Data mining and metagenomic analysis of 277 open reading frame sequences of bipartite RNA viruses of the genus Nepovirus, family Secoviridae, were performed, documenting how challenging it can be to unequivocally assign a virus to a particular species, especially those in subgroups A and C, based on some of the currently adopted taxonomic demarcation criteria. This work suggests a possible need for their amendment to accommodate pangenome information. In addition, we revealed a host-dependent structure of arabis mosaic virus (ArMV) populations at a cladistic level and confirmed a phylogeographic structure of grapevine fanleaf virus (GFLV) populations. We also identified new putative recombination events in members of subgroups A, B and C. The evolutionary specificity of some capsid regions of ArMV and GFLV that were described previously and biologically validated as determinants of nematode transmission was circumscribed in silico. Furthermore, a C-terminal segment of the RNA-dependent RNA polymerase of members of subgroup A was predicted to be a putative host range determinant based on statistically supported higher π (substitutions per site) values for GFLV and ArMV isolates infecting Vitis spp. compared with non-Vitis-infecting ArMV isolates. This study illustrates how sequence information obtained via high-throughput sequencing can increase our understanding of mechanisms that modulate virus diversity and evolution and create new opportunities for advancing studies on the biology of economically important plant viruses.

中文翻译：

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nepoviruses 的宏基因组分析：对宿主范围很重要的 A 亚组成员中基因组区域的多样性、进化和鉴定。

对 277 个开放阅读框序列的 Nepovirus 属， Secoviridae 家族的二分 RNA 病毒进行了数据挖掘和宏基因组分析，记录了明确地将病毒分配给特定物种的挑战，特别是 A 和 C 亚组中的病毒，基于目前采用的一些分类划分标准。这项工作表明可能需要对其进行修改以适应泛基因组信息。此外，我们在分支水平上揭示了阿拉伯花叶病毒 (ArMV) 种群的宿主依赖性结构，并证实了葡萄扇叶病毒 (GFLV) 种群的系统地理结构。我们还在亚组 A、B 和 C 的成员中发现了新的假定重组事件。ArMV 和 GFLV 的一些衣壳区域的进化特异性先前被描述和生物学验证为线虫传播的决定因素，但这些区域的进化特异性被限制在计算机上。此外，基于统计学支持的感染葡萄球菌属的 GFLV 和 ArMV 分离株的较高 π（每个位点的替换）值，预测 A 亚组成员的 RNA 依赖性 RNA 聚合酶的 C 末端片段是推定的宿主范围决定因素。与未感染葡萄球菌的 ArMV 分离株相比。这项研究说明了通过高通量测序获得的序列信息如何增加我们对调节病毒多样性和进化机制的理解，并为推进具有重要经济意义的植物病毒生物学研究创造新机会。