Real-time tracking of Tomato brown rugose fruit virus (ToBRFV) outbreaks in the Netherlands using Nextstrain.
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 in several countries in the Middle East, North-America, and Europe.In October 2019, the Dutch National Reference Centre for plant health received a tomato sample suspected to be infected with ToBRFV. Presence of the virus was confirmed with analysis of plant rRNA depleted Illumina RNAseq data, and a trace-back survey was initiated to 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 stock and scion varieties, seed batches and nurseries, and the source(s) of the Dutch outbreak remain unknown.At the time of publication, the Nextstrain build contains 63 ToBRFV genomes, but the Dutch National Plant Protection Organization 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 important virus. Other organizations are stimulated to share data or materials for inclusion in the Nextstrain build.