Department of Laboratory, Jining Center for Disease Control and Prevention, Jining, China.
Department of Laboratory, Rencheng Center for Disease Control and Prevention, Jining, China.
BMC Genomics. 2024 Apr 17;25(1):378. doi: 10.1186/s12864-024-10246-w.
This study aims to analyze the molecular characteristics of the novel coronavirus (SARS-CoV-2) Omicron variant BA.2.76 in Jining City, China.
Whole-genome sequencing was performed on 87 cases of SARS-CoV-2 infection. Evolutionary trees were constructed using bioinformatics software to analyze sequence homology, variant sites, N-glycosylation sites, and phosphorylation sites.
All 87 SARS-CoV-2 whole-genome sequences were classified under the evolutionary branch of the Omicron variant BA.2.76. Their similarity to the reference strain Wuhan-Hu-1 ranged from 99.72 to 99.74%. In comparison to the reference strain Wuhan-Hu-1, the 87 sequences exhibited 77-84 nucleotide differences and 27 nucleotide deletions. A total of 69 amino acid variant sites, 9 amino acid deletions, and 1 stop codon mutation were identified across 18 proteins. Among them, the spike (S) protein exhibited the highest number of variant sites, and the ORF8 protein showed a Q27 stop mutation. Multiple proteins displayed variations in glycosylation and phosphorylation sites.
SARS-CoV-2 continues to evolve, giving rise to new strains with enhanced transmission, stronger immune evasion capabilities, and reduced pathogenicity. The application of high-throughput sequencing technologies in the epidemic prevention and control of COVID-19 provides crucial insights into the evolutionary and variant characteristics of the virus at the genomic level, thereby holding significant implications for the prevention and control of the COVID-19 pandemic.
本研究旨在分析中国济宁市新型冠状病毒（SARS-CoV-2）奥密克戎变异株 BA.2.76 的分子特征。
对 87 例 SARS-CoV-2 感染病例进行全基因组测序。使用生物信息学软件构建进化树，分析序列同源性、变异位点、N-糖基化位点和磷酸化位点。
87 例 SARS-CoV-2 全基因组序列均归类于奥密克戎变异株 BA.2.76 的进化分支。与参考株武汉-Hu-1 的相似度为 99.72%至 99.74%。与参考株武汉-Hu-1 相比，87 个序列显示出 77-84 个核苷酸差异和 27 个核苷酸缺失。在 18 种蛋白中，共发现 69 个氨基酸变异位点、9 个氨基酸缺失和 1 个终止密码子突变。其中，刺突（S）蛋白的变异位点最多，ORF8 蛋白出现 Q27 终止突变。多个蛋白的糖基化和磷酸化位点发生变化。
SARS-CoV-2 持续进化，产生了传播力更强、免疫逃逸能力更强、致病性更低的新株。高通量测序技术在 COVID-19 疫情防控中的应用，为病毒在基因组水平上的进化和变异特征提供了重要的认识，对 COVID-19 大流行的防控具有重要意义。
