Rapid determination of HLA B07 ligands from the West Nile virus NY99 genome

• Published in: Emerging infectious diseases 2001-07, Vol.7 (4), p.706-713
• Main Authors: De Groot, A S, Saint-Aubin, C, Bosma, A, Sbai, H, Rayner, J, Martin, W
• Format: Article
• Language: English
• Subjects: bioinformatics; computational immunology; Costs and Cost Analysis; Cross Reactions; Epitope Mapping - economics; Epitope Mapping - methods; Epitopes, T-Lymphocyte - genetics; Epitopes, T-Lymphocyte - immunology; Genetic aspects; Genome, Viral; HLA B07; HLA-B7 Antigen - immunology; Humans; Ligands; MHC ligand; New York - epidemiology; Peptides - chemical synthesis; Peptides - immunology; Physiological aspects; Staining and Labeling - methods; T Cell epitope; T-Lymphocytes, Cytotoxic - immunology; Time Factors; Vaccines; Viruses; West Nile fever; West Nile Fever - epidemiology; West Nile Fever - virology; West Nile virus; West Nile virus - genetics; West Nile virus - immunology
• ISSN: 1080-6040; 1080-6059
• DOI: 10.3201/eid0704.017419

Defined T cell epitopes for West Nile (WN) virus may be useful for developing subunit vaccines against WN virus infection and diagnostic reagents to detect WN virus-specific immune response. We applied a bioinformatics (EpiMatrix) approach to search the WN virus NY99 genome for HLA B*07 restricted cytotoxic T cell (CTL) epitopes. Ninety-five of 3,433 WN virus peptides scored above a predetermined cutoff, suggesting that these would be likely to bind to HLA B*07 and would also be likely candidate CTL epitopes. Compared with other methods for genome mapping, derivation of these ligands was rapid and inexpensive. Major histocompatibility complex ligands identified by this method may be used to screen T cells from WN virus-exposed persons for cell-mediated response to WN virus or to develop diagnostic reagents for immunopathogenesis studies and epidemiologic surveillance.