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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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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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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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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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.
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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
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Related Experiment Video

Updated: Jul 6, 2025

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Analysis of SARS-CoV-2 genome evolutionary patterns.

Shubhangi Gupta1, Deepanshu Gupta2, Sonika Bhatnagar1,2

  • 1Department of Biological Sciences and Engineering, Computational and Structural Biology Laboratory, Netaji Subhas University of Technology, Dwarka, New Delhi, India.

Microbiology Spectrum
|January 10, 2024
PubMed
Summary
This summary is machine-generated.

SARS-CoV-2 evolution accelerated post-vaccination, with increased mutation rates and shifts in selection pressure. Omicron showed highest mutation rates, while Delta had the highest dN/dS ratio, impacting viral evolution insights.

Keywords:
SARS-CoV-2evolutiongenomemutation ratesselection pressurevaccination

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Area of Science:

  • Virology
  • Evolutionary Biology
  • Genomics

Background:

  • The SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) pandemic provided unprecedented genomic data for studying viral evolution.
  • Understanding viral evolutionary patterns is crucial for public health interventions, including diagnostics, therapeutics, and pharmacovigilance.

Purpose of the Study:

  • To analyze SARS-CoV-2 evolutionary patterns by comparing mutation rates, selection pressure (dN/dS ratio), and transition/transversion ratios across different time periods and variants.
  • To investigate the impact of vaccination on viral evolution across seven countries from January 2020 to December 2022.

Main Methods:

  • Collected and classified SARS-CoV-2 genome sequences into pre-vaccination, post-vaccination, and recent phases.
  • Compared mutation rates, dN/dS ratios, and Ti/Tv ratios across phases and variants.
  • Utilized Graphpad unpaired t-test for statistical significance testing.

Main Results:

  • Genomic mutation rates increased significantly post-vaccination and in the recent period across all studied countries.
  • Specific genes (NSP3, S, N, NSP12b, NSP4) showed notable increases in mutation rates after vaccination.
  • Selection pressure shifted from purifying to neutral selection post-vaccination, with variations observed across different genes and variants (Omicron, Delta).

Conclusions:

  • Vaccination and time significantly influenced SARS-CoV-2 evolution, leading to increased mutation rates and altered selection pressures.
  • The study provides a large-scale, time-course analysis of genomic and protein-wise mutation patterns, offering critical insights for SARS-CoV-2 management.
  • Findings underscore the importance of continuous genomic surveillance for understanding and combating evolving viral threats.