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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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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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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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Updated: Jul 18, 2025

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples
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SARS-CoV-2 genomic characterization and evolution in China.

Peng Zhang1, Dongzi Liu2, Lei Ji1

  • 1Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China.

Heliyon
|August 28, 2023
PubMed
Summary

This study analyzed SARS-CoV-2 genomic variations in China during nonpharmaceutical interventions (NPIs). Mutations in spike and nucleocapsid genes suggest increased contagiousness, impacting epidemic control strategies.

Keywords:
ChinaEvolutionGenomic characterizationNonpharmaceutical interventionSARS-CoV-2

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Area of Science:

  • Virology
  • Genomics
  • Epidemiology

Background:

  • The COVID-19 pandemic, caused by SARS-CoV-2, spread globally due to high contagiousness.
  • Mutations within the SARS-CoV-2 genome occurred during viral spread.
  • China implemented nonpharmaceutical interventions (NPIs) to control COVID-19 outbreaks.

Purpose of the Study:

  • To understand the evolution and genomic variation of SARS-CoV-2 in China under NPI policy.
  • To analyze SARS-CoV-2 genomic data collected between 2019 and 2022.
  • To provide a scientific basis for understanding NPI control effects.

Main Methods:

  • Downloaded 524 SARS-CoV-2 sequences from GISAID (2019-2022).
  • Performed time-scaled evolutionary analysis to cluster sequences.
  • Identified mutation sites and amino acid deletions.

Main Results:

  • Sequences clustered into three groups (A-C), with Groups B and C predominating around 2020.
  • Group A mainly comprised G variants isolated from multiple regions.
  • 191 mutation sites and 30 amino acid deletions were identified; spike and nucleocapsid genes showed positive selection.

Conclusions:

  • SARS-CoV-2 exhibited distinct evolutionary characteristics and genomic mutations under China's NPI policy.
  • Positive selection on spike and nucleocapsid genes suggests increased SARS-CoV-2 contagiousness.
  • Findings offer insights into the effectiveness of NPIs in controlling viral spread.