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 .

中文翻译：

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使用Nextstrain实时跟踪荷兰番茄褐色皱纹果病毒（ToBRFV）爆发

番茄褐色皱纹水果病毒（ToBRFV）是一种Tobamovirus，于2014年和2015年首次在以色列和约旦的番茄植株上观察到，导致叶片和果实变色和变形。除番茄外，还有辣椒果实受损的报道。自从第一次描述以来，该病毒已在除大洋洲和南极洲以外的所有大洲发现。2019年10月，荷兰国家植物保护组织收到了怀疑被ToBRFV感染的番茄样本，这是对荷兰番茄果农进行的官方专项调查的一部分，该调查于2019年7月至10月进行。在调查中，对124家公司进行了访问和检查。可能的ToBRFV症状。在测试的47个样品中，有一个样品在ELISA和测试植物中呈阳性，已通过实时RT-PCR和Illumina RNAseq数据进行了验证。已开始进行后续调查，以确定荷兰番茄园艺中ToBRFV的存在程度，并确定ToBRFV基因型，公司和流行病学特征之间的可能联系。我们使用Nextstrain可视化了这些潜在的联系。在荷兰组中发现的ToBRFV分离株的基因组多样性分布在三个主要的簇中，假设它们代表了三个来源。在基因型，公司和流行病学特征（例如砧木和接穗品种，种子批次和苗圃）之间未发现相关性，荷兰爆发的来源仍然未知。本文介绍了一个包含ToBRFV基因组的Nextstrain构建，直至2019年11月（含）.NPPO-NL致力于维护和改进该构建。使用此交互式在线工具共享数据将使调节植物病毒学领域能够更好地了解和交流这种新病毒的多样性和传播。鼓励其他组织共享要包含在Nextstrain版本中的数据或材料，可以在//40.91.255.14/ToBRFV/20191231进行访问。