Tian Zhongshuai, Hu Tao, Holmes Edward C, Ji Jingkai, Shi Weifeng
Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 6699 Qingdao Road, Ji'nan 250117, China.
Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqingnanlu, Shanghai 200025, China.
Virus Evol. 2024 Jul 25;10(1):veae059. doi: 10.1093/ve/veae059. eCollection 2024.
RNA viruses are characterized by a broad host range and high levels of genetic diversity. Despite a recent expansion in the known virosphere following metagenomic sequencing, our knowledge of the species rank genetic diversity of RNA viruses, and how often they are misassigned and misclassified, is limited. We performed a clustering analysis of 7801 RNA-directed RNA polymerase (RdRp) sequences representing 1897 established RNA virus species. From this, we identified substantial genetic divergence within some virus species and inconsistency in RNA virus assignment between the GenBank database and The International Committee on Taxonomy of Viruses (ICTV). In particular, 27.57% virus species comprised multiple virus operational taxonomic units (vOTUs), including , and , with each having over 100 vOTUs. In addition, the distribution of average amino acid identity between vOTUs within single assigned species showed a relatively low threshold: <90% and sometimes <50%. However, when only exemplar sequences from virus species were analyzed, 1889 of the ICTV-designated RNA virus species (99.58%) were clustered into a single vOTU. Clustering of the RdRp sequences from different virus species also revealed that 17 vOTUs contained two distinct virus species. These potential misassignments were confirmed by phylogenetic analysis. A further analysis of average nucleotide identity (ANI) values ranging from 70% to 97.5% revealed that at an ANI of 82.5%, 1559 (82.18%) of the 1897 virus species could be correctly clustered into one single vOTU. However, at ANI values >82.5%, an increasing number of species were clustered into two or more vOTUs. In sum, we have identified some inconsistency and misassignment of the RNA virus species based on the analysis of RdRp sequences alone, which has important implications for the development of an automated RNA virus classification system.
RNA病毒的特点是宿主范围广泛且遗传多样性水平高。尽管宏基因组测序使已知病毒圈最近有所扩展，但我们对RNA病毒物种水平的遗传多样性以及它们被错误分类和错误归属的频率的了解仍然有限。我们对代表1897种已确定的RNA病毒物种的7801个RNA依赖性RNA聚合酶（RdRp）序列进行了聚类分析。由此，我们发现一些病毒物种内存在显著的遗传差异，以及GenBank数据库与国际病毒分类委员会（ICTV）之间在RNA病毒归属上的不一致。特别是，27.57%的病毒物种包含多个病毒操作分类单元（vOTU），包括[此处原文缺失具体物种信息]，每个都有超过100个vOTU。此外，单个指定物种内vOTU之间的平均氨基酸同一性分布显示出相对较低的阈值：<90%，有时<50%。然而，当仅分析病毒物种的代表性序列时，ICTV指定的1889种RNA病毒物种（99.58%）被聚类到单个vOTU中。来自不同病毒物种的RdRp序列聚类还表明，17个vOTU包含两种不同的病毒物种。系统发育分析证实了这些潜在的错误归属。对70%至97.5%的平均核苷酸同一性（ANI）值的进一步分析表明，在ANI为82.5%时，1897种病毒物种中的1559种（82.18%）可以正确聚类到单个vOTU中。然而，在ANI值>82.5%时，越来越多的物种被聚类到两个或更多的vOTU中。总之，我们仅基于RdRp序列分析就发现了RNA病毒物种的一些不一致和错误归属情况，这对自动化RNA病毒分类系统的开发具有重要意义。
