Our approach represents an alternative to peptide selection by phage display [45, 46] . The bioinformatic selection avoids construction and handling of phage display libraries and panning procedures. The most important limitation to successful panning consists in the lack of selective antibodies. Antibody purification from human sera requires pure and specific antigen, which generally is not yet available. Our bioinformatic approach to peptide selection reduces complex lab work and is compatible with screening on peptide microarray. In our hands, this platform proved highly suitable for investigation of antigen-antibody interaction. Figure S1 Alignment of E. granulosus and E. multilocularis antigenB8/1 sequences with location of peptide D8, D9 and longD8-9.  Protective Efficacy of Cross-Reactive CD8(+) T Cells Recognising Mutant Viral Epitopes Depends on Peptide-MHC-I Structural Interactions and T Cell Activation Threshold Emergence of a new influenza strain leads to a rapid global spread of the virus due to minimal antibody immunity. Pre-existing CD8(+) T-cell immunity directed towards conserved internal viral regions can greatly ameliorate the disease. However, mutational escape within the T cell epitopes is a substantial issue for virus control and vaccine design. Although mutations can result in a loss of T cell recognition, some variants generate cross-reactive T cell responses. In this study, we used reverse genetics to modify the influenza NP(336–374) peptide at a partially-solvent exposed residue (N->A, NPN3A mutation) to assess the availability, effectiveness and mechanism underlying influenza-specific cross-reactive T cell responses. The engineered virus induced a diminished CD8(+) T cell response and selected a narrowed T cell receptor (TCR) repertoire within two Vβ regions (Vβ8.3 and Vβ9). This can be partially explained by the H-2D(b)NPN3A structure that showed a loss of several contacts between the NPN3A peptide and H-2D(b), including a contact with His155, a position known to play an important role in mediating TCR-pMHC-I interactions. Despite these differences, common cross-reactive TCRs were detected in both the naïve and immune NPN3A-specific TCR repertoires. However, while the NPN3A epitope primes memory T-cells that give an equivalent recall response to the mutant or wild-type (wt) virus, both are markedly lower than wt->wt challenge. Such decreased CD8(+) responses elicited after heterologous challenge resulted in delayed viral clearance from the infected lung. Furthermore, mice first exposed to the wt virus give a poor, low avidity response following secondary infection with the mutant. Thus, the protective efficacy of cross-reactive CD8(+) T cells recognising mutant viral epitopes depend on peptide-MHC-I structural interactions and functional avidity. Our study does not support vaccine strategies that include immunization against commonly selected cross-reactive variants with mutations at partially-solvent exposed residues that have characteristics comparable to NPN3A. Virus-specific CD8 + T cells play a critical role in host defence via the production of antiviral cytokines, the direct killing of virusinfected cells and the establishment of immunological memory [1] . The selection of CD8 + T cells into an immune response requires specific interaction between the T cell receptor (TCR) and virus peptide bound to Major Histocompatibility Complex class I (pMHC-I) molecules on the surface of infected host cells. The processing of virus proteins into short fragments generates thousands of peptides that might potentially form pMHC-I epitopes, but only a few elicit CTL responses [2] .