Lu Yunbiao, Wang Weixiu, Liu Hao, Li Yue, Yan Ge, Franzo Giovanni, Dai Jianjun, He Wan-Ting
School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, People's Republic of China.
Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, Legnaro 35020, PD, Italy.
Int J Biol Macromol. 2023 Oct 1;250:126080. doi: 10.1016/j.ijbiomac.2023.126080. Epub 2023 Aug 2.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is a heavily mutated virus and designated as a variant of concern. To investigate the codon usage pattern of this new variant, we performed mutation and codon bias analysis for Omicron as well as for its sub-lineages BA.1 and BA.2 and compared them with the original SARS-CoV-2 and the Delta variant sequences obtained in this study. Our results indicate that the sub-lineage BA.1 and BA.2 have up to 23 sites of difference on the spike protein, which have minimal impact on function. The Omicron variant and its sub-lineages have similar codon usage patterns and A/U ending codons appear to be preferred over G/C ending codons. The Omicron has a lower degree of codon usage bias in spite of evidence that natural selection, mutation pressure and dinucleotide abundance shape the codon usage bias of Omicron, with natural selection being more significant on BA.2 than the other sub-lineages of Omicron. The codon usage pattern of Omicron variant that we explored provides valid information for a clearer understanding of Omicron and its sub-lineages, which could find application in vaccine development and optimization.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）奥密克戎变种是一种高度变异的病毒，被列为受关注的变种。为了研究这种新变种的密码子使用模式，我们对奥密克戎及其亚谱系BA.1和BA.2进行了突变和密码子偏好性分析，并将它们与本研究中获得的原始SARS-CoV-2和德尔塔变种序列进行了比较。我们的结果表明，亚谱系BA.1和BA.2在刺突蛋白上有多达23个差异位点，对功能的影响最小。奥密克戎变种及其亚谱系具有相似的密码子使用模式，并且A/U结尾的密码子似乎比G/C结尾的密码子更受青睐。尽管有证据表明自然选择、突变压力和二核苷酸丰度塑造了奥密克戎的密码子使用偏好，但奥密克戎的密码子使用偏好程度较低，其中自然选择对BA.2的影响比对奥密克戎的其他亚谱系更为显著。我们探索的奥密克戎变种的密码子使用模式为更清楚地了解奥密克戎及其亚谱系提供了有效信息，这可能在疫苗开发和优化中得到应用。
