Virus-derived siRNAs (vsiRNAs) are generated in the host during infection by RNA viruses in both Drosophila click here and mosquitoes. The biogenesis of these vsiRNAs has been the focus of much research to discover the identity of the viral RNA precursor targeted, and to provide insight into how the RNAi pathway mechanistically responds to infection against distinct classes of viruses [1]. Figure 1A diagrams the potential RNA precursors of vsiRNAs generated during RNA virus infection, bearing in mind that these precursors must be in the form of dsRNA.

Small RNA sequencing of virus-infected cells or animals has revealed that the dsRNA replication intermediate of RNA viruses is a common target of the antiviral machinery [4, 7-9] (and Sabin and Cherry, unpublished observations). In addition, as RNA viruses have limited coding capacity, they often encode highly structured cis elements (structured viral RNA) with double-stranded character that direct transcription, replication, and packaging. Therefore, it is perhaps not surprising that the antiviral BGB324 price RNAi machinery is capable of targeting those regions with double-stranded character within the highly structured viral transcripts. Viruses such as Flock House virus, Drosophila C virus, and West Nile virus, appear

to expose such structures during infection; the majority Acyl CoA dehydrogenase of the small RNAs generated during their replication derive from only the genomic RNA strand [10-12] (and Sabin and Cherry, unpublished observations). This suggests that double-stranded structures within single-stranded RNAs can be processed into siRNAs during infection. Genetic studies have indicated that robust antiviral RNAi requires not only vsiRNA biogenesis by Dicer-2, but also the action of the core siRNA RISC effector, Ago2; however, only a fraction of vsiRNAs are specifically bound to Ago2 in infected cells [13, 14] with a large proportion of vsiRNAs being stable, but not bound to Ago2. Whether the

“free” vsiRNAs are loaded onto another RISC, such as Ago1 RISC, which normally binds miRNAs, or whether the vsiRNAs are stabilized elsewhere remains unknown. Furthermore, while some reporters that bear viral RNA target sequences can be silenced by vsiRNAs produced during infection, this is not always the case [8, 13, 15]. Altogether, these findings raise questions regarding which vsiRNAs reflect the active pool for viral silencing, and whether viral sequences are indeed generally targeted by Ago2-RISC. Additional studies of the effector step of antiviral RNAi are necessary to resolve these issues. Since viruses co-evolve with their hosts, one hallmark of an important antiviral pathway is the development of robust countermeasures against the host-encoded antiviral immune factors by viruses.