Tomato brown rugose fruit virus in the Netherlands: The rise of a novel clade

In the Netherlands, tomato brown rugose fruit virus (ToBRFV) was first identified in tomato crops in 2019. Since then, the National Plant Protection Organization (NPPO-NL) is performing surveys to track and trace this regulated virus aiming for its eradication. According to the EU implementing regulation, samples are tested with real-time RT-PCR for virus detection and confirmation. Additionally, to gain more insight in the epidemiology of this virus, for samples with sufficiently high virus concentration, whole genomes are assembled based on Illumina RNA sequencing data. We integrated whole-genome phylogenetics with meta-data such as host, variety, seed batch, geographic location, but found no associations. This indicates that multiple introductions may have accounted to the outbreaks in the Netherlands. Furthermore, our analyses suggested that that the virus was probably already present in the Netherlands in 2018 or 2017 and had been introduced at least three times (1). Thanks to strict hygiene measures, the majority of infested growers managed to eradicate the virus during crop rotation. Those who did not succeed, remained infested with the same virus sequence type, suggesting elimination was unsuccessful. Intriguingly, in 2021 this pattern changed, when many re-infestations concerned a common novel virus sequence type, indicating a shared source. Therefore, investigations on the epidemiology of ToBRFV will be continued, including the analysis of sequence data available from other countries.
NPPO-NL maintains a publicly available interactive ToBRFV Nextstrain webpage (2) displaying data from our tracing research supplemented with genome sequences that are either retrieved from NCBI GenBank or kindly shared by international partners. This dataset facilitates a better understanding of the global diversity and spread of ToBRFV.

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