Molecular phylogeny of coronaviruses including human SARS-CoV

Lei Gao; Ji Qi; Haibin Wei; Yigang Sun; Bailin Hao

doi:10.1007/BF03183929

Molecular phylogeny of coronaviruses including human SARS-CoV

Chin Sci Bull. 2003;48(12):1170-1174. doi: 10.1007/BF03183929.

Authors

Lei Gao^{1

2}, Ji Qi^{1

2}, Haibin Wei^{3

4}, Yigang Sun^{3

4}, Bailin Hao^{2

4}

Affiliations

¹ 1Institute of Theoretical Physics, Chinese Academy of Sciences, 100080 Beijing, China.
² 2T-Life Research Center, Fudan University, 200433 Shanghai, China.
³ 3Graduate School, Zhejiang University, 310027 Hangzhou, China.
⁴ 4Hangzhou Branch, Beijing Genomics Institute, Chinese Academy of Sciences, 310008 Hangzhou, China.

Abstract

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.

Keywords: composition distance; coronavirus; molecular phylogeny; severe acute respiratory syndrome (SARS); ultramericity.