Aim There are many factors that are thought to contribute to T-cell immunodominance hierarchies including timing and levels of antigen presentation to T-cells. One of the most potent tools for studying antigen presentation for a specific determinant are monoclonal antibodies that are specific for not only MHC but a specific ligand, similar to a T cell receptor. In this study we utilize these antibodies to study levels and timing of antigen presentation of immunodominant (SVG9), sub-dominant (SLF9), and super sub-dominant (YTM9) T-cell epitopes during West Nile virus (WNV) infection. Methods High avidity antibodies specific for peptide/HLA-A∗02:01 complexes, SVG9, SLF9, and YTM9 were generated by mouse immunization with peptide/HLA complexes. Specific antibody producing hybridomas were expanded and the antibodies were purified from the cell supernatant. The purified antibodies were then used to stain WNV infected HeLa cells transfected with HLA-A∗02:01. Relative number of complexes was measured using flow cytometry. TAP inhibition studies were performed using TAP inhibitor protein ICP47. Results In this study, we demonstrate that viral peptide ligands are differentially expressed by A∗02:01 on the surface of a cell infected with WNV. Specifically, the super sub-dominant ligand (YTM9) was presented earlier and at 20 times the levels of the immunodominant (SVG9) and subdominant (SLF9) ligands. Transfection of ICP47 in infected cells show that all three epitopes are TAP dependent. Conclusions Using these highly specific reagents we show that there is differential ligand presentation within the restrictive allele A∗02:01. High levels of peptide HLA complexes on the surface of an infected do not correspond with immunodominance hierarchies as the super subdominant epitope YTM9 was presented at higher levels than the most immune dominant epitope SVG9. We then show that this differential presentation was not due the TAP dependence of the ligands.