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POSTERS: Disease Detection and Diagnosis II

P-218 - Innovative e-probe design for targeted identification of 10 tomato viruses using EDNA electronic probes.

Tuesday, August 5, 2025
9:30 AM - 10:15 AM HST
Location: Exhibit Hall 3
Abstract Text: This research focuses on developing electronic probes (e-probes) applying the bioinformatic pipeline E-probes Diagnostic Nucleic-acids Analysis integrated with the Microbe Finder platform (EDNA-MiFi®) for detection of 11 tomato-infecting viruses in High-Throughput Sequencing (HTS) data. These include: Orthotospovirus arachinecrosis, Carlavirus pisi, Potexvirus pepini, Potyvirus nicotianainsculpentis, Nepovirus nigranuli, Tobamovirus fructirugosum, Blunervirus solani, Ipomovirus lycopersici, tomato necrotic streak virus (Ilarvirus), Nepovirus lycopersici and Torradovirus marchitezum. The virus selection considered their global economic impact on the horticultural sector. The MiFi® platform includes MiProbeTM, which generates specific e-probes, and MiDetectTM, which matches specific e-probes to accurately and rapidly detect viruses or other phytopathogens in HTS data sets. A large-scale multiple-sequence alignment of all targeted viral pathogens and their close neighbors was performed within this framework using MiProbeTM. The curation of e-probes eliminated non-specific e-probes, and the theoretical limit of detection (LoD) of the curated e-probe sets was predicted in silico. As a result, four sets of raw e-probes with different lengths (30, 40, 60, and 80 nucleotides) were generated for each virus. The LoD varied among virus species, ranging from 8 to 1030 reads. Remarkably, complete or partial genomes of ToBRFV, PepMV, and ToFBV were detected by EDNA-MiFi® in two HTS datasets obtained from tomato samples collected in Italy, and RT-PCR confirmed these findings.