CRISPR–Cas systems for plant virus management: detection, surveillance, and host resistance
TL;DR
A focused synthesis integrating CRISPR-mediated host resistance engineering with CRISPR-based diagnostic surveillance within a unified framework for plant virus management is presented, emphasizing their convergence in enabling early detection, real-time surveillance, and targeted intervention across the disease cycle.
Abstract
The CRISPR–Cas system has transformed genome manipulation by enabling precise and programmable modification of genetic material. Initially developed as a genome-editing tool, CRISPR technologies have expanded from fundamental research to applied use across plant, animal, and microbial systems due to their simplicity, accuracy, and versatility. In agriculture, CRISPR–Cas9 has progressed from crop improvement to host-directed strategies conferring resistance against a broad range of plant viruses. Concurrently, the discovery of additional Cas effector proteins, particularly Cas12a and Cas13a, has enabled highly sensitive nucleic acid–based diagnostic platforms supporting rapid, field-deployable pathogen detection. Here, we present a focused synthesis integrating CRISPR-mediated host resistance engineering with CRISPR-based diagnostic surveillance within a unified framework for plant virus management. Unlike previous reviews that treat these domains independently, we emphasize their convergence in enabling early detection, real-time surveillance, and targeted intervention across the disease cycle. Cas12a-based systems, currently the most widely implemented, have been coupled with isothermal amplification and visual readouts for rapid virus detection, whereas Cas13a-based platforms offer direct RNA targeting with potential for simplified workflows, although they remain less developed. We examine key design considerations, performance characteristics, and limitations of these platforms, including challenges related to sensitivity, multiplexing, and field deployment. Finally, we highlight future directions, including vector-based detection, multiplex diagnostics, and integration of CRISPR technologies into scalable surveillance systems. Collectively, this review positions CRISPR-based genome editing and diagnostics as complementary components of a next-generation strategy for plant virus detection, surveillance, and management.