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Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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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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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Spontaneous and Induced Mutations01:30

Spontaneous and Induced Mutations

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Spontaneous mutations arise infrequently during DNA replication due to errors in the process. A key factor behind these errors is tautomeric shifts in nitrogenous bases, where bases transition from keto to enol forms or amino to imino forms. This shift can alter base-pairing rules, leading to mutations. Additionally, reactive oxygen species (ROS) arising from aerobic metabolism can damage DNA, resulting in depurination (loss of a purine base) or depyrimidination (loss of a pyrimidine base).
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Point and Frameshift Mutations01:30

Point and Frameshift Mutations

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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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Mutations in Microorganisms01:18

Mutations in Microorganisms

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Mutations are heritable changes in an organism’s genome involving alterations in the base sequence of DNA or RNA. These changes can influence cellular processes and phenotypic traits, potentially transforming the unaltered wild type into a mutant form. Such changes, termed forward mutations, are pivotal in shaping the genetic diversity of organisms.RNA viruses exhibit the highest mutation rates due to the absence of robust proofreading mechanisms during genome replication. In contrast,...
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Mutations01:39

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Single Droplet Digital Polymerase Chain Reaction for Comprehensive and Simultaneous Detection of Mutations in Hotspot Regions
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Single Droplet Digital Polymerase Chain Reaction for Comprehensive and Simultaneous Detection of Mutations in Hotspot Regions

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Hotspot Mutations in SARS-CoV-2.

Indrajit Saha1, Nimisha Ghosh2, Nikhil Sharma3

  • 1Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, India.

Frontiers in Genetics
|December 16, 2021
PubMed
Summary
This summary is machine-generated.

This study analyzed 71,038 severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genomes to identify hotspot mutations. Researchers found 45 unique mutations, providing insights into the evolving virus strains and their characteristics.

Keywords:
COVID-19SARS-CoV-2 genomesdeletionsentropyhotspot mutationssubstitution

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Area of Science:

  • Virology
  • Genomics
  • Computational Biology

Background:

  • The global pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) necessitates continuous monitoring of viral evolution.
  • Understanding hotspot mutations is crucial for tracking emerging strains and informing public health strategies.

Purpose of the Study:

  • To identify and analyze hotspot mutations in SARS-CoV-2 genomes.
  • To visualize the evolution of these mutations and their impact on viral characteristics.
  • To assess the functional consequences of mutations on protein structure and binding affinity.

Main Methods:

  • Performed multiple sequence alignment of 71,038 SARS-CoV-2 genomes from 98 countries (January 2020-June 2021) using MAFFT.
  • Conducted phylogenetic analysis to visualize virus evolution and identify hotspot mutations (entropy ≥ 0.3).
  • Utilized PolyPhen-2, I-Mutant 2.0, and SSIPe to analyze functional consequences and binding affinities of key mutations.

Main Results:

  • Identified 45 unique hotspot mutations, including deletions and substitutions, across the global SARS-CoV-2 genome.
  • Detailed analysis of 10,286 Indian sequences revealed 52 unique hotspot mutations.
  • Characterized the evolution of hotspot mutations, including those in variants of concern, and their impact on Spike protein-ACE2 binding.

Conclusions:

  • The study successfully identified and characterized significant hotspot mutations in SARS-CoV-2, contributing to the understanding of viral evolution.
  • The findings highlight the importance of ongoing genomic surveillance for tracking evolving viral strains.
  • Functional analysis of mutations provides insights into potential mechanisms of viral adaptation and infectivity.