Efficient, Rapid, and Sensitive Detection of Plant RNA Viruses With One-Pot RT-RPA–CRISPR/Cas12a Assay

Rashid Aman, Ahmed Mahas, Tin Marsic, Norhan Hassan, Magdy M. Mahfouz*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

79 Scopus citations


Most viruses that infect plants use RNA to carry their genomic information; timely and robust detection methods are crucial for efficient control of these diverse pathogens. The RNA viruses, potexvirus (Potexvirus, family Alphaflexiviridae), potyvirus (Potyvirus, family Potyviridae), and tobamovirus (Tobamovirus, family Virgaviridae) are among the most economically damaging pathogenic plant viruses, as they are highly infectious and distributed worldwide. Their infection of crop plants, alone or together with other viruses, causes severe yield losses. Isothermal nucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), and others have been harnessed for the detection of DNA- and RNA-based viruses. However, they have a high rate of non-specific amplification and other drawbacks. The collateral activities of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated nuclease Cas systems such as Cas12 and Cas14 (which act on ssDNA) and Cas13 (which acts on ssRNA) have recently been exploited to develop highly sensitive, specific, and rapid detection platforms. Here, we report the development of a simple, rapid, and efficient RT- RPA method, coupled with a CRISPR/Cas12a-based one-step detection assay, to detect plant RNA viruses. This diagnostic method can be performed at a single temperature in less than 30 min and integrated with an inexpensive commercially available fluorescence visualizer to facilitate rapid, in-field diagnosis of plant RNA viruses. Our developed assay provides an efficient and robust detection platform to accelerate plant pathogen detection and fast-track containment strategies.

Original languageEnglish (US)
Article number610872
StatePublished - Dec 17 2020

Bibliographical note

Funding Information:
This research was supported by the King Abdullah University of Science and Technology (KAUST) Competitive Research Grants (CRG8) under Award No. CRG8-URF/1/4026-01-01.

Publisher Copyright:
© Copyright © 2020 Aman, Mahas, Marsic, Hassan and Mahfouz.


  • biosensors
  • CRISPR-Cas12a
  • diagnostics
  • plant virus RNA
  • RT-RPA

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)


Dive into the research topics of 'Efficient, Rapid, and Sensitive Detection of Plant RNA Viruses With One-Pot RT-RPA–CRISPR/Cas12a Assay'. Together they form a unique fingerprint.

Cite this