Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events.
Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events.
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DOI：
10.1038/s41392-022-00992-2
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发表时间：
2022-04-26
影响因子：
39.3
通讯作者：
Zhang Q
中科院分区：
文献类型：
--
作者：
Ou J;Lan W;Wu X;Zhao T;Duan B;Yang P;Ren Y;Quan L;Zhao W;Seto D;Chodosh J;Luo Z;Wu J;Zhang Q
当前的COVID-19大流行是由更具传染性的新出现的欧米克隆变体推动的。由于基因组重组是人类病毒病原体出现和再出现的重要进化机制，因此对突发性变异的持续关注包括可能的重组。在这项研究中，我们发现了两个Omicron主要亚变（BA.1和BA.2）与其他关注变异体（VOCs）和感兴趣变异体（VOIs）之间的多种重组事件，这表明共感染和随后的基因组重组在SARS-CoV-2的持续进化中发挥了重要作用。通过扫描高质量完整的Omicron刺突基因序列，鉴定出BA.1核心突变18个（频率bbbb99 %）， BA.2核心突变27个（比BA.1多9个），其中15个为Omicron特异性突变。BA.1亚变异体与大多数VOCs在刺突蛋白中有9个共同的氨基酸突变（比BA.2多3个），这表明Omicron可能来自这些VOCs的重组起源。BA.1中与α相关的突变比BA.2多3个，并且BA.1在系统发育上比其他变异更接近α。在BA.1的一些显性突变中发现了反向突变（频率为bb0 95%）。最值得注意的是，自2021年11月11日在南非分离的“Deltacron”样Omicron变体中也发现了Delta刺突蛋白的多个特征氨基酸突变，这意味着在Omicron和Delta变体之间发生了重组事件。监测SARS-CoV-2基因组的演变，特别是重组，对于识别病毒属性（包括其表位）的突变至关重要，这可能需要对疫苗进行修改。
The current pandemic of COVID-19 is fueled by more infectious emergent Omicron variants. Ongoing concerns of emergent variants include possible recombinants, as genome recombination is an important evolutionary mechanism for the emergence and re-emergence of human viral pathogens. In this study, we identified diverse recombination events between two Omicron major subvariants (BA.1 and BA.2) and other variants of concern (VOCs) and variants of interest (VOIs), suggesting that co-infection and subsequent genome recombination play important roles in the ongoing evolution of SARS-CoV-2. Through scanning high-quality completed Omicron spike gene sequences, 18 core mutations of BA.1 (frequency >99%) and 27 core mutations of BA.2 (nine more than BA.1) were identified, of which 15 are specific to Omicron. BA.1 subvariants share nine common amino acid mutations (three more than BA.2) in the spike protein with most VOCs, suggesting a possible recombination origin of Omicron from these VOCs. There are three more Alpha-related mutations in BA.1 than BA.2, and BA.1 is phylogenetically closer to Alpha than other variants. Revertant mutations are found in some dominant mutations (frequency >95%) in the BA.1. Most notably, multiple characteristic amino acid mutations in the Delta spike protein have been also identified in the “Deltacron”-like Omicron Variants isolated since November 11, 2021 in South Africa, which implies the recombination events occurring between the Omicron and Delta variants. Monitoring the evolving SARS-CoV-2 genomes especially for recombination is critically important for recognition of abrupt changes to viral attributes including its epitopes which may call for vaccine modifications.
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