Pros and Cons in the Use of Next-Generation Sequencing for Plant Virus Diagnosis

The security of the world’s food supply is of vital importance to everyone. Plant viruses, being a highly contagious pathogen, challenge the security of our food supply. Plant diseases, including viruses, result in the loss of $220 billion in agricultural food crops around the globe. However, viruses, unlike other plant diseases and pests, cannot be eradicated by chemical spraying. Once an individual plant is infected, it will carry that virus throughout its lifespan and can even act as a reservoir for insect vectors to cross-contaminate other plants. Diagnostic tools are useful for the management and control of plant viruses. These tools have evolved over recent decades and are becoming more sensitive and specific for virus detection. Early diagnostic procedures involved mechanical inoculation and grafting of sensitive indicator hosts with infected plants, which took days or even years to produce results. These initial techniques were followed by rapid and specific ELISA and PCR-based methods with various levels of sensitivity. The latest diagnostic procedure is next generation sequencing (NGS), which can detect the “virome” of a single sample without the need for previous sequence information. However, NGS appears to be too expensive and time consuming for routine analyses. The fact that most detected viruses in perennial crops like grapevine are symptomless is a cause for concern among biosecurity staff and growers alike. Here, we are seeking advice from expert colleagues on how to address the issue of the detection of the many viruses causing little or no symptoms in a single host by application of NGS.

Dr. Nuredin Habili
Guest Editor

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