MHCII

MHCII predicts MHC class II-binding epitopes and evaluates conservation and population coverage to support peptide vaccine design against Aichi virus (AiV).

Key Features:

• Epitope Prediction: Predicts potential epitopes from viral proteins, specifically targeting the VP1 protein of the AiV-1 strain.
• Conservation Analysis: Aligns 38 Aichi virus VP1 sequences retrieved from the NCBI database to identify conserved regions across strains.
• MHC Class II Epitope Prediction: Focuses on predicting MHC class II-binding epitopes and identifies epitopes including FTYIAADLR and YMAEVPVSA that show high affinity for frequent MHC class II alleles.
• Global Coverage Assessment: Evaluates predicted epitopes for their ability to cover diverse global populations.
• Integration with IEDB: Utilizes the Immune Epitope Database (IEDB) analysis resource to predict B-cell and T-cell epitopes.
• Support for Multiple Prediction Methods: Supports IEDB recommended (2.22, 2.18), Consensus (2.22, 2.18), NetMHCIIpan (3.2, 3.1), NN-align (2.3 / NetMHCII 2.3, 2.2 / NetMHCII 2.2), SMM-align (NetMHCII 1.1), and combinatorial library approaches.

Scientific Applications:

• Peptide Vaccine Design: Informs selection of VP1-derived MHC class II epitopes for peptide vaccine candidates against AiV.
• Cross-strain Epitope Selection: Uses conserved VP1 regions to prioritize epitopes with potential breadth across AiV strains.
• Population Coverage Estimation: Assesses HLA allele coverage of predicted epitopes to inform global vaccine applicability.
• Immunogenicity Assessment: Combines B-cell and T-cell epitope predictions to support evaluation of potential immune responses.

Methodology:

Aligns 38 Aichi virus VP1 sequences retrieved from NCBI and performs epitope prediction using the IEDB analysis resource with methods including IEDB recommended (2.22, 2.18), Consensus (2.22, 2.18), NetMHCIIpan (3.2, 3.1), NN-align (2.3, 2.2), SMM-align (NetMHCII 1.1), and combinatorial library approaches.