The citrus blight disease, citrus leprosis virus (CiLV), citrus tatter leaf virus (CTLV) and citrus yellow mosaic virus (CYMV), which are not present in the EPPO region, are included in the EPPO A1 List, whereas the citrus bark cracking viroid (CBCVd) and citrus tristeza virus (CTV) non-European isolates (non-EU CTV), and satsuma dwarf virus, are included in the EPPO A2 List. In addition, the genomes of two isolates of the citrus yellow vein clearing virus and the citrus tatter leaf virus, detected in a sample from China, are described.Īccording to the categorization of citrus virus and viroid diseases in the Euro-Mediterranean region, the European and Mediterranean Plant Protection Organization (EPPO) has drawn up two lists of pests whose regulation is relevant for the entire EPPO region or large parts of it. Molecular assays are valuable as confirmation tests of viruses and viroids but many pairs of primers are needed for a full screening and new or non-target pathogens remain undetected. Bioindexing checks each single virus infection but does not differentiate viroids on the Etrog citron indicator and is time-consuming. It also provides effective information on citrus tristeza virus mixed infections despite not being able to identify the non-EU variants of the virus. The results demonstrate that HTS provides a comprehensive phytosanitary status of citrus samples either in single and multiple infections of viruses and viroids. The HTS’s ability to detect other citrus viroids was also evaluated. In this study, we simulated the use of high throughput sequencing (HTS) and the bioinformatic analysis of small interfering RNAs (siRNA) as a pre-screening method to guide bioindexing and molecular detection to enhance the surveillance survey of some key or emerging citrus viruses, such as non-European citrus tristeza virus isolates (non-EU CTV), citrus tatter leaf virus, citrus leprosis virus, citrus yellow mosaic virus, and citrus bark cracking viroid, present in the EPPO lists, and the citrus yellow vein clearing virus. Citrus are affected by many viruses and viroids, some globally widespread and some restricted to particular countries or areas.

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