ArticleProceedings of the National Academy of Sciences of the United States of America2021
Ongoing global and regional adaptive evolution of SARS-CoV-2.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 175 papers.
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Who cites it
175 citing papers in PubMed.
- From sites to structure to serology: a roadmap for structure-aware molecular evolution of antigenically evolving viruses.Journal of virology · 2026Review
- Global disparities in COVID-19 vaccine coverage associated with trajectories of SARS-CoV-2 adaptation.BMC infectious diseases · 2026Article
- Genomic characterization of SARS-CoV-2 variants circulating in the population of Bangui, Central African Republic (CAR) in 2022.Virology journal · 2026Article
- Stringent selection drives convergence toward omicron-like SARS-CoV-2 receptor-binding motifs.Nature communications · 2026Article
- Multi-epitope vaccine targeting SARS-CoV-2 omicron S and N proteins promotes enhanced immunity: a computational approach.Frontiers in immunology · 2026Article
- Integrated Genomic and Epidemiological Surveillance to Monitor SARS-CoV-2 Variants in Italy: Insights From the JN.1 Case Study (2023-2024).Journal of medical virology · 2026Article
- The emergence of putative epistatic mutations and iSNVs in SARS-CoV-2 XBB.1.16 variants linked with alteration in immunogenic determinants.Frontiers in immunology · 2026Article
- "Fertile" Mutations in SARS-CoV-2 RNA More Frequently Occurred in Hairpin Loops That Determine Virus Evolution.APMIS : acta pathologica, microbiologica, et immunologica Scandinavica · 2025Article
- Unraveling Epistatic Interactions Between Sites Under Drug-Dependent Selection in the Mycobacterium tuberculosis Genome.Molecular biology and evolution · 2025Article
- Dynamic Allostery: Evolution's Double-Edged Sword in Protein Function and Disease.Journal of molecular biology · 2025Review
- Heterogeneous Evolution Among SARS-CoV-2 Genes and Variants of Concern.Journal of medical virology · 2025Article
- Predicting high-fitness viral protein variants with Bayesian active learning and biophysics.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Trans amplifying mRNA vaccine expressing consensus spike elicits broad neutralization of SARS CoV 2 variants.NPJ vaccines · 2025Article
- SARS-CoV-2 point mutations are over-represented in terminal loops of RNA stem-loop structures that can be resolved by Nsp13 helicase in a unique manner with respect to nucleotide dependence.Nucleic acids research · 2025Article
- Prediction of Prospective Mutational Landscape of SARS-CoV-2 Spike ssRNA and Evolutionary Basis of Its Host Interaction.Molecular biotechnology · 2025Article
- Behavior-driven forecasts of neighborhood-level COVID-19 spread in New York City.PLoS computational biology · 2025Article
- JN.1 variants circulating in Italy from October 2023 to April 2024: genetic diversity and immune recognition.BMC infectious diseases · 2025Article
- Combined immunization with SARS-CoV-2 spike and SARS-CoV nucleocapsid protects K18-hACE2 mice but increases lung pathology.NPJ vaccines · 2025Article
- Forecasting framework for dominant SARS-CoV-2 strains before clade replacement using phylogeny-informed genetic distances.Frontiers in microbiology · 2025Article
- A highly divergent sample from a nearly extinct SARS-CoV-2 lineage in a patient with long-term COVID-19.Frontiers in cellular and infection microbiology · 2025Article
115 more citing papers are in PubMed but not listed here.
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Funding
Abstract
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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