EVAg

Dr Luca Ferretti is a plant virologist working for the Council of Agricultural Research and Economics (CREA) at the Research centre for Plant Protection and Certification in Rome, Italy. With a background in environmental and agricultural science, Luca currently works on the development and validation of detection methods for plant pathogens, as well as their application on diagnostics in plant samples. His work involves molecular and epidemiological research on plant pathogenic viruses and phytoplasmas, the implementation of quality standards in Plant Virology, as well as the issuing of technical advice for national and international phytosanitary affairs.

Citrus tristeza virus (CTV, genus Closterovirus) is the most destructive viral pathogen of citrus. Inducing symptoms, such as quick-decline (tristeza) and stem pitting, CTV has caused severe outbreaks in citrus-growing areas all over the world, with an estimated loss of more than 100 million trees in the last century. Recently, previously undetected in Europe, Citrus Tristeza Virus (CTV) strains have appeared in Sardinia. As CTV still represents a high risk for the citrus production in many countries, non-european CTV isolates are categorized as A1 quarantine pests, according to EU Regulation 2019/2072. This implies that the country where they are identified has to control and contain the spreading of the virus. What’s more, these CTV strains are resistance-breaking (RB), which means that the virus replicates and spreads in plants that are otherwise resistant to CTV. It is a way for the virus to bypass plant resistance in order to proliferate. Adding insult to injury, CTV is known for its molecular variability that makes the association of a specific strain to a biological behaviour particularly difficult. As a result, the definitive identification of a CTV strain is complex. In this context, putting in place a robust diagnostics system for the identification of CTV in Italy and, consequently, in Europe is becoming of increasing importance.

As National reference laboratory for virology, CREA - Research centre for Plant Protection and Certification lead the first steps of investigation, performing analyses on 3 samples from asymptomatic four-year-old Citrus reticulata plants, belonging to a variety imported from South Africa that tested positive for CTV non-EU isolates, RB (Resistance breaking) genotype. As a next step, Luca is now implementing the use of Next Generation Sequencing (NGS) for the molecular characterization of the identified CTV strains, using the NGS services offered through EVA. To date, six major CTV phylogenetic groups have been delineated, based on the nucleotide sequences of complete genomes.

‘Our work will generate newly identified full genome sequences of CTV RB isolates that will be made available to the scientific community, in order to better understand their molecular profile and phylogenetic features ‘ Luca points out.

‘Due to the unsurpassed capacity of HTS for high accuracy full genome sequencing of viruses, this tool provides insight into genome diversity among isolates, enabling the rapid and precise determination of the phytosanitary status of samples. This is especially critical when diagnostic bioassays are not available or obtaining results is time consuming, as it can help elucidate the likely risk associated with these isolates’ he concludes.

Text by Semeli Platsaki, PhD