Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus

Antigenic diversity in dengue virus strains has been studied, but large-scale and detailed systematic analyses have not been reported. In this study, we report a bioinformatics method for analyzing viral antigenic diversity in the context of T-cell mediated immune responses. We applied this method t...

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Bibliographic Details
Published in:BMC bioinformatics 2006-12, Vol.7 Suppl 5 (S5), p.S4-S4, Article S4
Main Authors: Khan, Asif M, Heiny, A T, Lee, Kenneth X, Srinivasan, K N, Tan, Tin Wee, August, J Thomas, Brusic, Vladimir
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Antigenic Variation
Computational Biology - methods
Databases, Protein
Dengue virus
Dengue Virus - immunology
Epitopes, T-Lymphocyte - analysis
Human immunodeficiency virus
Influenza A virus
Molecular Sequence Data
Peptide Fragments - immunology
Proceedings
Sequence Homology, Amino Acid
Serotyping
Viral Proteins - immunology
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Summary:Antigenic diversity in dengue virus strains has been studied, but large-scale and detailed systematic analyses have not been reported. In this study, we report a bioinformatics method for analyzing viral antigenic diversity in the context of T-cell mediated immune responses. We applied this method to study the relationship between short-peptide antigenic diversity and protein sequence diversity of dengue virus. We also studied the effects of sequence determinants on viral antigenic diversity. Short peptides, principally 9-mers were studied because they represent the predominant length of binding cores of T-cell epitopes, which are important for formulation of vaccines. Our analysis showed that the number of unique protein sequences required to represent complete antigenic diversity of short peptides in dengue virus is significantly smaller than that required to represent complete protein sequence diversity. Short-peptide antigenic diversity shows an asymptotic relationship to the number of unique protein sequences, indicating that for large sequence sets (approximately 200) the addition of new protein sequences has marginal effect to increasing antigenic diversity. A near-linear relationship was observed between the extent of antigenic diversity and the length of protein sequences, suggesting that, for the practical purpose of vaccine development, antigenic diversity of short peptides from dengue virus can be represented by short regions of sequences (approximately
ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-7-S5-S4