新型冠状病毒Omicron变异株密码子偏爱性及其进化分析

目的 分析新型冠状病毒(SARS-CoV-2)Omicron变异株各蛋白密码子偏爱性的变化,探索Omicron与其他关切变异株(Variant of Concern,VOC)密码子偏爱性的差异及进化关系。方法 从NCBI SARS-CoV-2数据库中收集标准株Wuhan-Hu-1及5种VOC全基因组编码序列,使用 EMBOSS 子程序CUSP、MEGA 11.0、Codon W等分析软件进行相关密码子偏爱性数据的计算,通过SigmaPlot 14.0、SPSS 22.0等软件进行数据统计分析并绘图。结果 Omicron变异株ENC均值为46.05±7.80,其S、E、ORF1ab、ORF1a蛋白编码基因密码子较其他VOC使用偏性减弱。相比Wuhan-Hu-1,Omicron关键蛋白RSCU与人类基因密码子更接近。基于密码子使用偏性的聚类分析结-果显示,Omicron毒株S、ORF1a蛋白密码子与其他VOC毒株变异最大。结论 新现Omicron变异株S、ORF1ab等关键蛋白的密码子偏爱性减弱,密码子使用模式较Wuhan-Hu-1更接近人类基因,可能是其感染效率增加的原因。

Analysis of the codon usage bias and evolution of the SARS-CoV-2 Omicron variant

This study aimed to analyze the changes in the codon usage of the SARS-CoV-2 Omicron variant, and to explore its evolution and the differences in codon usage with respect to other variants of concern (VOC). The whole genome coding sequences of the standard strain Wuhan-Hu-1 and five VOCs were collected from the NCBI SARS-CoV-2 database, and the relevant codon preference data were calculated with the EMBOSS subprograms CUSP, MEGA 11.0, Codon W and other analytic software. SigmaPlot 14.0 and SPSS 22.0 were used for analysis and plotting. The average ENC value of the Omicron variant strain was 46.05±7.80, and its S, E, ORF1ab and ORF1a protein coding gene codons were less biased than those of other VOCs. The key proteins’ RSCU in the Omicron variant was closer to that of human gene codons than to that of Wuhan-Hu-1 codons. The results of cluster analysis based on codon usage bias showed that the S and ORF1a protein codons of the Omicron strain had greater variation than those in other VOC strains. In conclusion, the codon usage bias of key proteins such as S and ORF1ab in the Omicron variant strain is weaker that in other VOC strains, and the codon usage pattern is closer to that of human genes than to that of Wuhan-Hu-1, thus potentially explaining the strain’s greater infection efficiency.