
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