An evaluation of nucleic acid-based molecular methods for the detection of plant viruses: a systematic review

Abstract

Precise and timely diagnosis of plant viruses is a prerequisite for the implementation of efficient management strategies, considering factors like globalization of trade and climate change facilitating the spread of viruses that lead to agriculture yield losses of billions yearly worldwide. Symptomatic diagnosis alone may not be reliable due to the diverse symptoms and confusion with plant abiotic stresses. It is crucial to detect plant viruses accurately and reliably and do so with little time. A complete understanding of the various detection methods is necessary to achieve this. Enzyme-linked immunosorbent assay (ELISA), has become more popular as a method for detecting viruses but faces limitations such as antibody availability, cost, sample volume, and time. Advanced techniques like polymerase chain reaction (PCR) have surpassed ELISA with its various sensitive variants. Over the last decade, nucleic acid-based molecular methods have gained popularity and have quickly replaced other techniques, such as serological techniques for detecting plant viruses due to their specificity and accuracy. Hence, this review enables the reader to understand the strengths and weaknesses of each molecular technique starting with PCR and its variations, along with various isothermal amplification followed by DNA microarrays, and next-generation sequencing (NGS). As a result of the development of new technologies, NGS is becoming more and more accessible and cheaper, and it looks possible that this approach will replace others as a favoured approach for carrying out regular diagnosis. NGS is also becoming the method of choice for identifying novel viruses.

Supplementary information: The online version contains supplementary material available at 10.1007/s13337-024-00863-0.

Keywords: Isothermal amplification; Molecular techniques; PCR; Plant virus detection; Virus diagnosis.

Fig. 1

Diagrammatic representation showing transmission of a plant virus from virus infected plant to an uninfected host plant; red dotted lines in the diagram represent the transmission of the virus horizontally, blue dotted lines represent vertical virus transmission

Fig. 2

Diagrammatic representation of various plant virus detection methods

Fig. 3

Diagrammatic representation of various PCR amplification techniques; a conventional PCR amplification of dsDNA target, b amplification of RNA template using reverse transcription PCR (rt-PCR), c fluorescent dye-based real-time PCR (qPCR), d multiplex PCR using multiple DNA targets; S1–S5 signifies DNA of different strains, P signifies strain-specific primers, e nested PCR with target DNA template, f amplification of RNA target using co-operational PCR (Co-PCR)