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

Abstract

Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time, faces now substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory, and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios.

Using high‐throughput sequencing in support of a plant health outbreak reveals novel viruses in Ullucus tuberosus (Basellaceae)

“…In this respect the framework by Massart et al . () gave a general set of parameters to consider during the initial phases of risk assessment.…”

Application of HTS for Routine Plant Virus Diagnostics: State of the Art and Challenges

“…From that point onwards more familiar techniques such as PCR or ELISA could be used to provide a definitive diagnosis (Massart et al, 2017). For use in front line detection an unambiguous result is however required to avoid, where possible, multiphasic confirmatory testing.…”

Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses

“…They also provide a simple, standardized inoculation mode that improves reproducibility and facilitates host-virus interaction studies and crop breeding; this is especially useful for viruses that cannot be transmitted to host plants by mechanical inoculation of virions. Use of infectious clones is part of a proposed framework for the biological characterization of viral agents discovered by high-throughput sequencing technologies (Massart et al, 2017). In one case, full-length virus clones assembled from 700-year-old DNA samples restored the infectivity of an ancient plant virus identified in a metagenomic survey (Ng et al, 2014).…”