Analysis of the codon usage Bias and evolution of the SARS-CoV-2 omicron variant

ABSTRACT

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+or-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.