In silico detection and characterization of novel Picornavirales mined from publicly available insect RNA-seq datasets

Authors: LAHEY, ZACHARY - Oak Ridge Institute For Science And Education (ORISE); JONES, TARA-KAY - Corteva Agriscience; Simmons, Alvin; Andreason, Sharon

Submitted to: Journal of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/21/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary: A wide variety of viruses infect insects, and sometimes these viruses are inadvertently discovered during insect sequencing experiments. In this study, a bioinformatics pipeline was developed for the detection of viruses in insect sequencing datasets. Publicly available datasets were screened using the pipeline, and 40 new insect-infecting viruses were discovered. These discoveries and the new pipeline will be of interest and useful to the scientific community and provides a new means of discovery of viruses that can be explored for pest control.

Technical Abstract: Picornavirales is a hyperdiverse order of viruses that infect assorted hosts, including arthropods. Members of this group contain a positive-sense, single-stranded RNA genome with a polyadenylated tail. As such, they are often sequenced as ‘bycatch’ in RNA-seq experiments targeting other organisms. We developed a simple-to-follow bioinformatic pipeline to assemble and annotate genomes of Picornavirales using publicly available insect metatranscriptome datasets. Using our pipeline, 40 novel viruses were discovered, including members of Dicistroviridae, Iflaviridae, and Polycipiviridae. The hosts of the new picornaviruses include beetles (two families), crickets, parasitic wasps, sap-sucking hemipterans (members of all suborders), and thrips. We validated each virus as new in silico by performing a sequence similarity (BLAST) search of each virus against the NCBI non-redundant database and by phylogenetic reconstruction of the RNA-dependent RNA polymerase amino acid sequence from each novel virus and other members of Picornavirales. A newly characterized psyllid iflavirus displays an inverted genome architecture and forms a clade with other psyllid-infecting iflaviruses that share this feature. Our pipeline demonstrates the ease with which novel viruses can be discovered, assembled, annotated, and submitted to nucleotide sequence archives.