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EDNA-Water, using deep sequencing and bioinformatics approach for water-borne plant virus detection

Lizbeth Pena Zuniga: Oklahoma State University

<div>Agriculture is adversely affected by viral infections. Water-borne plant viruses: <em>Potexvirus, Tobamovirus</em> and <em>Tombusvirus</em>, have been reported worldwide and a number of them occur in the U.S. Viral infections in irrigated fields or hydroponic crops are not detected until symptoms are evident. Single-virus serological and molecular assays are used for detection. Third-generation sequencing (TGS) offers a broad detection capability to identify multiple unique Nucleic Acid signatures in metagenomic data from a single sample. Electronic probe Diagnostic Nucleic acid Analysis (EDNA) was developed to detect water-borne plant viruses in simulated mock metagenomic sequence databases (MSDs), assembled with reference positive controls and host genome sequences. MSDs were generated using MetaSim and configured to simulate Illumina average read length and error rates. Virus E-probes ranging 20-60 nucleotides lengths were designed using EDNA MiProbe software. MSDs containing host and the target viral genome were used as positive controls. MSDs mimicking single and multiple infections were also generated. EDNA E-probes proved to be a relatively rapid diagnostic method for specific and discrete targeted viruses in water if compared with other TGS bioinformatics analyses. This provides the framework for a new sequence-based diagnosis system to make disease management decisions.</div>