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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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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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Evolutionary Relationships through Genome Comparisons02:54

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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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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Mismatch Repair01:20

Mismatch Repair

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Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
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Point and Frameshift Mutations01:30

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Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Detecting Potentially Adaptive Mutations from the Parallel and Fixed Patterns in SARS-CoV-2 Evolution.

Cheng-Yang Ji1,2, Na Han1,2, Ye-Xiao Cheng1,2,3

  • 1Institute of Systems Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China.

Viruses
|May 28, 2022
PubMed
Summary
This summary is machine-generated.

Identifying fixed and parallel mutations in SARS-CoV-2, termed paraFix mutations, aids early detection of adaptive mutations. This computational strategy helps track viral evolution for COVID-19 pandemic control.

Keywords:
COVID-19SARS-CoV-2evolutionmutation

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Area of Science:

  • Genomics
  • Virology
  • Computational Biology

Background:

  • Early detection of adaptive mutations is crucial for controlling the COVID-19 pandemic.
  • The rapid increase in SARS-CoV-2 sequencing data presents challenges for identifying adaptive mutations.

Purpose of the Study:

  • To propose a computational strategy for detecting potentially adaptive mutations.
  • To integrate fixed substitution and parallel mutation patterns for enhanced mutation identification.

Main Methods:

  • Developed a computational strategy analyzing fixed and parallel mutation patterns in phylogenetic trajectories.
  • Defined and applied the concept of 'fixed and parallel' (paraFix) mutations.

Main Results:

  • Identified 37 sites in the SARS-CoV-2 spike protein exhibiting paraFix mutations.
  • Confirmed that 70% of identified paraFix mutations were experimentally validated as adaptive.
  • Inferred paraFix mutations up to a month earlier than their regional dominance.

Conclusions:

  • The paraFix mutation concept enables rapid and accurate identification of potentially adaptive mutations.
  • This approach provides valuable insights for COVID-19 pandemic control and prevention strategies.