Development and application of EpitopeScan, a Python3 toolset for mutation tracking in SARS-CoV-2 immunogenic...

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.