Gao Lei, Qi Ji, Wei Haibin, Sun Yigang, Hao Bailin
1Institute of Theoretical Physics, Chinese Academy of Sciences, 100080 Beijing, China.
2T-Life Research Center, Fudan University, 200433 Shanghai, China.
Chin Sci Bull. 2003;48(12):1170-1174. doi: 10.1007/BF03183929.
Phylogenetic tree of coronaviruses (CoVs) including the human SARS-associated virus is reconstructed from complete genomes by using our newly developed K-string composition approach. The relation of the human SARS-CoV to other coronaviruses, i.e. the rooting of the tree is suggested by choosing an appropriate outgroup. SARS-CoV makes a separate group closer but still distant from G2 (CoVs in mammalian host). The relation between different isolates of the human SARS virus is inferred by first constructing an ultrametric distance matrix from counting sequence variations in the genomes. The resulting tree is consistent with clinic relations between the SARS-CoV isolates. In addition to a larger variety of coronavirus genomes these results provide phylogenetic knowledge based on independent novel methodology as compared to recent phylogenetic studies on SARS-CoV.
通过使用我们新开发的K串组成方法，从完整基因组重建了包括人类SARS相关病毒在内的冠状病毒（CoV）系统发育树。通过选择合适的外类群来表明人类SARS-CoV与其他冠状病毒的关系，即树的根。SARS-CoV形成一个单独的组，与G2（哺乳动物宿主中的冠状病毒）更接近但仍有距离。通过首先从基因组中的计数序列变异构建一个超度量距离矩阵，推断人类SARS病毒不同分离株之间的关系。所得的树与SARS-CoV分离株之间的临床关系一致。与最近关于SARS-CoV的系统发育研究相比，除了更多种类的冠状病毒基因组外，这些结果还基于独立的新方法提供了系统发育知识。
