Figure - available from: Frontiers in Genetics
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(A) Organization of functional motifs on the polypeptide chain of CPs of the Solemoviridae and Alphaflexiviridae family. The functional motifs at the N-terminal ATPase domain are represented in different colors, whereas the C-terminal end occupies the putative DNA-binding domain. Schematics are drawn approximately to the scale and represent the approximate consensus of representative homologs of RNA viruses infecting plants. (B) Interaction of the ATP molecule with the I-TASSER-predicted atomic model of CP. All the putative ATP catalysis motifs are highlighted in different colors. For details, refer to Kumar et al., 2022.
Source publication
Genome packaging is the crucial step for maturation of plant viruses containing an RNA genome. Viruses exhibit a remarkable degree of packaging specificity, despite the probability of co-packaging cellular RNAs. Three different types of viral genome packaging systems are reported so far. The recently upgraded type I genome packaging system involves...
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Background
Transcriptome data from a plant sample frequently include numerous reads originating from RNA virus genomes that were concurrently isolated during RNA preparation. These high-throughput sequencing reads from the virus can be assembled to form a new sequence for the plant RNA genome.
Methods and results
Here, we identify putative novel m...
Citations
Plant viruses threaten global food security by infecting commercial crops, highlighting the critical need for
efficient virus detection to enable timely preventive measures. Current techniques rely on polymerase chain
reaction (PCR) for viral genome amplification and require laboratory conditions. This review explores the applications
of CRISPR-Cas assisted diagnostic tools, specifically CRISPR-Cas12a and CRISPR-Cas13a/d systems for
plant virus detection and analysis. The CRISPR-Cas12a system can detect viral DNA/RNA amplicons and can be
coupled with PCR or isothermal amplification, allowing multiplexed detection in plants with mixed infections.
Recent studies have eliminated the need for expensive RNA purification, streamlining the process by providing a
visible readout through lateral flow strips. The CRISPR-Cas13a/d system can directly detect viral RNA with
minimal preamplification, offering a proportional readout to the viral load. These approaches enable rapid viral
diagnostics within 30 min of leaf harvest, making them valuable for onsite field applications. Timely identification
of diseases associated with pathogens is crucial for effective treatment; yet developing rapid, specific,
sensitive, and cost-effective diagnostic technologies remains challenging. The current gold standard, PCR technology,
has drawbacks such as lengthy operational cycles, high costs, and demanding requirements. Here we
update the technical advancements of CRISPR-Cas in viral detection, providing insights into future developments,
versatile applications, and potential clinical translation. There is a need for approaches enabling
field plant viral nucleic acid detection with high sensitivity, specificity, affordability, and portability. Despite
challenges, CRISPR-Cas-mediated pathogen diagnostic solutions hold robust capabilities, paving the way for
ideal diagnostic tools. Alternative applications in virus research are also explored, acknowledging the technology’s
limitations and challenges.
