Diagnostic methods for Synchytrium endobioticum, especially for pathotype identification (SENDO)
van Leeuwen, Gerard; van de Vossenberg, Bart; Flath, Kerstin; Przetakiewicz, Jaroslaw; Boerma, Margriet; Heungens, Kurt; Dimitrova, Lidia; Besheva, Ani; Beniusis, Arunas; Adams, Ian; Afanaseko, Olga; Yakovleva, Vera; Schlenzig, Alexandra; Choiseul, James; Bonants, Peter
The main parts of the project consisted of testing new differential cultivars for pathotype identification (bioassays), and the generation of validation data for three molecular S. endobioticum detection and identification assays. As a bioassay, the partners in the project agreed upon the use of the Glynne-Lemmerzahl method to identify pathotypes. In the second year of the project (2013) a test performance study (TPS) was organised. Two different pathotypes were tested, pathotype 6(O1) and 18(T1), and five partners joined in. The cultivars Talent and Logo were chosen to replace cv Miriam in the actual set of differential cultivars (EPPO, 2004). In former research, cv Miriam proved to be less suitable for separating pathotypes 6(O1) and 18(T1), results were inconsistent. As a result, we concluded that cv Talent was the best replacement of cv Miriam in the actual set of differential cultivars. Also, the cultivar Gawin can be added to the set of differentials in a new version of the EPPO Diagnostic Protocol on Synchytrium endobioticum. An international test performance study was organised to generate validation data for three molecular S. endobioticum detection and identification assays: Boogert et al. (2005), van GentPelzer et al. (2010), and Bonants et al. (2015). Two TPS rounds were organised focussing on different test matrices: round 1: wart material, and round 2: winter spore suspensions. When using the assays for detection and identification of S. endobioticum in warted potato tissue, no significant differences were observed for diagnostic sensitivity, diagnostic specificity, overall accuracy, analytical sensitivity and robustness. After applying a Ct cut-off value for the GentPelzer assay, all assays are regarded equal. When using the assays for detection and identification of S. endobioticum in winter spore suspensions, the Boogert and Gent-Pelzer assays significantly outperform the Bonants assay for diagnostic sensitivity and diagnostic specificity. For overall accuracy and analytical sensitivity, the Gent-Pelzer assay significantly outperforms the Boogert and Bonants assays and is regarded as the assay of choice when identifying S. endobioticum winter spores. The tests included in this TPS are regarded fit for purpose for routine testing of wart material and winter spore suspensions with ≥ 500 spores per sample.