Integrating AI and CRISPR Cas13a for rapid detection of tomato brown rugose fruit virus

The Tomato Brown Rugose Fruit Virus (ToBRFV) has recently emerged as a serious threat to global tomato production, underscoring the need for rapid and sensitive diagnostic tools. Here, we present an AI-driven CRISPR-Cas13a pipeline for designing crRNAs with high specificity to enable the detection o...

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Bibliographic Details
Published in:Scientific reports Vol. 15; no. 1; pp. 25422 - 15
Main Authors: Karimi, Marzieh, Ghorbani, Abozar, Niazi, Ali, Rostami, Mahsa, Tahmasebi, Ahmad
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 14.07.2025
Nature Publishing Group
Nature Portfolio
Subjects:
631/208
631/326
631/337
631/61
Automation
Bioinformatics
Cas13
Computational Biology - methods
Conserved sequence
CRISPR
CRISPR-Cas Systems
CrRNA
Design
Enzymes
Fruits
Genomes
Humanities and Social Sciences
Machine learning
multidisciplinary
Pathogens
Plant Diseases - virology
Plant viruses
Plant Viruses - genetics
Plant Viruses - isolation & purification
Rapid detection
RNA, Viral - genetics
Science
Science (multidisciplinary)
Sensitive diagnostic
Solanum lycopersicum - virology
ToBRFV
Tomatoes
Viral infections
Viruses
ToBRFV
Cas13
CrRNA
Sensitive diagnostic
Rapid detection
ISSN:2045-2322, 2045-2322
Online Access:Get full text
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Summary:The Tomato Brown Rugose Fruit Virus (ToBRFV) has recently emerged as a serious threat to global tomato production, underscoring the need for rapid and sensitive diagnostic tools. Here, we present an AI-driven CRISPR-Cas13a pipeline for designing crRNAs with high specificity to enable the detection of ToBRFV. A computational pipeline that retrieves viral sequences, aligns them in multiple sequence alignments, analyzes their conservation, and screens for off-targets—all coupled with machine learning to optimize crRNA sequences. Experimentally validated crRNAs were evaluated with a fluorescence-based Cas13a assay and showed better sensitivity than RT-PCR, RT-qPCR, and RT-LAMP. By the CRISPR-Cas13a system, ToBRFV was detected at 1:200 (1 ng/µL) dilutions, which performed superior to conventional methods. Integrating bioinformatics with experimental workflows, this pipeline provides a powerful framework for rapid diagnostics that can be deployed in the field, addressing significant challenges in plant virus surveillance and management.
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ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-025-11405-z