SHANG Fang-jian1, 2, SHI Zhe-fang1, 2, WANG Cong1, 2, LIU Qi1, 2
1.Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D (Dali University),Dali 671000,China; 2. Integrated Lab of Pathology Biology, College of Basic Medical, Dali University,Dali 671000,China;
Abstract：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.
尚方建, 石哲芳, 王聪, 刘奇. 新型冠状病毒(SARS-CoV-2)的密码子偏爱性分析[J]. 中国人兽共患病学报, 2021, 37(1): 15-21.
SHANG Fang-jian, SHI Zhe-fang, WANG Cong, LIU Qi. Analysis of SARS-CoV-2 codon usage preference. Chinese Journal of Zoonoses, 2021, 37(1): 15-21.
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