Genetics-based classification of filoviruses calls for expanded sampling of genomic sequences.
Genetics-based classification of filoviruses calls for expanded sampling of genomic sequences.
复制标题
基于遗传学的丝状病毒分类需要扩大基因组序列的采样。
DOI：
10.3390/v4091425
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发表时间：
2012-09
期刊：
影响因子：
--
通讯作者：
Gorbalenya AE
中科院分区：
文献类型：
--
作者：
Lauber C;Gorbalenya AE
我们最近开发了一种基于基因组的病毒家族分层分类的计算方法（DEmARC）。在DEmARC中，通过对每个分类水平特异性的病毒簇内遗传趋异设计通用的全家族阈值，客观地划分病毒簇。在这里，我们将DEmARC应用于一组56个具有完整基因组序列的丝状病毒，并将所得分类与丝状病毒科的ICTV分类进行比较。我们发现，在总共6个候选分类单元的水平，其中两个对应的科的种和属的行列。在这两个层面上，ICTV正式确认的六个丝状病毒种和两个属，以及Lloviu病毒的第七个暂定种和第三个属的原型，都被复制。DEmARC为这两个级别以及其他四个级别提供了最高可能的支持，这意味着有效分类单元级别的实际数量仍然不确定，丝状病毒种属级别的选择是任意的。根据我们对其他病毒家族的经验，我们得出结论，目前丝状病毒基因组序列的采样需要大大扩大，以解决这些不确定性的框架内基于遗传学的分类。
We have recently developed a computational approach for hierarchical, genome-based classification of viruses of a family (DEmARC). In DEmARC, virus clusters are delimited objectively by devising a universal family-wide threshold on intra-cluster genetic divergence of viruses that is specific for each level of the classification. Here, we apply DEmARC to a set of 56 filoviruses with complete genome sequences and compare the resulting classification to the ICTV taxonomy of the family Filoviridae. We find in total six candidate taxon levels two of which correspond to the species and genus ranks of the family. At these two levels, the six filovirus species and two genera officially recognized by ICTV, as well as a seventh tentative species for Lloviu virus and prototyping a third genus, are reproduced. DEmARC lends the highest possible support for these two as well as the four other levels, implying that the actual number of valid taxon levels remains uncertain and the choice of levels for filovirus species and genera is arbitrary. Based on our experience with other virus families, we conclude that the current sampling of filovirus genomic sequences needs to be considerably expanded in order to resolve these uncertainties in the framework of genetics-based classification.
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