Development of a virus detection and discovery pipeline using next generation sequencing

- Viruses present a major threat to humans, agriculture and the ecosystem in general with new viruses emerging every year.
- Major bottlenecks: virus identification and high throughput sequence data analysis.
- This pipeline can process multiple samples, detecting known and discovering novel viruses.
- The bioinformatics tool can be used by the general virology community.

Next generation sequencing (NGS) has revolutionized virus discovery. Notwithstanding, a vertical pipeline, from sample preparation to data analysis, has not been available to the plant virology community. We developed a degenerate oligonucleotide primed RT-PCR method with multiple barcodes for NGS, and constructed VirFind, a bioinformatics tool specifically for virus detection and discovery able to: (i) map and filter out host reads, (ii) deliver files of virus reads with taxonomic information and corresponding Blastn and Blastx reports, and (iii) perform conserved domain search for reads of unknown origin. The pipeline was used to process more than 30 samples resulting in the detection of all viruses known to infect the processed samples, the extension of the genomic sequences of others, and the discovery of several novel viruses. VirFind was tested by four external users with datasets from plants or insects, demonstrating its potential as a universal virus detection and discovery tool.