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.

Key words: SARS, coronavirus, evolution distance, most recent common ancestor

摘要： 发展了一种研究基因序列进化的随机替代模型，根据一组从某个最近共同祖先演化而来的若干序列，可以预测此共同祖先序列，并计算随机替代概率矩阵，确定了从祖先序列的各个碱基到进化序列的各个碱基之间的替代概率。将这一模型应用于分析包括SARS冠状病毒在内的4种冠状病毒全基因组的演化规律，确定了在若干较保守的编码蛋白基因序列中同义替代位点的最近共同祖先序列以及分歧进化后的累计同义替代数目。结果表明，SARS病毒和其他几种已知的冠状病毒具有相当的进化历程，但存在不同的进化途径，支持了SARS病毒在造成此次大规模感染人体之前已经历了较长的进化历程的猜测。

关键词: SARS, 冠状病毒, 进化距离, 最近共同祖先