Anti-RNA virus crRNA targets efficient screening platform based on bioinformatics and CRISPR detection

The mutation and evolution of RNA viruses pose significant challenges in treatment efforts. The CRISPR-Cas system is a promising antiviral tool because of its powerful programmability. However, traditional cell screening methods for CRISPR targets are time-consuming, limiting their application. Here, we developed a rapid and efficient screening platform for crRNA targets by combining the CaSilico-based bioinformatics method with CRISPR in vitro detection technology. Using a bioinformational approach to design and screen crRNAs, the characteristics of crRNAs and the corresponding target sequences can be rapidly determined. CRISPR is used for secondary screening in vitro, enabling swift identification of the target site with optimal cleavage efficiency. This method significantly reduces the screening time for antiviral targets compared with traditional cell screening. We successfully designed and screened effective crRNA targeting SARS-CoV-2 conserved N gene regions and demonstrated its inhibition function in HEK 293T cells. We also designed and screened crRNAs targeting DENV to validate the feasibility of the platform. E-2330 crRNA reduced more than 90% of the DENV RNA load in multiple mammalian cell lines and effectively inhibited the replication of all four DENV serotypes. This study provides a new approach for screening antiviral crRNAs for antivirus research.