云南新现蝙蝠SARS样冠状病毒密码子偏性及其聚类分析

目的 探索云南新现蝙蝠SARS样冠状病毒(SARSr-CoV)密码子偏性及其与SARS冠状病毒(SARS-CoV)及其他地区SARSr-CoV密码子偏性的进化关系。方法 运用Lasergene、EMBOSS、CodonW等生物信息软件,以SARS-CoV为对照,对云南新现蝙蝠SARSr-CoV各蛋白的编码序列进行密码子偏性分析,并基于此与不同时期报道的SARSr-CoV及SARS-CoV进行聚类分析。结果 11株云南新现蝙蝠SARSr-CoV各蛋白有效密码子数目均接近61,密码子偏性较弱;各蛋白偏性的密码子有差异,但均以A、U结尾的密码子为主。ENC-Plot、中性绘图分析与PR2规则分析均提示新现蝙蝠SARSr-CoV在进化过程中主要受到自然选择因素的影响。基于密码子偏性的聚类分析发现,部分云南蝙蝠SARSr-CoV与SARS-CoV关系极为密切。同时,其他云南SARSr-CoV分散聚类于其他地区的SARSr-CoV中。结论 新报道的蝙蝠SARSr-CoV的密码子偏性与SARS-CoV相似度较高,在进化过程中主要受到自然选择因素的影响,跨种传播至人的风险较高。

Codon usage bias studies and cluster analysis on emerging bat SARS-related coronaviruses in Yunnan Province,China

To explore the codon usage bias of the emerging bat SARS-related coronavirus (SARSr-CoV) in Yunnan Province and its evolutionary relationship with SARS-CoVs and other SARSr-CoVs, we used Lasergene, EMBOSS, CodonW and other biological information software to analyze codon usage bias and cluster analysis of the protein coding sequences of the emerging bat SARSr-CoVs in Yunnan Province, SARS-CoVs, and other SARSr-CoVs. Results showed that the number of effective codons (ENC) of these emerging bat SARSr-CoVs proteins were close to 61, their codon usage bias were weak. The Relative Synonymous Codon Usage (RSCU) analysis showed that the preferred codons of each protein were different, but tending to use the codons ending with A or U. In the choice of preferred codons, these new emerging bat SARSr-CoVs were highly consistent with SARS-CoVs. ENC-Plot, neutral plot analysis and PR2 rule analysis indicated that the natural selection factors mainly influenced the evolution of these emerging bat SARSr-CoVs. Clustering analysis based on codon usage bias indicated that the emerging bat SARSr-CoVs were closely related to SARS-CoVs. In addition, these emerging bat SARSr-CoVs were dispersedly clustered with SARSr-CoVs found in other regions. All of these shown that the new emerging bat SARSr-CoVs in Yunnan have higher degree of similarity to SARS-CoVs and have higher risks of cross species transmission. This further indicated that the bat SARSr-CoVs in Yunnan may be the natural gene reservoir of SARS-CoVs and SARSr-CoVs for other regions from the perspective of codon usage preference.