新型冠状病毒(SARS-CoV-2)的密码子偏爱性分析  

Analysis of SARS-CoV-2 codon usage preference

作　　者：尚方建 石哲芳 王聪 刘奇 SHANG Fang-jian;SHI Zhe-fang;WANG Cong;LIU Qi(Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D(Dali University),Dali 671000,China;Integrated Lab of Pathology Biology,College of Basic Medical,Dali University,Dali 671000,China)

机构地区：[1]云南省昆虫生物医药研发重点实验室(大理大学),大理671000 [2]大理大学基础医学院病原生物学综合实验室,大理671000

出　　处：《中国人兽共患病学报》2021年第1期15-21,38,共8页Chinese Journal of Zoonoses

基　　金：国家自然科学基金资助项目(No.81660337,No.81703573);大理大学创新团队(No.ZKLX2019105)联合资助。

摘　　要：目的分析SARS-CoV-2密码子使用的偏爱性及不同国家和地区流行株的密码子之间的聚类关系。方法使用CodonW、EMBOSS、SigmaPlot14.0、SPSS 22.0等软件分析SARS-CoV-2的密码子偏爱性及其影响因素,在此基础上对不同国家毒株的密码子偏爱性进行聚类分析。结果SARS-CoV-2的各蛋白ENC值在26.60~57.81之间;密码子以A/U结尾(RSCU>1),约占84.98%。ACA、ACU、AGA、AUU、CCU、CUU、GCU、GGU、GUU、UCA、UCU、UUA为多数基因共有的高频密码子,ORF10基因没有偏爱密码子。ENC-Plot、中性分析、PR2绘图分析显示,SARS-CoV-2的各蛋白密码子使用偏爱性受不同因素影响,但是主要因素是自然选择,突变次之。基于密码子偏性的聚类分析发现,来源全球20多个国家和地区的SARS-CoV-2密码子偏爱性有明显差异。部分蛋白的密码子偏爱性聚类分析显示,西班牙、法国、韩国、美国和越南等国家单独聚类。S和ORF1ab的聚类分析显示,中国SARS-CoV-2流行株与美国的流行株的密码子使用偏性分属不同聚类。结论SARS-CoV-2的密码子使用偏性在发生变化,目前主要受环境选择影响。这种改变可能是病毒的跨物种传播造成的,需对其加强动态监控,并对其密码子偏爱性改变的意义进行深入研究。This work aimed to research the codon usage preference of SARS-CoV-2 and the codon clustering relationship of epidemic strains in different countries.CodonW,EMBOSS,SigmaPlot14.0 and SPSS 22.0 were used to analyze the codon usage preference of SARS-CoV-2 and the codon clustering relationship of epidemic strains in different countries.The ENC value of SARS-CoV-2 was found to be between 26.60 and 57.81.Approximately 84.98%of the codon preference involved codons ending with A/U.ACA,ACU,AGA,AUU,CCU,CUU,GCU,GGU,GUU,UCA,UCU,UUA were the high-frequency codons used in most proteins,and ORF10 had no high-frequency codons.ENC-Plot,neutrality and PR2 analyses showed that the codon usage preference of SARS-CoV-2 was affected by different factors.The main factor was natural selection,followed by mutation.According to cluster analysis,the codon preference of SARS-CoV-2 in 20 countries has changed significantly.Spain,France,South Korea,the United States,and Vietnam clustered separately.Cluster analysis of S and ORF1ab indicated that the usage bias of SARS-CoV-2 strains in China and in the United States belonged to different clusters.Thus,the main factor affecting the codon usage preference of SARS-CoV-2 is natural selection.The codon usage preference of SARS-CoV-2 has changed significantly,possibly because of cross-species transmission.Dynamic monitoring of SARS-CoV-2 codon usage must be strengthened,and further study the significance of codon changes is needed.

关 键 词：SARS-CoV-2 密码子偏爱性 聚类分析 

分 类 号：R373.1[医药卫生—病原生物学]