Impact of NGS-based diagnosis on sugarcane quarantine processes

Quarantine processes are essentially performed for detecting known pathogens. In the last decade, Next Generation Sequencing (NGS) approaches have proved to be reliable methods for detecting and identifying both known and unknown viruses. The Cirad Sugarcane Quarantine (CSQ) had set up several pilot projects based on these NGS approaches aiming at evaluating their strength and reliability for sugarcane virus detection. For instance, we have used the so-called VANA (virion-associated nuclear acids) approach to detect viruses from CSQ material and CIRAD Sugarcane collection (CSC) material supplied by the Biological Resources Centre of Tropical Plants INRA-CIRAD. Leaf samples from 300 CSC and 245 CSQ cultivars were processed, respectively. Sequences generated by this study were filtered and assembled using in-house bioinformatics pipelines. Known viruses, such as Sugarcane yellow leaf virus (SCYLV), Sugarcane baciliform virus (SCBV), sugarcane infecting streak viruses (SSV, SSRV, SSEV) and Sugarcane mosaic virus (SCMV) were reliably detected using the VANA approach. In addition, several unknown viruses were found, including viruses from the Geminiviridae and the Tombusviridae families. Another virus belonging to the Ampelovirus genus (Closteroviridae family), which is likely to correspond to Sugarcane mild mosaic virus(SCMMV) described by B.E.L Lockhart et al. was also found in both CSQ and CSC plants. The discovery of these new sugarcane viruses stresses the need to better and dynamically adapt quarantine processes to the emergence of unknown viruses. A full characterization of these novel viruses must be carried out before figuring out whether the detection and sanitation of these novel viruses have to be included within CSQ processes. The full characterization of these novel viruses includes several complementary studies, such as virus genomics, virus epidemiology, virus detection, risk analysis and plant sanitation. This approach is already applied for a novel Mastrevirus (Geminivridae) and will be next extend to the other new detected viruses. (Texte intégral