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Related Concept Videos

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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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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Updated: Jul 16, 2025

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The Single-Nucleotide Polymorphism (SNP) Validity to Detect Omicron Variants.

Lia Gardenia Partakusuma1, Luhung Budiailmiawan2, Budiman3

  • 1Faculty of Medicine and Post Graduate Programme, YARSI University, Jakarta, West Java, Indonesia.

Advances in Virology
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The single-nucleotide polymorphism (SNP) method accurately detects SARS-CoV-2 omicron variants and sublineages. This PCR-based approach offers a faster, more accessible alternative to whole genome sequencing for genomic surveillance.

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Area of Science:

  • Virology
  • Genomics
  • Molecular Diagnostics

Background:

  • SARS-CoV-2 variants of concern (VOCs) necessitate rapid global surveillance strategies.
  • Whole genome sequencing (WGS) is the gold standard for variant detection but is time-consuming and has limited accessibility.
  • Faster, more accessible diagnostic methods are crucial for effective COVID-19 pandemic management.

Purpose of the Study:

  • To evaluate the diagnostic validity of the single-nucleotide polymorphism (SNP) method using PCR for detecting SARS-CoV-2 omicron variants.
  • To compare the SNP method's performance against the gold standard whole genome sequencing (WGS).

Main Methods:

  • Diagnostic analysis of 140 nasopharyngeal COVID-19 samples.
  • Utilized the single-nucleotide polymorphism (SNP) method with PCR.
  • Compared SNP results with whole genome sequencing (WGS) data.
  • Employed Cohen's kappa coefficient test for conformity analysis.

Main Results:

  • High conformity observed between SNP and WGS methods (kappa coefficient = 0.948, p < 0.001).
  • SNP method demonstrated excellent validity for omicron BA.1 (90% sensitivity, 100% specificity).
  • SNP method showed high validity for omicron BA.2 (100% sensitivity, 99% specificity) and BA.4/5 (99.2% sensitivity, 100% specificity).

Conclusions:

  • The SNP method is a valid and time-efficient alternative for detecting SARS-CoV-2 omicron variants.
  • SNP analysis, using specific gene mutations (ΔH69/V70 and Q493R), can differentiate between omicron sublineages (BA.1, BA.2, BA.4/5).
  • This method enhances genomic surveillance capabilities for emerging SARS-CoV-2 variants.