Ongoing global and regional adaptive evolution of SARS-CoV-2.
Adaptation, Physiological
/ genetics
Amino Acid Substitution
COVID-19
/ diagnosis
COVID-19 Testing
Coronavirus Nucleocapsid Proteins
/ genetics
Epistasis, Genetic
Evolution, Molecular
Genome, Viral
/ genetics
Humans
Immune Evasion
/ genetics
Mutation
Nuclear Localization Signals
/ genetics
Phosphoproteins
/ genetics
Phylogeny
Protein Interaction Domains and Motifs
/ genetics
SARS-CoV-2
/ classification
Selection, Genetic
Spike Glycoprotein, Coronavirus
/ genetics
Vaccination
SARS-Cov-2
ancestral reconstruction
epistasis
globalization
phylogeny
Journal
Proceedings of the National Academy of Sciences of the United States of America
ISSN: 1091-6490
Titre abrégé: Proc Natl Acad Sci U S A
Pays: United States
ID NLM: 7505876
Informations de publication
Date de publication:
20 07 2021
20 07 2021
Historique:
entrez:
22
7
2021
pubmed:
23
7
2021
medline:
7
8
2021
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 34292871
pii: 2104241118
doi: 10.1073/pnas.2104241118
pmc: PMC8307621
pii:
doi:
Substances chimiques
Coronavirus Nucleocapsid Proteins
0
Nuclear Localization Signals
0
Phosphoproteins
0
Spike Glycoprotein, Coronavirus
0
nucleocapsid phosphoprotein, SARS-CoV-2
0
spike protein, SARS-CoV-2
0
Types de publication
Journal Article
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Intramural NIH HHS
ID : 1DP1 HL141201
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
Organisme : NHLBI NIH HHS
ID : DP1 HL141201
Pays : United States
Organisme : Intramural NIH HHS
ID : 1R01 HG009761
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG009761
Pays : United States
Organisme : NHGRI NIH HHS
ID : RM1 HG006193
Pays : United States
Commentaires et corrections
Type : UpdateOf
Informations de copyright
Copyright © 2021 the Author(s). Published by PNAS.
Déclaration de conflit d'intérêts
The authors declare no competing interest.
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