气候变化领域集成服务门户(CCPortal): Ongoing global and regional adaptive evolution of SARS-CoV-2

CCPortal

DOI	10.1073/pnas.2104241118
	Ongoing global and regional adaptive evolution of SARS-CoV-2
	Rochman N.D.; Wolf Y.I.; Faure G.; Mutz P.; Zhang F.; Koonin E.V.
发表日期	2021
ISSN	0027-8424
卷号	118 期号:29
英文摘要	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. © 2021 National Academy of Sciences. All rights reserved.
英文关键词	Ancestral reconstruction; Epistasis; Globalization; Phylogeny; SARS-Cov-2
语种	英语
scopus关键词	coronavirus spike glycoprotein; nucleocapsid phosphoprotein, SARS-CoV-2; phosphoprotein; spike protein, SARS-CoV-2; adaptation; amino acid substitution; classification; diagnosis; epidemiology; epistasis; genetic selection; genetics; human; immune evasion; molecular evolution; mutation; nuclear localization signal; phylogeny; prevention and control; protein domain; vaccination; virology; virus genome; Adaptation, Physiological; Amino Acid Substitution; Coronavirus Nucleocapsid Proteins; COVID-19; COVID-19 Testing; Epistasis, Genetic; Evolution, Molecular; Genome, Viral; Humans; Immune Evasion; Mutation; Nuclear Localization Signals; Phosphoproteins; Phylogeny; Protein Interaction Domains and Motifs; SARS-CoV-2; Selection, Genetic; Spike Glycoprotein, Coronavirus; Vaccination
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/238862
作者单位	National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, United States; Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States; HHMI, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
推荐引用方式 GB/T 7714	Rochman N.D.,Wolf Y.I.,Faure G.,et al. Ongoing global and regional adaptive evolution of SARS-CoV-2[J],2021,118(29).
APA	Rochman N.D.,Wolf Y.I.,Faure G.,Mutz P.,Zhang F.,&Koonin E.V..(2021).Ongoing global and regional adaptive evolution of SARS-CoV-2.Proceedings of the National Academy of Sciences of the United States of America,118(29).
MLA	Rochman N.D.,et al."Ongoing global and regional adaptive evolution of SARS-CoV-2".Proceedings of the National Academy of Sciences of the United States of America 118.29(2021).