National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA.
Microbiol Mol Biol Rev. 2020 Mar 4;84(2). doi: 10.1128/MMBR.00061-19. Print 2020 May 20.
Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve with nearly all forms of cellular life. The route of virus replication and protein expression is determined by the viral genome type. Comparison of these routes led to the classification of viruses into seven "Baltimore classes" (BCs) that define the major features of virus reproduction. However, recent phylogenomic studies identified multiple evolutionary connections among viruses within each of the BCs as well as between different classes. Due to the modular organization of virus genomes, these relationships defy simple representation as lines of descent but rather form complex networks. Phylogenetic analyses of virus hallmark genes combined with analyses of gene-sharing networks show that replication modules of five BCs (three classes of RNA viruses and two classes of reverse-transcribing viruses) evolved from a common ancestor that encoded an RNA-directed RNA polymerase or a reverse transcriptase. Bona fide viruses evolved from this ancestor on multiple, independent occasions via the recruitment of distinct cellular proteins as capsid subunits and other structural components of virions. The single-stranded DNA (ssDNA) viruses are a polyphyletic class, with different groups evolving by recombination between rolling-circle-replicating plasmids, which contributed the replication protein, and positive-sense RNA viruses, which contributed the capsid protein. The double-stranded DNA (dsDNA) viruses are distributed among several large monophyletic groups and arose via the combination of distinct structural modules with equally diverse replication modules. Phylogenomic analyses reveal the finer structure of evolutionary connections among RNA viruses and reverse-transcribing viruses, ssDNA viruses, and large subsets of dsDNA viruses. Taken together, these analyses allow us to outline the global organization of the virus world. Here, we describe the key aspects of this organization and propose a comprehensive hierarchical taxonomy of viruses.
病毒和移动遗传元件是与几乎所有形式的细胞生命共同进化的分子寄生虫或共生体。病毒复制和蛋白质表达的途径由病毒基因组类型决定。对这些途径的比较导致了将病毒分为七种“巴尔的摩分类”（BC），这定义了病毒繁殖的主要特征。然而，最近的系统基因组学研究在每个 BC 内以及不同类别之间的病毒之间确定了多个进化联系。由于病毒基因组的模块化组织，这些关系难以简单地表示为血统线，而是形成复杂的网络。病毒特征基因的系统发育分析结合基因共享网络的分析表明，五个 BC 的复制模块（三种 RNA 病毒类和两种逆转录病毒类）从编码 RNA 指导的 RNA 聚合酶或逆转录酶的共同祖先进化而来。真正的病毒通过从不同的细胞蛋白招募作为衣壳亚基和病毒粒子的其他结构成分，从这个祖先在多个独立的场合进化而来。单链 DNA（ssDNA）病毒是一个多系类群，不同的群体通过滚动环复制质粒之间的重组进化，该质粒贡献了复制蛋白，而正链 RNA 病毒贡献了衣壳蛋白。双链 DNA（dsDNA）病毒分布在几个大的单系群中，通过不同结构模块与同样多样化的复制模块的组合而产生。系统基因组学分析揭示了 RNA 病毒和逆转录病毒、ssDNA 病毒以及 dsDNA 病毒的大部分亚组之间进化联系的更精细结构。总的来说，这些分析使我们能够概述病毒世界的整体结构。在这里，我们描述了这个组织的关键方面，并提出了一个全面的病毒层次分类法。
