ISSN 1002-1027　　CN 11-2952/G2

### A Preliminary Study to the Origin and Evolution of SARS-CoV

SHE Zhensu, YANG Zhu, OUYANG Zhengqing, ZHU Huaiqiu, WANG Chao, YIN Jianxin

1. Center for Theoretical Biology, State Key Laboratory for Turbulence and Complex Systems, Peking University, Beijing，100871, Email: she@mech.pku.edu.cn
• Received:2003-06-16 Online:2003-11-20 Published:2003-11-20

Abstract: A random substitution model for the study of the evolution of virus genomes, which is able to determine self-consistently the ancestral genome, as well as the substitution matrix have been developed in this paper. The model is applied to analyze the evolution of four coronavirus genomes including the newly discovered SARS-CoV genome. The nucleotide sequences of the most recent common ancestor are determined at a set of synonymous substitution sites of several conserved protein-coding genes, the substitution matrix is found, and the total variation rate of each sequence since the divergent evolution of the common ancestor is determined. The results suggest that the SARS-CoV has undergone an independent evolution path from the beginning of the divergent evolution from the common ancestor (e.g. the SARS-CoV is as old as any other known coronaviruses). It can be speculated that the SARS-CoV may have stayed silent in its natural host long before it spreads the current large-scale epidemic in human.