T-CoV

T-CoV analyzes how mutations in SARS-CoV-2 affect HLA-peptide binding to assess impacts on CD8 and CD4 T-cell epitope recognition.

Key Features:

• Mutation impact analysis: Evaluates how specific SARS-CoV-2 mutations alter HLA-peptide interactions.
• HLA class coverage: Includes analysis across HLA class I and II alleles to capture allele diversity.
• T-cell epitope context: Considers both CD8 and CD4 T-cell recognition of viral peptides.
• Binding affinity prediction: Uses in silico techniques to assess binding affinities between HLA molecules and viral peptides.
• Variant comparison: Compares common SARS-CoV-2 variants, including Wuhan, Delta (Indian) and Alpha (UK), for changes in peptide binding.
• Allele-specific findings: Reports allele-specific effects such as loss of binding of peptides tightly bound to HLA-B*07:02 in the Wuhan variant in Delta and Alpha variants.

Scientific Applications:

• Susceptibility prediction: Predicts individual susceptibility to SARS-CoV-2 variants based on HLA genotype.
• Severity forecasting: Informs potential infection severity by identifying variant-induced changes in epitope presentation.
• Immune response tailoring: Supports tailoring immune response strategies by highlighting allele-specific epitope changes.
• Viral immunology research: Advances understanding of how SARS-CoV-2 mutations affect antigen presentation and T-cell recognition.

Methodology:

In silico assessment of HLA–peptide binding affinities for SARS-CoV-2 peptides, comparing variants and HLA class I and II alleles to identify changes in predicted epitope presentation.