REGENTS OF THE UNIVERSITY OF CALIFORNIA AT RIVERSIDE
RNA interference (RNAi) functions as an antiviral immunity in fungi, plants, insects and nematodes. In this immunity, dsRNA produced during replication of viral RNA genomes or convergent transcription of viral DNA genomes is processed into 21- to 24-nucleotide virus-derived small interfering RNAs (siRNAs) by Dicer to guide specific antiviral silencing. We have recently cloned and sequenced by the next generation sequencing technologies viral siRNAs produced in plants and fruitflies infected with positive-strand RNA viruses. Our results show that viral siRNAs produced by the host immune system in response to viral infection are overlapping and can be assembled back into long continuous fragments (contigs) of the infecting viral RNA genome using assembly programs developed for short reads genome sequencing. Thus, we propose that deep sequencing and assembly of virus-derived siRNAs can be employed as a new culture-independent approach for virus discovery. Indeed, examination of the small RNA population of a Drosophila cell line from Gerald M Rubin lab in our proof-of-the-concept experiments shows that the cell line is infected with at least five RNA viruses. These include two known viruses and three new viruses belonging to different genera not previously described. Since many important human and animal viruses are transmitted by arthropod vectors and many human diseases have no identified etiology, we propose to develop the pipeline for discovering new arthropod-borne viruses (arboviruses) in nosquitoes.