Filling the gaps in diagnostics of Pepino mosaic virus and Potato spindle tuber viroid in water and tomato seeds and leaves

Waterborne and seedborne Pepino mosaic virus (Pep MV ) and Potato spindle tuber viroid ( PSTV d) pose serious threats to tomato production due to seed transmission and mechanical transmission, coupled with their long‐term stability outside the host plant. Therefore, rapid and sensitive diagnostic procedures are needed to prevent the spread of these quarantine pathogens. In particular, water and seed contamination are difficult to detect and confirm without efficient concentration methods. This study presents procedures that improve detection of PSTV d from tomato seeds and leaf tissue, and Pep MV from water and tomato leaf tissue. For efficient concentration of Pep MV from water samples, a procedure was optimized using convective interaction media monolithic chromatography columns, which provides concentration by three orders of magnitude. For concentration of PSTV d from seed extracts, an easy‐to‐use and efficient method was developed based on RNA binding to positively charged anion‐exchange resin beads that provides up to 100‐fold more sensitive detection in comparison with procedures without a concentration step. This thus allows confirmation of RT ‐ qPCR results with sequencing of RT ‐ PCR products in samples with low viroid levels. In addition, reverse‐transcription loop‐mediated isothermal amplification assays for detection of PSTV d and Pep MV were optimized and adapted to both laboratory and on‐site testing requirements. This allows rapid detection of these pathogens in crude leaf homogenates, in under 30 min. These procedures of concentration and detection are shown to be efficient and to fill the gaps in diagnostics of Pep MV and PSTV d, especially when these pathogens are present at low levels in difficult matrices such as water and seeds.