Viral surveillance and discovery

•Improvements in high throughput sequencing are enabling new insights into viral ecology, evolution and pathogenesis.•Finding genetic footprints of an agent is only the first step in proving linkage to disease.•Future success depends on the integration of molecular methods for pathogen discovery and host response characterization.

The field of virus discovery has burgeoned with the advent of high throughput sequencing platforms and bioinformatics programs that enable rapid identification and molecular characterization of known and novel agents, investments in global microbial surveillance that include wildlife and domestic animals as well as humans, and recognition that viruses may be implicated in chronic as well as acute diseases. Here we review methods for viral surveillance and discovery, strategies and pitfalls in linking discoveries to disease, and identify opportunities for improvements in sequencing instrumentation and analysis, the use of social media and medical informatics that will further advance clinical medicine and public health.