Successful disease management relies on rapid and accurate identification of the causal agent. Begomoviruses (family Geminiviridae) cause severe economic losses and pose a serious threat to sustainable agriculture. Here, we describe a clustered regularly interspaced short palindromic repeats (CRISPR)-based nucleic acid detection method utilizing the CRISPR/Cas12a and CRISPR/Cas13a system for begomoviruses used in our laboratory. CRISPR-based diagnostic tools are very precise and sensitive and visual readout-compatible reporters do not need expensive laboratory equipment such as qRT-PCR. The assay detects the targeted begomoviruses in infected plants with high sensitivity and specificity, and can provide highly sensitive and specific detection visual readouts using a simple, low-cost blue light lamp, ideal for on-site use.
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