Tomato brown rugose fruit virus (ToBRFV) Nextstrain build version 3; 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. To gain more insight in the epidemiology of this virus, complete genomes were assembled from Illumina sequence data. Whole-genome phylogenetics was integrated with epidemiological meta-data. Two new clades were defined, one of which displayed a rapid increase relative to the previous version of the Nextstrain build. This rapid increase could be attributed to the illegal application of a supposedly mild isolate of ToBRFV as a cross-protection agent. Sample analyses suggest that both deliberate application or accidental introduction occurred at different tomato production sites. In this report we announce the inclusion of 61 new (near) complete ToBRFV genomes in version three of the Nextstrain build, available from https://nextstrain.nrcnvwa.nl/ToBRFV/20220412.