The CRISPR/Cas system is an extremely powerful tool in molecular biology. In plants, the CRISPR/Cas system is mainly focused on introducing new traits to plants by DNA modifications and to diversity the CRISPR toolbox for enhanced gene editing. Nevertheless, the CRISPR/Cas system is versatile. At NIBIO, we have been exploring novel applications of the CRISPR/Cas system, specifically utilizing the RNA-binding Cas proteins Cas13a and Cas13BT3. Employing transient vector transfections with fluorescent-labeled Cas13 proteins and specific guide RNAs, we have developed a protoplast-based system that allows detection and localization of viral RNA within plant cells. This protoplast-based system is capable of localizing and discriminating positive and negative strand viral RNA. In our laboratory, we have used this system to show that the negative strand of Poinsettia mosaic virus (PnMV, a single-stranded, positive-sense RNA virus) localizes in the chloroplasts, whereas the positive strand localizes in the chloroplast and in the cytoplasm. Our prior investigations have shown the localization of the coat protein of PnMV at the periphery of the chloroplast. This collective data suggests that the assembly of the viral replication complex takes place on the chloroplast membranes, subsequently facilitating virus multiplication.