Detecting virus-carrying Xiphinema spp. as an alternative to Xiphinema identification up to species level in trade

General introduction

Nematodes can in some cases transmit viruses that are not desirable - or are even prohibited - in the plant trade sector. The XiphiVIR project aimed to develop a way to detect these so-called nepoviruses, with the following research questions: 1) Which methods are currently already available to detect (nepo)viruses in plants and nematodes, and which of these offer the best options as a performant generic method to detect the different neopviruses (in subgroups)? 2) Can we provide an optimized and validated method(s) for the detection of viruses in the nematodes, with an emphasis on specificity, sensitivity and robustness of the method? 3) How does this method perform for the detection of viruses in nematodes in the context of an interlaboratory test? Through this interlaboratory test, other parameters such as repeatability and reproducibility were assessed. 4) Is nanopore sequencing (MinION strategy) an alternative option for the future as a rapid method to identify (nepo)viruses in nematode samples? 

Research approach

The first step was to screen current methods for detecting nepoviruses in plants and nematodes, both from the scientific literature, inter-laboratory test reports and from practical experience. The best performing generic methods were selected for the detection of the different subgroups of nepoviruses. Xiphinema spp. were collected and cultures were initiated. Methods were optimized and validated for virus detection in the nematodes, establishing a standardised all-inclusive protocol starting with nematode extraction, RNA extraction, virus detection and virus identification. Through an inter-laboratory test, the methods for virus detection in nematodes were validated. Finally, the potential of MinION nanopore sequencing was investigated in a short initial trial with a small number of selected nematode samples with known virus status.

Relevance/Valorisation

Plant growers and traders benefit from a quick and reliable diagnostic method on the matter. The research about virus detection method in nematodes aimed to lead to a more favourable phytosanitary regulation: Currently, no plants may be imported that contain the species of the X. americanum group recognised as capable of transmitting certain viruses. This could be made more flexible by requiring confirmation of the (real) presence of a nepovirus in the nematode. On the methodological-scientific front, the relevance of this project lay in the fact that its approach could later be applied to other nematode genera that transmit viruses.