Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant.
Genomic Perspectives on the Emerging SARS-CoV-2 Omicron Variant.
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DOI：
10.1016/j.gpb.2022.01.001
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发表时间：
2022-03
期刊：
影响因子：
--
通讯作者：
Li M
中科院分区：
文献类型：
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作者：
Ma W;Yang J;Fu H;Su C;Yu C;Wang Q;de Vasconcelos ATR;Bazykin GA;Bao Y;Li M
2021年11月26日，世界卫生组织指定了一种新的SARS-CoV-2变异株Omicron（B.1.1.529）。本研究分析了从Omicron感染患者中收集的108份样本的病毒基因组测序数据。首先，我们发现病毒核酸的富集效率由于引物退火区域的突变而降低。其次，与同时循环的其他变体相比，Omicron变体具有过多数量的突变（中位数：62 vs. 45），特别是在Spike基因中。Spike基因的突变导致32个氨基酸残基的改变，比在其他SARS-CoV-2变体中观察到的要多。此外，位于刺突蛋白表面的氨基酸残基的密码子中发生了大量的非同义突变，这可能会影响SARS-CoV-2的复制、感染性和抗原性。第三，在Omicron变体和公共数据库中可获得的其最接近的序列之间存在53个突变。其中许多突变在公共数据库中很少观察到，突变率很低。此外，这些突变之间的连锁不平衡很低，在同一基因组中同时观察到的突变数量有限，这表明Omicron变体将处于与目前流行的变体不同的进化分支。为了提高我们快速发现和追踪新变异来源的能力，必须及时在全球范围内进一步加强基因组监测和数据共享。
A new variant of concern for SARS-CoV-2, Omicron (B.1.1.529), was designated by the World Health Organization on November 26, 2021. This study analyzed the viral genome sequencing data of 108 samples collected from patients infected with Omicron. First, we found that the enrichment efficiency of viral nucleic acids was reduced due to mutations in the region where the primers anneal to. Second, the Omicron variant possesses an excessive number of mutations compared to other variants circulating at the same time (median: 62 vs. 45), especially in the Spike gene. Mutations in the Spike gene confer alterations in 32 amino acid residues, more than those observed in other SARS-CoV-2 variants. Moreover, a large number of nonsynonymous mutations occur in the codons for the amino acid residues located on the surface of the Spike protein, which could potentially affect the replication, infectivity, and antigenicity of SARS-CoV-2. Third, there are 53 mutations between the Omicron variant and its closest sequences available in public databases. Many of these mutations were rarely observed in public databases and had a low mutation rate. In addition, the linkage disequilibrium between these mutations was low, with a limited number of mutations concurrently observed in the same genome, suggesting that the Omicron variant would be in a different evolutionary branch from the currently prevalent variants. To improve our ability to detect and track the source of new variants rapidly, it is imperative to further strengthen genomic surveillance and data sharing globally in a timely manner.