ABSTRACT
Viral pathogens of livestock evolve rapidly and exist in complex microbial communities that interact with the host and the environment in causing disease. These habits of viral pathogens challenge us to keep our understanding of viruses in pace with their changes and interactions. This chapter describes how next-generation sequencing (NGS) technologies and bioinformatics analysis are beginning to help address this challenge. NGS has been instrumental in facilitating the uptake of metagenomic approaches to understanding viral communities, their members and activities as well as in expanding public collections of whole genome sequences, including pathogenic viral genomes. Metagenomics and viral genomics increase the precision and accuracy of our assessments of livestock health and disease. In livestock, they have applications in virus discovery, understanding of virus emergence, investigation of disease outbreaks, disease diagnosis, and disease prevention strategies such as vaccination programs.
