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Prospects and challenges of High Throughput Sequencing for viral pathogen diagnosis and expedited release of quarantined propagative plant material

Maher Al Rwahnih: Foundation Plant Services Facility, University of California

<div>High Throughput Sequencing (HTS) provides a rapid, robust approach for viral plant pathogen identification. Recent studies found HTS superior to conventional methods for detecting viruses of economic significance in grapevine and fruit trees. As such, Foundation Plant Services has an import permit that allows provisional release of propagative plant material that has been HTS screened for pathogens. When HTS is used in conjunction with current conventional methods, growers of certified and registered material can initiate propagative increase and virus elimination programs with new accessions years earlier. While HTS remains a powerful new technology with significant benefits for plant certification and quarantine programs, there are challenges to consider. Since detecting a given pathogen sequence does not mean that pathogen is responsible for the disease, establishing biological significance for viruses identified via HTS analysis is necessary. Biological effects are assessed by graft transmission, completion of Koch’s postulates, spread and distribution studies, and determining the agronomic significance of the symptoms. In addition, efficient sample preparation methods for large scale application and bioinformatics algorithms to efficiently separate pathogen and host sequences must be developed, validated, and standardized across laboratories. No regulatory decision can be made on the importance of a novel virus without information on its biological effects.</div>