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

Asif M. Khan, A. T. Heiny, Kenneth X. Lee, K. N. Srinivasan, Tin Wee Tan, J. Thomas August, Vladimir Brusic

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

Background: 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 shortpeptide 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. Results: 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 (∼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 (∼

Original languageEnglish
Article numberS4
JournalBMC Bioinformatics
Volume7
Issue numberSUPPL.5
DOIs
Publication statusPublished - Dec 18 2006
Externally publishedYes

Fingerprint

Epitopes
Antigenic Variation
antigenic variation
Dengue virus
Dengue Virus
T-Lymphocyte Epitopes
T-cells
Viruses
epitopes
Virus
T-lymphocytes
Proteins
Peptides
Protein Sequence
amino acid sequences
Vaccines
peptides
Vaccine
Bioinformatics
vaccine development

ASJC Scopus subject areas

  • Medicine(all)
  • Structural Biology
  • Applied Mathematics
  • Agricultural and Biological Sciences (miscellaneous)
  • Artificial Intelligence
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Software

Cite this

Khan, A. M., Heiny, A. T., Lee, K. X., Srinivasan, K. N., Tan, T. W., August, J. T., & Brusic, V. (2006). Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus. BMC Bioinformatics, 7(SUPPL.5), [S4]. https://doi.org/10.1186/1471-2105-7-S5-S4

Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus. / Khan, Asif M.; Heiny, A. T.; Lee, Kenneth X.; Srinivasan, K. N.; Tan, Tin Wee; August, J. Thomas; Brusic, Vladimir.

In: BMC Bioinformatics, Vol. 7, No. SUPPL.5, S4, 18.12.2006.

Research output: Contribution to journalArticle

Khan, AM, Heiny, AT, Lee, KX, Srinivasan, KN, Tan, TW, August, JT & Brusic, V 2006, 'Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus', BMC Bioinformatics, vol. 7, no. SUPPL.5, S4. https://doi.org/10.1186/1471-2105-7-S5-S4
Khan AM, Heiny AT, Lee KX, Srinivasan KN, Tan TW, August JT et al. Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus. BMC Bioinformatics. 2006 Dec 18;7(SUPPL.5). S4. https://doi.org/10.1186/1471-2105-7-S5-S4
Khan, Asif M. ; Heiny, A. T. ; Lee, Kenneth X. ; Srinivasan, K. N. ; Tan, Tin Wee ; August, J. Thomas ; Brusic, Vladimir. / Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus. In: BMC Bioinformatics. 2006 ; Vol. 7, No. SUPPL.5.
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