PopCover-2.0

PopCover-2.0 selects minimal peptide sets that maximize population and pathogen coverage for vaccine design and T cell diagnostics.

Key Features:

• Input Parameters: Accepts predicted CD8 and/or CD4 T cell epitopes annotated with HLA restriction and pathogen strain information and uses HLA allele frequency data.
• Optimization Methodology: Identifies peptide sets that optimize coverage across HLA alleles (class I and II) and multiple pathogen strains.
• Benchmarking and Validation: Has been benchmarked using historical HIV and SARS-CoV-2 datasets and includes peptide sets experimentally validated to elicit T cell responses in SARS-CoV-2–infected individuals.

Scientific Applications:

• Vaccine epitope selection: Facilitates selection of epitopes with broad HLA and strain coverage for rational vaccine design.
• Diagnostic and immunogenicity studies: Supports selection of T cell epitopes for diagnostics and for assessing population-level immunogenicity in infectious diseases such as HIV and SARS-CoV-2.

Methodology:

Integrates epitope prediction annotations with population HLA allele frequency data and systematically identifies peptide sets that maximize coverage across HLA class I and II alleles and pathogen strains.