新型冠状病毒基因组的适应性进化研究进展

doi:10.16288/j.yczz.24-231

遗传 ›› 2025, Vol. 47 ›› Issue (2): 211-227.doi: 10.16288/j.yczz.24-231

新型冠状病毒基因组的适应性进化研究进展

张林(), 姚卓成(), 陆剑(), 唐小鹿()

北京大学生命科学学院生物信息学中心，蛋白质与植物基因研究国家重点实验室，北京 100871

收稿日期:2024-08-08 修回日期:2024-09-26 出版日期:2025-02-20 发布日期:2024-11-18
通讯作者: 陆剑，博士，教授，研究方向：基因组学和分子进化。E-mail: luj@pku.edu.cn;
唐小鹿，博士，助理研究员，研究方向：基因组学和分子进化。E-mail: tangxiaolu@pku.edu.cn
作者简介:张林，博士研究生，专业方向：生物信息学。E-mail: allan_z@stu.pku.edu.cn
姚卓成，博士研究生，专业方向：生物信息学。E-mail: yao15705723159@163.com
第一联系人：
张林和姚卓成并列第一作者。
基金资助:
中华人民共和国科学技术部国家重点研发项目(2021YFC2301300);中华人民共和国科学技术部国家重点研发项目(2023YFC3041500);中华人民共和国科学技术部国家重点研发项目(2021YFC0863400)

Current understanding of the adaptive evolution of the SARS-CoV-2 genome

Lin Zhang(), Zhuocheng Yao(), Jian Lu(), Xiaolu Tang()

State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China

Received:2024-08-08 Revised:2024-09-26 Published:2025-02-20 Online:2024-11-18
Supported by:
National Key Research and Development Projects of the Ministry of Science and Technology of the People's Republic of China(2021YFC2301300);National Key Research and Development Projects of the Ministry of Science and Technology of the People's Republic of China(2023YFC3041500);National Key Research and Development Projects of the Ministry of Science and Technology of the People's Republic of China(2021YFC0863400)

摘要/Abstract

摘要：

由严重急性呼吸综合征冠状病毒2 (severe acute respiratory syndrome coronavirus 2，SARS-CoV-2)引起的2019冠状病毒病(coronavirus disease 2019，COVID-19)大流行给人类生命安全和全球经济造成了巨大冲击。SARS-CoV-2基因组的快速变异引起了广泛关注，基因组中几乎每个位点都发生过单核苷酸变异(single nucleotide variants，SNVs)，其中刺突蛋白上的变异在病毒的适应性进化和传播中起着尤为关键的作用。本文综述了SARS-CoV-2及非人类动物中相关冠状病毒的系统发生关系，并深入分析了SARS-CoV-2的谱系划分以及关键氨基酸变异对病毒生物学特性的影响。此外，本文还概述了当前面临的挑战，并展望了深度突变扫描(deep mutational scanning，DMS)结合人工智能方法在预测新冠病毒变异株流行趋势中的广阔应用前景。

关键词: 新冠病毒, 谱系划分, 分子进化, 适应性变异, 流行趋势

Abstract:

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has significantly impacted human life safety and the global economy. The rapid mutation of the SARS-CoV-2 genome has attracted widespread attention, with almost every site in the genome experiencing single nucleotide variants (SNVs). Among these, the mutations in the spike (S) protein are of particular importance, as they play a more critical role in the virus's adaptive evolution and transmission. In this review, we summarize the phylogenetic relationships between SARS-CoV-2 and related coronaviruses in non-human animals, and delves into the lineage classification of SARS-CoV-2 and the impact of key amino acid variations on viral biological characteristics. Furthermore, it outlines the current challenges and looks forward to the promising application of deep mutational scanning (DMS) combined with artificial intelligence methods in predicting the prevalence trends of SARS-CoV-2 variants.

Key words: SARS-CoV-2, lineage designation, molecular evolution, adaptive mutations, pandemic trend

张林, 姚卓成, 陆剑, 唐小鹿. 新型冠状病毒基因组的适应性进化研究进展[J]. 遗传, 2025, 47(2): 211-227.

Lin Zhang, Zhuocheng Yao, Jian Lu, Xiaolu Tang. Current understanding of the adaptive evolution of the SARS-CoV-2 genome[J]. Hereditas(Beijing), 2025, 47(2): 211-227.

图/表 3

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新型冠状病毒基因组的适应性进化研究进展

Current understanding of the adaptive evolution of the SARS-CoV-2 genome

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