Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review

Abstract

Plant viral diseases are the foremost threat to sustainable agriculture, leading to several billion dollars in losses every year. Many viruses infecting several crops have been described in the literature; however, new infectious viruses are emerging frequently through outbreaks. For the effective treatment and prevention of viral diseases, there is great demand for new techniques that can provide accurate identification on the causative agents. With the advancements in biochemical and molecular biology techniques, several diagnostic methods with improved sensitivity and specificity for the detection of prevalent and/or unknown plant viruses are being continuously developed. Currently, serological and nucleic acid methods are the most widely used for plant viral diagnosis. Nucleic acid-based techniques that amplify target DNA/RNA have been evolved with many variants. However, there is growing interest in developing techniques that can be based in real-time and thus facilitate in-field diagnosis. Next-generation sequencing (NGS)-based innovative methods have shown great potential to detect multiple viruses simultaneously; however, such techniques are in the preliminary stages in plant viral disease diagnostics. This review discusses the recent progress in the use of NGS-based techniques for the detection, diagnosis, and identification of plant viral diseases. New portable devices and technologies that could provide real-time analyses in a relatively short period of time are prime important for in-field diagnostics. Current development and application of such tools and techniques along with their potential limitations in plant virology are likewise discussed in detail.

High-Throughput Sequencing of Small RNAs for the Sanitary Certification of Viruses in Grapevine

“…In the last years, performing RNA-sequencing analysis for determination and discovery of plant viruses in crop plants has become widespread ( Rott et al, 2017 ; Zheng et al, 2017 ; Maliogka et al, 2018 ; Massart et al, 2019 ; Rajamäki et al, 2019 ; Mehetre et al, 2021 ). More specifically, Al Rwahnih et al (2009) pioneered the use of HTS for virus determination in grapevine; and since then, it has proved a valuable tool ( Coetzee et al, 2010 ; Pantaleo et al, 2010 ; Al Rwahnih et al, 2015 ; Maree et al, 2015 ; Jo et al, 2015 ; Czotter et al, 2018 ; Hily et al, 2018 ; Vigne et al, 2018 ).…”

Evolution of Plant Virus Diagnostics Used in Australian Post Entry Quarantine

“…The department has been conducting extensive comparisons of HTS against existing bioassays and PCR techniques used in PEQ since 2014. The expert panel relies on scientific data to clearly demonstrate how the benefits of HTS outweigh the potential risks noted above, as discussed by several authors in recent years from multiple jurisdictions [ 10 , 11 , 12 , 13 , 14 ], as well as findings from research already in progress in DAWE to directly compare the efficacy of HTS to existing PEQ testing platforms.…”

Advanced and Commonly Used Serological Techniques for Detection and Diagnosis of Plant Virus: Review

“…Management or to minimize the disease-induced damage in crops during growth, harvest and postharvest processing, as well as to maximize productivity, and ensure agricultural sustainability, advanced disease detection and prevention in crops are highly important. The prevention measures demand pathogen detection methods of high sensitivity, specificity and reliability (Mehetre et al, 2021).…”