DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, 69120 Heidelberg, Germany.
Biomolecules. 2023 Jan 19;13(2):204. doi: 10.3390/biom13020204.
Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of "hyperparasitism" in the viral world. While only a handful of virophages have been isolated, a vast diversity of virophage-like sequences have been uncovered from diverse metagenomes. Their wide ecological distribution, idiosyncratic infection and replication strategy, ability to integrate into protist and giant virus genomes and potential role in antiviral defense have made virophages a topic of broad interest. However, one limitation for further studies is the lack of clarity regarding the nomenclature and taxonomy of this group of viruses. Specifically, virophages have been linked in the literature to other "virophage-like" mobile genetic elements and viruses, including polinton-like viruses (PLVs), but there are no formal demarcation criteria and proper nomenclature for either group, i.e., virophage or PLVs. Here, as part of the ICTV Virophage Study Group, we leverage a large set of genomes gathered from published datasets as well as newly generated protist genomes to propose delineation criteria and classification methods at multiple taxonomic ranks for virophages 'sensu stricto', i.e., genomes related to the prototype isolates Sputnik and mavirus. Based on a combination of comparative genomics and phylogenetic analyses, we show that this group of virophages forms a cohesive taxon that we propose to establish at the class level and suggest a subdivision into four orders and seven families with distinctive ecogenomic features. Finally, to illustrate how the proposed delineation criteria and classification method would be used, we apply these to two recently published datasets, which we show include both virophages and other virophage-related elements. Overall, we see this proposed classification as a necessary first step to provide a robust taxonomic framework in this area of the virosphere, which will need to be expanded in the future to cover other virophage-related viruses such as PLVs.
噬病毒体是一种小型 dsDNA 病毒，在原生生物（即微真核生物）宿主的共同感染过程中劫持巨型病毒的机器，代表了病毒世界中一种特殊的“超寄生”现象。虽然已经分离出少数噬病毒体，但从各种宏基因组中发现了大量噬病毒样序列。它们广泛的生态分布、特殊的感染和复制策略、能够整合到原生生物和巨型病毒基因组中以及在抗病毒防御中的潜在作用，使得噬病毒体成为一个广泛关注的话题。然而，进一步研究的一个限制是缺乏对该病毒群命名法和分类学的明确性。具体来说，噬病毒体在文献中与其他“噬病毒样”移动遗传元件和病毒（包括多利顿样病毒 (PLV)）有关联，但这两个群体（即噬病毒体或 PLV）都没有正式的划分标准和适当的命名法。在这里，作为 ICTV 噬病毒体研究小组的一部分，我们利用从已发表数据集以及新生成的原生生物基因组中收集的大量基因组，提出了“严格意义上的噬病毒体”（即与原型分离物 Sputnik 和 mavirus 相关的基因组）的多个分类等级的划分标准和分类方法。基于比较基因组学和系统发育分析，我们表明，这组噬病毒体形成了一个有凝聚力的分类群，我们建议将其确立为一个类别，并建议将其细分为四个目和七个科，具有独特的生态基因组特征。最后，为了说明所提出的划分标准和分类方法的应用，我们将其应用于最近发表的两个数据集，结果表明这两个数据集中既包括噬病毒体，也包括其他噬病毒体相关元件。总体而言，我们认为这种分类方法是提供该病毒领域稳健分类框架的必要第一步，未来需要扩展以涵盖其他噬病毒体相关病毒，如 PLV。
