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Related Concept Videos

Viral Mutations00:36

Viral Mutations

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A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
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Gene Evolution - Fast or Slow?02:05

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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
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Mutation, Gene Flow, and Genetic Drift01:09

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In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
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The Evidence for Evolution02:55

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Genetic variations accumulating within populations over generations give rise to biological evolution. Evolutionary changes can result in the formation of novel varieties and entire new species. These changes are responsible for the diverse forms of life inhabiting the planet. The evidence for evolution suggests that all living organisms descended from common ancestors.
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Single Nucleotide Polymorphisms-SNPs01:05

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Related Experiment Video

Updated: Oct 31, 2025

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Following the Dynamics of Structural Variants in Experimentally Evolved Populations

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Evolution, correlation, structural impact and dynamics of emerging SARS-CoV-2 variants.

Austin N Spratt1, Saathvik R Kannan1, Lucas T Woods1,2

  • 1Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.

Computational and Structural Biotechnology Journal
|June 30, 2021
PubMed
Summary

New Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) variants evolved with mutations like D614G and P323L. Their increased transmissibility is complex, influenced by multiple factors beyond simple ACE2 binding affinity.

Keywords:
B.1.1.7B.1.351, P.1, CAL.20CCOVID-19SARS-CoVSARS-CoV-2

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Area of Science:

  • Virology and Molecular Biology
  • Bioinformatics and Structural Analysis
  • Epidemiology

Background:

  • Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infections continue to pose global health challenges.
  • Continuous evolution of RNA viruses, including SARS-CoV-2, leads to the emergence of new variants.
  • Four significant SARS-CoV-2 variants (B.1.1.7, B.1.351, P.1, and CAL.20C) exhibit increased infectiousness and transmissibility.

Purpose of the Study:

  • To investigate the genetic and structural basis of newly identified SARS-CoV-2 variants.
  • To analyze the evolutionary relationships and potential mechanisms driving the increased infectivity and transmissibility of these variants.

Main Methods:

  • Phylogenetic analysis to determine evolutionary relationships among SARS-CoV-2 variants.
  • Bioinformatics and structural analyses of mutations in the Spike protein and RNA polymerase.
  • Comparison of ACE2/Spike complex structures and calculation of free energy changes to assess binding affinity and protein stability.

Main Results:

  • New SARS-CoV-2 variants emerged with pre-existing D614G (Spike protein) and P323L (RNA polymerase) mutations.
  • Phylogenetic analysis revealed distinct ancestral origins for variant groups (CAL.20C/B.1.351 and B.1.1.7/P.1).
  • While N501Y mutation may enhance hydrophobic interactions, other mutations (R417T, K417N) disrupt salt-bridge interactions, indicating complex effects on ACE2 binding. Free energy calculations did not show clear trends in S protein stability.

Conclusions:

  • The evolution of SARS-CoV-2 variants is a complex process influenced by multiple genetic and structural factors.
  • Increased infectivity and transmissibility are not solely attributable to enhanced ACE2 binding affinity.
  • The geographical spread of variants, such as CAL.20C across the USA, highlights ongoing viral dynamics.