The flavivirus nonstructural protein NS3 is a dominant source of cytotoxic T cell peptide determinants.

Vaccinia virus recombinants encoding regions of the Murray Valley encephalitis virus (MVE) genome, which together cover the entire viral coding region, were employed to identify the MVE protein which is the dominant source of CD8+, cytotoxic, T cell antigenic determinant(s) presented by the mouse H-2Kk major histocompatibility antigen. MVE and West Nile virus-immune, H-2k-restricted, effector cells recognized peptides derived from the MVE nonstructural polyprotein segment, and in this region the immunodominant determinant mapped to protein NS3. Interestingly, mapping of cytotoxic T cell antigenic determinants of other flaviviruses also identified the NS3 protein as the dominant source of antigenic peptides (A. B. Hill, A. Müllbacher, C. Parrish, G. Coia, E. G. Westaway, and R. V. Blanden, 1992, J. Gen. Virol. 73, 1115-1123; A. L. Rothman, I. Kurane, C.-J. Lai, M. Bray, B. Falgout, R. Men, and F. A. Ennis, 1993, J. Virol. 67, 801-806). Using an allele-specific peptide motiff for H-2Kk, we predicted 12 peptides in the MVE NS3 protein as ligands for the restriction element and identified three peptides which were recognized in association with H-2Kk by MVE-immune cytotoxic T cells. We also examined the effect of proteolytic processing in the MVE nonstructural polyprotein segment mediated by the viral proteinase NS3 on antigen processing and presentation of the MVE H-2Kk-restricted T cell determinant. Processing of the MVE polyprotein by the viral proteinase did not markedly influence the availability of this peptide determinant.