Xu Zhongtian, Zheng Luping, Gao Fangluan, Li Yiyuan, Sun Zongtao, Chen Jianping, Zhang Chuanxi, Li Junmin, Wang Xifeng
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
Virus Evol. 2025 Jan 3;11(1):veaf001. doi: 10.1093/ve/veaf001. eCollection 2025.
Advancements in high-throughput sequencing and associated bioinformatics methods have significantly expanded the RNA virus repertoire, including novel viruses with highly divergent genomes encoding "orphan" proteins that apparently lack homologous sequences. This absence of homologs in routine sequence similarity search complicates their taxonomic classification and raises a fundamental question: Do these orphan viral genomes represent viruses? In 2022, an orphan viral genome encoding a large polyprotein was identified in alfalfa () and thrips (), and named Snake River alfalfa virus (SRAV). SRAV was initially proposed as an uncommon flavi-like virus identified in a plant host distantly related to family . Subsequently, another research group showed its common occurrence in alfalfa but challenged its taxonomic position, suggesting it belongs to the family . In this study, a large-scale analysis of 77 publicly available small RNA datasets indicates that SRAV could be detected across various tissues and cultivars of alfalfa, and has a broad geographical distribution. Moreover, profiles of the SRAV-derived small interfering RNAs (vsiRNAs) exhibited typical characteristics of viruses in plant hosts. The evolutionary analysis suggests that SRAV represents a unique class of plant-hosted flavi-like viruses with an unusual genome organization and evolutionary status, distinct from previously identified flavi-like viruses documented to infect plants. The latter shows a close evolutionary relationship to flavi-like viruses primarily found in plant-feeding invertebrates and lacks evidence of triggering host RNA interference (RNAi) responses so far. Moreover, mining the transcriptome shotgun assembly (TSA) database identified two novel viral sequences with a similar genome organization and evolutionary status to SRAV. In summary, our study resolves the disagreement regarding the taxonomic status of SRAV and suggests the potential existence of two distinct clades of plant-hosted flavi-like viruses with independent evolutionary origins. Furthermore, our research provides the first evidence of plant-hosted flavi-like viruses triggering the host's RNAi antiviral response. The widespread occurrence of SRAV underscores its potential ecological significance in alfalfa, a crop of substantial economic importance.
高通量测序及相关生物信息学方法的进步显著扩充了RNA病毒库，其中包括具有高度分化基因组、编码明显缺乏同源序列的“孤儿”蛋白的新型病毒。在常规序列相似性搜索中缺乏同源物使得它们的分类学分类变得复杂，并引发了一个基本问题：这些孤儿病毒基因组代表病毒吗？2022年，在苜蓿（Medicago sativa）和蓟马（Frankliniella occidentalis）中鉴定出一个编码大型多聚蛋白的孤儿病毒基因组，并将其命名为蛇河苜蓿病毒（SRAV）。SRAV最初被提议作为一种在与黄病毒科关系较远的植物宿主中发现的罕见类黄病毒。随后，另一个研究小组表明它在苜蓿中普遍存在，但对其分类地位提出质疑，认为它属于黄病毒科。在本研究中，对77个公开可用的小RNA数据集进行的大规模分析表明，SRAV可在苜蓿的各种组织和品种中检测到，并且具有广泛的地理分布。此外，源自SRAV的小干扰RNA（vsiRNA）图谱表现出植物宿主中病毒的典型特征。进化分析表明，SRAV代表一类独特的植物宿主类黄病毒，具有不寻常的基因组组织和进化地位，与先前鉴定的感染植物的类黄病毒不同。后者与主要在取食植物的无脊椎动物中发现的类黄病毒具有密切的进化关系，并且迄今为止缺乏引发宿主RNA干扰（RNAi）反应的证据。此外，挖掘转录组鸟枪法组装（TSA）数据库鉴定出两个与SRAV具有相似基因组组织和进化地位的新型病毒序列。总之，我们的研究解决了关于SRAV分类地位的分歧，并表明可能存在两个具有独立进化起源的不同类群的植物宿主类黄病毒。此外，我们的研究提供了植物宿主类黄病毒触发宿主RNAi抗病毒反应的首个证据。SRAV的广泛存在凸显了其在苜蓿中的潜在生态意义，苜蓿是一种具有重要经济价值的作物。
