Massive detection of tomato brown rugose fruit virus by high-throughput sequencing (ToViPoRe)

Description

Swiss agriculture is at risk with the emergence of a new viral disease epidemic caused by the Tomato Brown Rugose Fruit Virus (ToBRFV), also know as Jordan virus. This plant disease attacking tomato and peppers can lead to a complete yield loss thus generating significant economic losses for Swiss growers. This highly contagious virus only for plants and not for humans can spread easily over small distances for example via agricultural tools, transport boxes or hands whereas the virus spreads by seeds or young plants over longer distances.

Mainly driven by the rising global trade of plants and seeds, disease outbreaks have been reported already from several countries around the world leading to a pandemic situation. Switzerland is not an exception as the virus has been already identified in 2021 on imported plants. Multiple interceptions on seedlings entering the country also occurred in 2022. Swiss tomato growers are therefore now requesting for an intensification of the diagnostics of this virus during the planting season to minimize the risk. The need for a reliable mass testing diagnostic tool is thus evident but current detection methods are incompatible with this intensification.

Our research project aims at two detection strategies:

the development of a fast, cheap, and specific molecular assay to ease the diagnostics and
the combination of this molecular assay with high-throughput sequencing.

The latter not only allows the unequivocal detection of the virus or closely related tomato viruses, but also the parallel analysis of many samples. To this end, four Swiss research partners are working closely with various stakeholders from research, vegetable sector and enforcement.

Funded by the Federal Office for Agriculture, this two years project has just started in February 2023 and aims at breaking new technological ground in pest and plant pathogen diagnostics. If this proof-of-concept is successful, future diagnostics will benefit greatly from this research project.