Vegetables are an important part of human diets but are frequently threatened by a broad range of viral pathogens that cause severe losses in yield, quality, and ultimately, food security. With increasing global trade and climate variability, the incidence of mixed and emerging infections such as begomoviruses, tobamoviruses, and potyviruses in tomato, pepper, cucumber, and other vegetables has surged, necessitating rapid and on-site diagnostic capabilities. While current diagnostic methods, such as qPCR and HTS, are reliable, they remain impractical for routine surveillance in both seed health testing and disease management at the farm level due to high cost, time-intensive workflow, and infrastructure requirements. The recent advances in CRISPR-based diagnostics have provided a revolutionary alternative in the detection of vegetable viruses. Cas9, Cas12, and Cas13 are used on platforms that can detect a range of DNA and RNA viruses with great sensitivity and specificity. Also, the development of one-pot assays that combine amplification and detection in a single reaction, as well as amplification-free technologies that offer visual outputs with fluorescence or lateral-flow assays, is making point-of-care diagnostics more available. Also, the combination of artificial intelligence (AI)/machine learning (ML), microfluidic-based equipment, and portable fluorescence sensors is improving speed, accuracy, and scalability. This chapter provides a systematic review of recent developments in CRISPR diagnostics of vegetable viruses. It puts focus on major technical advances in the Cas9, Cas12, and Cas13 platforms, along with case studies. Also, it addresses the issues and outlook of the translation of these technologies into agricultural biosecurity that could be practised and scaled into tangible tools.

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Revolutionizing Vegetable Virus Detection: A Systematic Review of Cas9, Cas12, and Cas13 Diagnostic Platforms

  • Nilim Kumar Saikia,
  • Arpita Talukdar,
  • Debojit Debnath,
  • Channakeshavaiah Chikkaputtaiah,
  • Shridhar Shivakumar Hiremath

摘要

Vegetables are an important part of human diets but are frequently threatened by a broad range of viral pathogens that cause severe losses in yield, quality, and ultimately, food security. With increasing global trade and climate variability, the incidence of mixed and emerging infections such as begomoviruses, tobamoviruses, and potyviruses in tomato, pepper, cucumber, and other vegetables has surged, necessitating rapid and on-site diagnostic capabilities. While current diagnostic methods, such as qPCR and HTS, are reliable, they remain impractical for routine surveillance in both seed health testing and disease management at the farm level due to high cost, time-intensive workflow, and infrastructure requirements. The recent advances in CRISPR-based diagnostics have provided a revolutionary alternative in the detection of vegetable viruses. Cas9, Cas12, and Cas13 are used on platforms that can detect a range of DNA and RNA viruses with great sensitivity and specificity. Also, the development of one-pot assays that combine amplification and detection in a single reaction, as well as amplification-free technologies that offer visual outputs with fluorescence or lateral-flow assays, is making point-of-care diagnostics more available. Also, the combination of artificial intelligence (AI)/machine learning (ML), microfluidic-based equipment, and portable fluorescence sensors is improving speed, accuracy, and scalability. This chapter provides a systematic review of recent developments in CRISPR diagnostics of vegetable viruses. It puts focus on major technical advances in the Cas9, Cas12, and Cas13 platforms, along with case studies. Also, it addresses the issues and outlook of the translation of these technologies into agricultural biosecurity that could be practised and scaled into tangible tools.