Challenges and Advances in the Detection of Plant Viral Pathogens

Post Entry Quarantine (PEQ) facilities in Australia and New Zealand play pivotal roles in preventing entry of viral pathogens in imported plants that could impact local, national and international markets. Current testing methods of plants held in PEQ rely mainly on biological indexing and specific PCR assays to screen an ever-increasing number of plant viruses and viroids. To enable PEQ plant pathologists to cope with the large volume of imported plants within a competitive timeframe and operational costs, we have implemented a web-based bioinformatics toolkit. This toolkit uses next generation sequencing data from small RNAs which are produced by the plant immune system upon infection with viruses and viroids.. We have implemented a computational framework that enables the surveillance and diagnosis of all known viruses and viroids in a single experiment. To date we have identified a diverse range of viruses in a broad spectrum of quarantined plant material. We envisage that this resource, generated with the support from the Plant Biosecurity CRC, will benefit not only PEQ agencies but also benefit academia and industry stakeholders worldwide.