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Related Concept Videos

Viral Mutations00:36

Viral Mutations

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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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Large-Scale SARS-CoV-2 Testing Utilizing Saliva and Transposition Sample Pooling
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Two-Period Study Results from a Large Italian Hospital Laboratory Attesting SARS-CoV-2 Variant PCR Assay Evolution.

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|November 21, 2022
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Summary

The Seegene Allplex SARS-CoV-2 Variants I assay accurately identified most major variants, including Alpha, Beta, Gamma, and Delta. However, the combination of Variants I and II assays showed limitations in detecting Omicron mutations, suggesting Variants I alone may be more suitable for current SARS-CoV-2 variant detection.

Keywords:
PCR assaySARS-CoV-2amino acid mutationnext-generation sequencingspike proteinvariant detection

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Area of Science:

  • Virology
  • Molecular Biology
  • Public Health

Background:

  • The emergence of SARS-CoV-2 variants necessitates rapid detection methods.
  • PCR assays have been developed to identify specific SARS-CoV-2 spike protein mutations characteristic of different variants.
  • Seegene Allplex SARS-CoV-2 Variants I and II assays were designed to detect key mutations in Alpha, Beta, Gamma, Delta, and Omicron variants.

Purpose of the Study:

  • To evaluate the performance of Seegene Allplex SARS-CoV-2 Variants I and II assays in identifying SARS-CoV-2 variants.
  • To compare the accuracy of Variants I assay alone versus the combination of Variants I and II assays for variant detection.
  • To assess the suitability of existing PCR assays for identifying currently circulating SARS-CoV-2 variants, including Omicron.

Main Methods:

  • Next-generation sequencing (NGS) of the S gene was used as the reference method for SARS-CoV-2 variant identification.
  • Results from SARS-CoV-2-positive nasopharyngeal swab samples were analyzed from two distinct testing periods.
  • The performance of the Variants I assay and the combined Variants I and II assays was assessed against NGS data.

Main Results:

  • The Variants I assay correctly identified Alpha, Beta/Gamma, and Delta variants with high accuracy.
  • The combined Variants I and II assays correctly identified 61 out of 77 Omicron variant-positive samples.
  • The Variants II assay failed to detect the K417N mutation in 16 Omicron samples, while Variants I detected key mutations like ΔH69/V70 and N501Y in most Omicron samples.
  • The Variants I assay alone resulted in fewer incorrect identifications (6/365) compared to the combined assay's performance on Omicron.

Conclusions:

  • The Seegene Allplex SARS-CoV-2 Variants I assay alone demonstrated better suitability for identifying currently circulating SARS-CoV-2 variants than the combination of Variants I and II assays.
  • The mutation panel in the Seegene Variants II assay may be suboptimal for detecting emerging SARS-CoV-2 variants like Omicron.
  • Future PCR assay development for SARS-CoV-2 variant detection should incorporate additional variant-specific mutations to maintain performance as the virus evolves.