Next-generation sequencing (NGS) as a tool in virus diagnostics: a case study for the identification of new harmful plant viruses in Belgium

Main research question/goal

The aim of this project was to make the non-targeted and therefore very broad 'High Throughput Sequencing' technique, which is emerging in the world of diagnostics, available for plant viruses. As a case study, the researchers focused on Solanaceae (nightshade family), an important plant family to which potato, and also tomato, sweet pepper and aubergine (eggplant) belong. These crops are important in Flemish agricultural production, so the accumulated knowledge about the virus status in Belgium in this plant family has a great impact. The central question, "Which viruses are present in food, ornamental and wild Solanaceae in Belgium?" was answered via high-throughput sequencing. This technique not only gave us a good picture of which viruses were present in the various plant species sampled, but also provided the complete genomes of many of these viruses. New viruses were found for Belgium, new viruses for various host plants, and for some of these new viruses, a risk assessment could be made for the plant health of the crops in which they were found.

Research approach

The technology that was used in this project was high-throughput sequencing (HTS). Several protocols were tested, optimized and standardized in order to identify both known and unknown viruses in each sample. The focus was particularly on the simultaneous analysis of multiple samples ("higher pooling degree"). Based on the genetic information obtained for the viruses that were found, phytosanitary risks were assessed and, if applicable, experiments to study the biological characteristics of certain viruses (for which little knowledge is available, e.g. in terms of vector transfer and host plant range) were set up. This approach allowed us to draw more targeted conclusions about the risk of virus damage in our agricultural and horticultural sector.

Relevance/Valorisation

The scientific relevance is that a significant contribution was made to the EU virome inventory in Solanaceae, and the framework for biological characterisation is being optimized. This project helps to improve risk management policies in plant health (important for the import and export of plant products). The researchers expect that in the short term, validated and internationally ring-tested HTS protocols for potato virus tests will become available for the Belgian, and by extension European, diagnostic labs. For the first time, a detailed "List of viruses infecting Solanaceae in Belgium" will be published. For the international exchange of knowledge, this project can provide preliminary biological characterization data for the newly found viruses. Reporting to EPPO and the EU is carried out.