Quarantine Regulations and the Impact of Modern Detection Methods

Abstract

Producers worldwide need access to the best plant varieties and cultivars available to be competitive in global markets. This often means moving plants across international borders as soon as they are available. At the same time, quarantine agencies are tasked with minimizing the risk of introducing exotic pests and pathogens along with imported plant material, with the goal to protect domestic agriculture and native fauna and flora. These two drivers, the movement of more plant material and reduced risk of pathogen introduction, are at odds. Improvements in large-scale or next-generation sequencing (NGS) and bioinformatics for data analysis have resulted in improved speed and accuracy of pathogen detection that could facilitate plant trade with reduced risk of pathogen movement. There are concerns to be addressed before NGS can replace existing tools used for pathogen detection in plant quarantine and certification programs. Here, we discuss the advantages and possible pitfalls of this technology for meeting the needs of plant quarantine and certification.

Generic Amplicon Deep Sequencing to Determine Ilarvirus Species Diversity in Australian Prunus

“…Similar concerns have also been raised by other authors regarding metagenomic NGS virus diagnostic sensitivity and what constitutes a virus infection (Martin et al, 2016). Currently, there is no standardized approach to accurately determine what constitutes an extant and active virus infection when analyzing an NGS dataset, especially where varied results and partial virus detection by molecular based methods is concerned, as in the case of Ilarvirus -S1 and Ilarvirus -S2 detection in this study.…”

Plant Disease Diagnosis: Technological Advancements and Challenges

“…At the same time mispriming can result from genetic similarity between different pathogens at primer/probe binding sites. Though, PCR has greater sensitivity than other pest detection methods, as more sensitivity is required for important pathogens like Magnaporthe grisea (Balodi and Kumar, 2015) and reliability of the result depends on sampling methods (Martin et al, 2016). The limitations of the hybridisation approach have largely been overcome by the PCR.…”

“…Detection protocols used for the diagnosis or quarantine measures should be reproducible, repeatable and should have minimum false results. All detection methods should be sensitive to pathogen concentration, genetic variability within a target pathogen population, and similarities between the target and other organisms (Candresse et al, 2014;Martin et al, 2016).…”

A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies

“…In the last few years, however, the advent of next generation sequencing (NGS) has revolutionized the study of plant viruses by providing a powerful alternative for their detection and identification, without any a priori knowledge. NGS technologies are progressively reaching the diagnostic field (Massart et al, 2014), impacting also quarantine regulations (Martin et al, 2016). Their use allows the continuous discovery of new plant viruses, the observation of an increasing diversity of variants for known viruses and the frequent existence of a complex of different viruses.…”