Real-time tracking of Tomato brown rugose fruit virus (ToBRFV) outbreaks in the Netherlands using Nextstrain

Abstract

Tomato brown rugose fruit virus (ToBRFV) is a Tobamovirus that was first observed in 2014 and 2015 on tomato plants in Israel and Jordan causing discolorations and deformation of leaves and fruits. Apart from tomato, damage in pepper fruits has been reported. Since the first description, the virus has been found on all continents except Oceania and Antarctica. In October 2019, the Dutch National Plant Protection Organization received a tomato sample suspected to be infected with ToBRFV as part of an official specific survey of tomato fruit growers in the Netherlands carried out July to October 2019. During the survey 124 companies were visited and inspected for possible ToBRFV symptoms. Of the 47 samples tested, one sample tested positive with ELISA and test plants, which was verified using real-time RT-PCR and Illumina RNAseq data. A follow-up survey was initiated to determine the extent of ToBRFV presence in the Dutch tomato horticulture and identify possible linkages between ToBRFV genotypes, companies and epidemiological traits. We used Nextstrain to visualize these potential connections. Genomic diversity of ToBRFV isolates found in the Netherlands group in three main clusters which are hypothesized to represent three sources. No correlation was found between genotypes, companies and epidemiological traits such as rootstock and scion varieties, seed batches and nurseries, and the source(s) of the Dutch outbreak remain unknown. This paper describes a Nextstrain build containing ToBRFV genomes up to and including November 2019. The NPPO-NL has committed itself to maintain and improve the build. Sharing data with this interactive online tool will enable the regulatory plant virology field to better understand and communicate the diversity and spread of this new virus. Other organizations are stimulated to share data or materials for inclusion in the Nextstrain build, which can be accessed at //40.91.255.14/ToBRFV/20191231.