ArticlePeerJ2020
Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function.
Article in PeerJ, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 57 citations in OpenAlex.
- Evolving fitness and immune escape: a retrospective analysis of SARS-CoV-2 spike protein (2020-2024) using protein language model.Frontiers in immunology · 2025Article
- Sequence signatures within the genome of SARS-CoV-2 can be used to predict host source.Microbiology spectrum · 2024Article
- Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations.Virology journal · 2023Article
- Review
- Article
- Tracking the evolution of the SARS-CoV-2 Delta variant of concern: analysis of genetic diversity and selection across the whole viral genome.Frontiers in microbiology · 2023Article
- Sequence Analysis of Hot Spot Regions of Spike and RNA-dependent-RNA polymerase (RdRp) Genes of SARS-CoV-2 in Kerman, Iran.Mediterranean journal of hematology and infectious diseases · 2023Article
- Review
- Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes.Genomics, proteomics & bioinformatics · 2022Article
- Epistasis-Driven Evolution of the SARS-CoV-2 Secondary Structure.Journal of molecular evolution · 2022Article
- Boosting the detection performance of severe acute respiratory syndrome coronavirus 2 test through a sensitive optical biosensor with new superior antibody.Bioengineering & translational medicine · 2022Article
- Promotion of neutralizing antibody-independent immunity to wild-type and SARS-CoV-2 variants of concern using an RBD-Nucleocapsid fusion protein.Nature communications · 2022Article
- Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica.Gene reports · 2022Article
- Statistical modeling of SARS-CoV-2 substitution processes: predicting the next variant.Communications biology · 2022Article
- Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model.Journal of medical virology · 2022Article
- Continuous genomic diversification of long polynucleotide fragments drives the emergence of new SARS-CoV-2 variants of concern.PNAS nexus · 2022Article
- Data-driven platform for identifying variants of interest in COVID-19 virus.Computational and structural biotechnology journal · 2022Article
- A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations.Frontiers in immunology · 2022Review
- RNA structure-altering mutations underlying positive selection on Spike protein reveal novel putative signatures to trace crossing host-species barriers inRNA biology · 2022Article
- Age and sex effects on DNA methylation sites linked to genes implicated in severe COVID-19 and SARS-CoV-2 host cell entry.PloS one · 2022Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. Such tests cannot, however, detect changes in the function of RNA molecules.
methodsHere we apply a test for branch-specific oversubstitution of mutations within narrow windows of the genome without reference to the genetic code.
resultsWe recapitulate the finding that the gene encoding Spike protein has been a target of both purifying and positive selection. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. Homology-directed modeling indicates no change in either Nsp4 or Nsp16 protein structure relative to the most recent common ancestor. These SARS-CoV-2-specific mutations may affect molecular processes mediated by the positive or negative RNA molecules, including transcription, translation, RNA stability, and evasion of the host innate immune system. Our results highlight the importance of considering mutations in viral genomes not only from the perspective of their impact on protein structure, but also how they may impact other molecular processes critical to the viral life cycle.
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