Genome Sequence, Phylogenetic Relationship and Host Range of Tomato Brown Rugose Fruit Virus U.S. Isolate

Tomato brown rugose fruit virus (ToBRFV), first identified in 2014 in the Middle East, has caused serious disease outbreaks on greenhouse tomatoes in many countries in Asia, Europe and North America. With its seed-borne, easy mechanical transmission and resistance breaking to the popular Tm-22 gene, ToBRFV could potentially cause serious economic losses to tomato industries worldwide if not managed timely. In the U.S., the first ToBRFV outbreak on tomato plants was identified in 2018 in a greenhouse facility in California. The objective of this study is to characterize the molecular and biological properties of this emerging ToBRFV isolate and to achieve a sensitive, species-specific detection. In the current study, high throughput sequencing is used to obtain a complete genome sequence of the US isolate of ToBRFV. The strong nucleotide sequence identity (99%) to other known ToBRFV isolates around the world suggests a high possibility of sharing the same or similar origin. Comparative evaluation of potential host ranges among tomato-infecting tobamoviruses (ToBRFV, tomato mosaic virus and tomato mottle mosaic virus) showed many similarities, but some unique plant species were also identified for each respective virus. Due to serological cross reactivity among tomato-infecting tobamoviruses, a species-specific real-time RT-PCR was developed, which was shown to provide sensitive and specific detection of ToBRFV.

番茄棕色皱缩果病毒（ToBRFV），首次于2014年在中东地区被发现，已导致亚洲、欧洲和北美多国温室番茄上爆发严重病害。鉴于其种子传播、易于机械传播及对流行Tm-22基因的抗性突破，若不及时管理，ToBRFV有可能对全球番茄产业造成严重经济损失。在美国，加利福尼亚州一温室设施于2018年首次确认番茄植株上的ToBRFV疫情。本研究旨在对这一新兴的ToBRFV分离株进行分子和生物学特性分析，并实现对该病毒的高灵敏度、种属特异性检测。在当前研究中，采用高通量测序技术获取了美国ToBRFV分离株的完整基因组序列。与其他全球已知ToBRFV分离株的强核苷酸序列同源性（99%）表明，存在高度共享相同或相似起源的可能性。对番茄侵染性番茄花叶病毒（ToBRFV、番茄花叶病毒和番茄斑驳花叶病毒）的潜在宿主范围进行对比评估，显示出许多相似之处，但每个病毒分别也识别出一些独特的植物物种。鉴于番茄侵染性番茄花叶病毒之间的血清学交叉反应，开发了一种种属特异性实时反转录聚合酶链反应（real-time RT-PCR），该技术已被证明能够提供对ToBRFV的高灵敏度和特异性检测。