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 respectively. Since the first description, the virus has been reported from all continents except Oceania and Antarctica, and has been found infecting both tomato and pepper crops. In October 2019, the Dutch National Plant Protection Organization received a ToBRFV infected tomato sample as part of a generic survey targeting tomato pests. Presence of the virus was verified using Illumina sequencing. 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. Nextstrain was used to visualize these potential connections. By November 2019, 68 companies had been visited of which 17 companies were found to be infected. The 50 ToBRFV genomes from these outbreak locations group in three main clusters, which are hypothesized to represent three original sources. No correlation was found between genotypes, companies and epidemiological traits, and the source(s) of the Dutch ToBRFV outbreak remain unknown. This paper describes a Nextstrain build containing ToBRFV genomes up to and including November 2019. Sharing data with this interactive online tool will enable the plant virology field to better understand and communicate the diversity and spread of this new virus. Organizations are invited to share data or materials for inclusion in the Nextstrain build, which can be accessed at https://nextstrain.nrcnvwa.nl/ToBRFV/20191231.
Highlights
Tomato brown rugose fruit virus belongs to the genus Tobamovirus
Of the 135 samples taken during the follow-up survey, and the two fruit samples intercepted during import inspections, 70 samples produced positive real-time RT-PCR results in one or both assays with Cq values ranging from 5.0 to 30.1 in the coat protein (CP) assay and from 4.5 to 31.2 in the movement protein (MP) assay
An overview of the samples that tested positive with the real-time RT-PCRs is provided in S1 Table
Summary
Tomato brown rugose fruit virus belongs to the genus Tobamovirus. The virus was first described by Salem et al in 2016 after a finding in tomato (Solanum lycopersicum) plants in Jordan [1]. Symptoms appeared to be consistent with a virus that was causing problems in Israel since 2014, with tomato plants showing mosaic patterns on leaves, and occasionally narrowing of leaves and yellow spotted fruits. Tracking Tomato brown rugose fruit virus (ToBRFV) using Nextstrain containing public ToBRFV genomes and the ToBRFV genomes generated in this study dating from November 2014 to November 2019, is available via https://nextstrain.nrcnvwa.nl/ToBRFV/ 20191231
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