Phytopathogens are one of the major causes of low agricultural productivity worldwide. Their reasons are new variants of plant infectious diseases resulting from mutation or recombination. The mutation and recombination take place due to heavy use of pesticides and other control measures (Hawkins et al., 2018). Even human mobility across the border causes a temporal and spatial spread of infectious pathogens (Changruenngam et al., 2020). Infectious diseases in plants are caused by microorganisms such as Viruses, Bacteria, Fungi and Nematodes. The rates of their spread have become a major threat to the sustainability of the world food supply (Pimentel et al., 2005; Oerke, 2006; Roberts et al., 2006; Savary et al., 2012). Worldwide, plant-pathogen infections are the main factors limiting crop productivity and incurring economic loss (Massart et al., 2014). Their precise and rapid detection of these phytopathogens is essential for integrated pest management strategies. The detection of plant pathogen is the first step to disease management in greenhouses, open field conditions and at the country borders. Several Nucleic acid Amplification Techniques (NAT) are available for detecting these plant pathogens, among which PCR and quantitative Real Time PCR are readily used worldwide (Rahimi et al., 2021). These methods are cost-effective and trained personnel are available as the COVID-19 pandemic has taught this very well. The challenge comes when there is the requirement for a robust method with almost no processing step, one step detection and point of care (POC) solutions are needed.

Recent development in diagnostic technology based on clustered regularly interspaced short palindromic repeats (CRISPR) is well suited for testing at the site, POC and remote places. The CRISPR technology known for genome editing tool has not been explored for phytopathogen monitoring and detection. Recently CRISPR associated proteins (Cas) such as Cas9, Cas12a, Cas13a and Cas13b are used with the CRISPR system for identifying the target gene sequences (Gootenberg et al., 2018, Harrington et al., 2018, Hu et al., 2021). This group of Cas proteins has emerged to be a cost-effective and miniature diagnostic tool. The characteristic of these enzymes is their highly specific nucleic acid sequence recognition and simultaneous nonspecific cleavage of the reporter nucleic acid. Together this process is termed collateral cleavage activity (Murugan et al., 2017, Aman et al., 2020).

The story of the CRISPR/Cas system begins as early as 1987 when Nakata and his co-worker reported different sets of nucleotide repeats in E. coli during their study in iap gene. Later several similar sequences were reported throughout the archaeal and bacterial strains and were termed as clustered repeats elements. The term CRISPR was first given by Mojica et al., (2000); and Jansen et al., (2002). The clues that these spacers were part of bacteriophage and conjugative plasmids were deciphered by Mojical et al., (2005). CRISPR associated proteins (Cas) is a multidomain endonuclease that makes a double-strand break (DSB) into the target DNA. The DSB is further repaired by host mediated DNA repair mechanism either by non-homologous end joining repair or homologous direct repair. The repair mechanism can be programmed to obtain a desire sequence of DNA at specific location in genome. This mechanism has revolutionized the genome engineering and clinical medicine field. The variants of CRISPR/Cas system are known for their diverse role with innovative application in different domain of Biotechnology.

Naturally, when foreign genetic elements invade a bacterial cell, the protospacer sequence is cleaved and incorporated into the CRISPR array. The recognition and incorporation of protospacer are governed by Cas1 and Cas2 endonucleases. The space sequence enables the host organism to track and identify the invader during the subsequent infections. To facilitate immunity, the CRISPR array is transcribed into a long precursor CRISPR RNA (crRNA). Downstream processing of long precursor crRNA gives rise to a mature guide RNA (gRNA) containing the complementary protospacer sequence of the invader. The gRNA along with the Cas protein complex identifies the target sequence and cleaves it at specific location, finally disrupting the DNA integration onto the host genome. The defence mechanism against virus has wider application in selectively destroying plasmids harbouring multidrug resistance in bacteria (Strich and Chertow 2019). Taking the advantage of Collateral cleavage activity of CRISPR/Cas12 and CRISPR/Cas13, new strategies are being employed for detection of specific nucleic acids. The ability to discriminate single nucleotide mutation in viruses and the flexibility to detect DNA as well as RNA make it suitable for in phytopathogenic virus monitoring.

The use of CRISPR/Cas technology (CCT) enables rapid detection of viral pathogens such as SARS CoV2 (Li et al., 2022), Ebola (Qin et al., 2019) in humans. Information related to phytopathogenic virus detection through CCT is scanty. However, the literature are available where in CCT has been utilized for inducing adaptive immunity in plants against viral disease (Chaparro et al., 2015; Chandrasekharan et al., 2016; Peng et al., 2019; Karmakar et al., 2022).