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Related Concept Videos

Viral Mutations00:36

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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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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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Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.
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The endosymbiont theory is the most widely accepted theory of eukaryotic evolution; however, its progression is still somewhat debated. According to the nucleus-first hypothesis, the ancestral prokaryote first evolved a membrane to enclose DNA and form the nucleus. Conversely, the mitochondria-first hypothesis suggests that the nucleus was formed after endosymbiosis of mitochondria.
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John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
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Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
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Updated: Jun 14, 2025

Analysis of Simian Immunodeficiency Virus-specific CD8+ T-cells in Rhesus Macaques by Peptide-MHC-I Tetramer Staining
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Mutational dynamics and phylogenetic insights into monkeypox virus clade I evolution.

Tamizhini Loganathan1, Karthick Vasudevan2, John Fletcher3

  • 1Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014, India.

Computational Biology and Chemistry
|June 12, 2025
PubMed
Summary

Monkeypox virus (MPXV) evolution is a global concern, with clade I re-emerging. This study analyzes MPXV clade evolutionary paths, genetic diversity, and mutations to inform public health strategies.

Keywords:
Clade IMonkeypoxMutation analysisPhylogenomics

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Area of Science:

  • Virology
  • Evolutionary Biology
  • Genomics

Background:

  • Monkeypox virus (MPXV) has transitioned from sporadic outbreaks to a global health threat.
  • The re-emergence of MPXV clade I in 2023, including the first reported case in India, highlights an urgent need for evolutionary insights.
  • Understanding MPXV clade diversity is critical for effective public health interventions.

Purpose of the Study:

  • To investigate the distinct evolutionary trajectories of MPXV clades I, Ia, and Ib.
  • To analyze the genetic diversity, mutational signatures, and phylogenetic relationships among these MPXV clades.
  • To provide data crucial for developing targeted MPXV diagnostics, therapies, and vaccines.

Main Methods:

  • Comparative genomic analysis of MPXV clades I, Ia, and Ib.
  • Examination of mutational profiles, including APOBEC3-type mutations.
  • Time-scaled phylogenetic analysis to reconstruct evolutionary history and divergence times.

Main Results:

  • Clade Ia exhibited a slightly higher frequency of APOBEC3-type mutations (39.88%) than Clade Ib (39.25%).
  • Phylogenetic analysis revealed distinct evolutionary patterns and divergence periods for the clades.
  • Identified variations in mutational profiles potentially linked to host immune pressure and epidemiological factors.

Conclusions:

  • The study elucidates the evolutionary divergence of MPXV clades, offering insights into viral adaptation.
  • Findings are essential for enhancing molecular diagnostics and developing effective vaccines and therapeutics for MPXV.
  • Understanding MPXV evolution is key to managing current and future outbreaks and mitigating global health risks.