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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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Related Experiment Video

Updated: Apr 9, 2026

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes
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Development and application of EpitopeScan, a Python3 toolset for mutation tracking in SARS-CoV-2 immunogenic

Alexander Kovalenko1, Sebastien Viatte1,2,3

  • 1Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.

Frontiers in Immunology
|June 6, 2024
PubMed
Summary

A new bioinformatics tool, EpitopeScan, tracks mutations in SARS-CoV-2 immunogenic epitopes. This tool aids in monitoring T-cell responses against the virus, particularly in rheumatoid arthritis patients, by analyzing viral genome data.

Keywords:
SARS-CoV-2epitopeimmune monitoringmutation trackingrheumatoid arthritissoftwarevaccine design

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Area of Science:

  • Immunology
  • Bioinformatics
  • Genomics

Background:

  • The COVID-19 pandemic highlights the need for advanced immunological research and bioinformatics tools for virus surveillance.
  • Existing software is insufficient for tracking mutations within SARS-CoV-2's immunogenic epitopes.

Purpose of the Study:

  • To develop EpitopeScan, a mutation tracker for SARS-CoV-2 immunogenic epitopes.
  • To analyze mutation dynamics in specific T-cell epitopes, particularly in the context of rheumatoid arthritis (RA).

Main Methods:

  • Developed EpitopeScan, a Python3 package with command-line and GUI tools.
  • Analyzed mutation dynamics in SARS-CoV-2 epitopes using multiple-sequence alignments of over 2.3 million genomes from England.
  • Focused on three Spike protein-derived CD4+ T-cell epitopes restricted by HLA-DRB1*04:01.

Main Results:

  • Observed epitope conservation, partial loss of conservation, and divergence from the wild type.
  • Identified the N969K Omicron-specific mutation's impact starting November 2021.
  • Demonstrated EpitopeScan's utility in tracking variant-specific T-cell responses.

Conclusions:

  • EpitopeScan facilitates the investigation of mutation dynamics in SARS-CoV-2 epitopes.
  • The tool aids in monitoring immune responses against SARS-CoV-2, with implications for RA patients.
  • EpitopeScan is publicly available on GitHub for broader research use.