Ongoing global and regional adaptive evolution of SARS-CoV-2.
Ongoing global and regional adaptive evolution of SARS-CoV-2.
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DOI：
10.1073/pnas.2104241118
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发表时间：
2021-07-20
影响因子：
11.1
通讯作者：
Koonin EV
中科院分区：
文献类型：
--
作者：
Rochman ND;Wolf YI;Faure G;Mutz P;Zhang F;Koonin EV
了解SARS-CoV-2的持续演变对于控制并最终结束大流行至关重要。我们分析了截至2021年1月的30多万个SARS-CoV-2基因组，并证明了病毒的适应性进化主要影响刺突和核衣壳蛋白中的多个位点。选择似乎作用于这些和其他SARS-CoV-2基因的突变组合。病毒的进化伴随着地理区域内和地理区域之间不断的适应性多样化。这种多样化可能会大大延长大流行和疫苗接种运动，其中可能需要变异特异性疫苗。了解严重急性呼吸道综合征冠状病毒2型（SARS-CoV-2）的演变趋势对于控制COVID-19大流行至关重要。我们分析了截至2021年1月可用的超过30万个SARS-CoV-2变异体的高质量基因组序列。结果表明，在大流行期间，SARS-CoV-2的持续进化主要以纯化选择为特征，但一小部分位点似乎在正选择下进化。刺突蛋白的受体结合结构域和与核定位信号（NLS）相关的核衣壳蛋白的区域富含正选择的氨基酸置换。这些替换形成了一个明显上位相互作用的强连接网络，是SARS-CoV-2系统发生中主要分区的特征。在整个大流行期间，每个地理区域内的病毒多样性一直在稳步增长，但对区域对之间的系统发育距离的分析显示，基于树的全球划分和关键突变的出现，有四个不同的时期。在2020年2月结束的快速多样化到区域特异性遗传的最初阶段之后，伴随着D 614 G在刺突蛋白中的传播，发生了一次重大的灭绝事件和全球同质化，于2020年3月结束。跨多个分区的NLS相关变异在3月至7月上升到全球显著水平，这是在区域间多样性停滞期间。最后，从2020年7月开始，多个突变（其中一些已被证明能够逃避抗体）开始出现，与持续的区域多样化有关，这可能表明物种形成。
Understanding the ongoing evolution of SARS-CoV-2 is essential to control and ultimately end the pandemic. We analyzed more than 300,000 SARS-CoV-2 genomes available as of January 2021 and demonstrate adaptive evolution of the virus that affects, primarily, multiple sites in the spike and nucleocapsid protein. Selection appears to act on combinations of mutations in these and other SARS-CoV-2 genes. Evolution of the virus is accompanied by ongoing adaptive diversification within and between geographic regions. This diversification could substantially prolong the pandemic and the vaccination campaign, in which variant-specific vaccines are likely to be required. Understanding the trends in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution is paramount to control the COVID-19 pandemic. We analyzed more than 300,000 high-quality genome sequences of SARS-CoV-2 variants available as of January 2021. The results show that the ongoing evolution of SARS-CoV-2 during the pandemic is characterized primarily by purifying selection, but a small set of sites appear to evolve under positive selection. The receptor-binding domain of the spike protein and the region of the nucleocapsid protein associated with nuclear localization signals (NLS) are enriched with positively selected amino acid replacements. These replacements form a strongly connected network of apparent epistatic interactions and are signatures of major partitions in the SARS-CoV-2 phylogeny. Virus diversity within each geographic region has been steadily growing for the entirety of the pandemic, but analysis of the phylogenetic distances between pairs of regions reveals four distinct periods based on global partitioning of the tree and the emergence of key mutations. The initial period of rapid diversification into region-specific phylogenies that ended in February 2020 was followed by a major extinction event and global homogenization concomitant with the spread of D614G in the spike protein, ending in March 2020. The NLS-associated variants across multiple partitions rose to global prominence in March to July, during a period of stasis in terms of interregional diversity. Finally, beginning in July 2020, multiple mutations, some of which have since been demonstrated to enable antibody evasion, began to emerge associated with ongoing regional diversification, which might be indicative of speciation.
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影响因子：
6.7
作者：
Brueggemann, Angela B.;Pai, Rekha;Beall, Bernard
通讯作者：
Beall, Bernard
影响因子：
5.4
作者：
Holmes, EC
通讯作者：
Holmes, EC
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
DOI：
10.1073/pnas.96.24.13910
发表时间：
1999-11-23
影响因子：
11.1
作者：
Drake, JW;Holland, JJ
通讯作者：
Holland, JJ
DOI：
10.1038/s41576-018-0055-5
发表时间：
2018-12
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
Geoghegan JL;Holmes EC
通讯作者：
Holmes EC