A Simulation of the Use of High Throughput Sequencing as Pre-Screening Assay to Enhance the Surveillance of Citrus Viruses and Viroids in the EPPO Region

Citrus are affected by many viruses and viroids, some globally widespread restricted to particular countries or areas. In this study, we simulated the use of high throughput sequencing (HTS) bioinformatic analysis small interfering RNAs (siRNA) as a pre-screening method guide bioindexing molecular detection enhance surveillance survey key emerging citrus viruses, such non-European tristeza virus isolates (non-EU CTV), tatter leaf virus, leprosis yellow mosaic bark cracking viroid, present in EPPO lists, vein clearing virus. The HTS’s ability detect other viroids was also evaluated. results demonstrate that HTS provides comprehensive phytosanitary status samples either single multiple infections viroids. It effective information on mixed despite not being able identify non-EU variants Bioindexing checks each infection but does differentiate Etrog citron indicator is time-consuming. Molecular assays valuable confirmation tests pairs primers needed for full screening new non-target pathogens remain undetected . addition, genomes two detected sample from China, described.