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Conserved amino acids 193–324 of non-structural protein 3 are a dominant source of peptide determinants for CD4⁺ and CD8⁺ T cells in a healthy Japanese encephalitis virus-endemic cohort

¹ Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka 560012, India
² Department of Pediatrics, Vijayanagar Institute of Medical Sciences, Bellary, Karnataka 583104, India

Correspondence
Vijaya Satchidanandam
vijaya{at}mcbl.iisc.ernet.in

Our earlier identification of the non-structural protein 3 (NS3) of Japanese encephalitis virus (JEV) as a dominant CD4⁺ as well as CD8⁺ T cell-eliciting antigen in a healthy JEV-endemic cohort with a wide HLA distribution implied the presence of several epitopes dispersed over the length of the protein. Use of various truncated versions of NS3 in lymphocyte stimulation and interferon (IFN)- secretion assays revealed that amino acids (aa) 193–324 of NS3 were comparable with, if not superior to, the full-length protein in evoking Th1 responses. The potential of this 14·4 kDa stretch to stimulate IFN- production from both subtypes of T cells in a manner qualitatively and quantitatively similar to the 68 kDa parent protein suggested the presence within it of both class I and II epitopes and demonstrated that the entire immunogenicity of NS3 was focused on aa 193–324. Interestingly, this segment contained five of the eight helicase motifs of NS3. Analysis of variability of the NS3 protein sequence across 16 JEV isolates revealed complete identity of aa 219–318, which is contained within the above segment, suggesting that NS3-specific epitopes tend to cluster in relatively conserved regions that harbour functionally critical domains of the protein.

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