Grass carp reovirus encoding circular RNAs with antiviral activity

Abstract Circular RNAs (circRNAs) are novel, single-stranded, non-coding RNAs that play important roles in many biological processes. CircRNAs have not only been identified in eukaryotes, they have also been identified in some DNA viruses. Grass carp reovirus (GCRV) is a dsRNA virus; the genome of this virus contains 11 segmented dsRNAs. Infection of grass carp with GCRV leads to haemorrhagic disease, one of the most serious diseases in the grass carp aquaculture industry. To investigate the expression of circRNAs in this dsRNA virus, and their potential role in viral infection, we performed transcriptome analysis of GCRV-infected Ctenopharyngodon idelluskidney (CIK) cells. In total, 32 GCRV-derived circRNAs (vcircRNAs) were identified using a back-splicing strategy. Thirty-one vcircRNAs were derived from antisense strands of dsRNA segments; only one vcircRNA was derived from the sense strand. Our analysis predicted that some vcircRNAs, with the same 5′ terminal and variable 3′ terminal regions, were generated via alternative splicing events. The expression levels of vcircRNAs increased in CIK cells following GCRV infection. Competing endogenous RNA analysis further showed that the effects of vcircRNAs on host or viral genes may act via miRNAs. Furthermore, some vcircRNAs, that were transfected into cells via in vitro syntheses, caused a significant increase in cell apoptosis when compared with linear sequences of vcircRNAs or circRNA-GFP (as controls). Finally, we found that the expression levels of GCRV genes in CIK cells were significantly suppressed following the transfection of vcircRNAs. Collectively, our findings indicate that vcircRNAs are a novel form of viral transcript that are expressed in virus-infected cells. Our data also indicate that vcircRNAs may sequester the functions of host miRNAs or viral miRNAs in order to regulate genes in the host or virus to inhibit viral infection.