Cytotoxic T lymphocytes (CTL) play an important role in the control and elimination of
infection by West Nile virus (WNV), yet the class I
human leukocyte antigen (HLA)-presented
peptide epitopes that enable CTL recognition of WNV-infected cells remain uncharacterized. The goals of this work were first to discover the
peptide epitopes that distinguish the class I HLA of WNV-infected cells and then to test the T cell reactivity of newly discovered WNV
epitopes. To discover WNV-immune
epitopes, class I HLA was harvested from WNV (NY99 strain)-infected and uninfected HeLa cells. Then
peptide epitopes were eluted from affinity-purified HLA, and
peptide epitopes from infected and uninfected cells were comparatively mapped by mass spectroscopy. Six virus-derived
peptides from five different
viral proteins (E, NS2b, NS3, NS4b, and NS5) were discovered as unique to
HLA-A*0201 of infected cells, demonstrating that the
peptides sampled by class I HLA are distributed widely throughout the WNV
proteome. When tested with CTL from infected individuals, one dominant WNV target was apparent, two
epitopes were subdominant, and three demonstrated little CTL reactivity. Finally, a sequence comparison of these
epitopes with the hundreds of viral isolates shows that
HLA-A*0201 presents
epitopes derived from conserved regions of the virus. Detection and recovery from
WNV infection are therefore functions of the ability of class I HLA molecules to reveal conserved WNV
epitopes to an intact cellular immune system that subsequently recognizes infected cells.