Weng Shenghui, Shang Jingzhe, Cheng Yexiao, Zhou Hangyu, Ji Chengyang, Yang Rong, Wu Aiping
Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China.
Suzhou Institute of Systems Medicine, Suzhou 215123, China.
Biosaf Health. 2022 Jun;4(3):171-178. doi: 10.1016/j.bsheal.2022.04.004. Epub 2022 Apr 25.
The recently emerged Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has quickly spread around the world. Although many consensus mutations of the Omicron variant have been recognized, little is known about its genetic variation during its transmission in the population. Here, we comprehensively analyzed the genetic differentiation and diversity of the Omicron variant during its early outbreak. We found that Omicron achieved more structural variations, especially deletions, on the SARS-CoV-2 genome than the other four variants of concern (Alpha, Beta, Gamma, and Delta) in the same timescale. In addition, the Omicron variant acquired, except for 50 consensus mutations, seven great new non-synonymous nucleotide substitutions during its spread. Three of them are on the S protein, including S_A701V, S_L1081V, and S_R346K, which belong to the receptor-binding domain (RBD). The Omicron BA.1 branch could be divided into five divergent groups spreading across different countries and regions based on these seven novel mutations. Furthermore, we found that the Omicron variant possesses more mutations related to a faster transmission rate than the other SARS-CoV-2 variants by assessing the relationship between the genetic diversity and transmission rate. The findings indicated that more attention should be paid to the significant genetic differentiation and diversity of the Omicron variant for better disease prevention and control.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）最近出现的奥密克戎变种已迅速在全球传播。尽管奥密克戎变种的许多共有突变已被识别，但其在人群传播过程中的基因变异情况却知之甚少。在此，我们全面分析了奥密克戎变种在早期爆发期间的基因分化和多样性。我们发现，在相同时间尺度上，奥密克戎在SARS-CoV-2基因组上实现了比其他四种关注变种（阿尔法、贝塔、伽马和德尔塔）更多的结构变异，尤其是缺失。此外，奥密克戎变种在传播过程中除了50个共有突变外，还获得了7个新的非同义核苷酸替换。其中3个位于S蛋白上，包括S_A701V、S_L1081V和S_R346K，它们属于受体结合域（RBD）。基于这7个新突变，奥密克戎BA.1分支可分为五个不同的组，分布在不同的国家和地区。此外，通过评估基因多样性与传播率之间的关系，我们发现奥密克戎变种比其他SARS-CoV-2变种拥有更多与更快传播率相关的突变。这些发现表明，为了更好地预防和控制疾病，应更加关注奥密克戎变种显著的基因分化和多样性。
