Metagenomic identification of viral pathogens

The target-independent identification of viral pathogens using ‘shotgun’ metagenomic sequencing is an emerging approach with potentially wide applications in clinical diagnostics, public health monitoring, and viral discovery. In this approach, all viral nucleic acids present in a sample are sequenced in a random, shotgun manner. Pathogens are then identified without the prerequisite of searching for a specific viral pathogen. In this opinion article, I discuss the current state and future research directions for this emerging and disruptive technology. With further technical developments, viral metagenomics has the potential to be deployed as a powerful and widely adopted tool, transforming the way that viral disease is researched, monitored, and treated.

► Viral metagenomics is an emerging method of identifying viral pathogens.
► Current methods of identifying viral pathogens are inherently limited.
► Viral metagenomics has wide utility in clinical and public health applications.