BACKGROUND
in  <dig>  the outbreak of a new swine-origin strain of influenza a h1n <dig> caused widespread human infection  <cit> .
one of the most important surface proteins, hemagglutinin  permits the virus to bind to cell membrane and infect the cells.
since mutations enable the virus to escape from either t cell or antibody recognition, current flu vaccines were not effective against the emerging virus.
sequence analyses showed that the ha sequence of the pandemic 2009-h1n <dig> underwent an antigenic shift  <cit>  that altered its antigenicity in context of the seasonal flu vaccine.
the antigenicity of ha 2009-h1n <dig> remained highly conserved to pandemic 1918-h1n <dig> and partially conserved to seasonal flu strains of the 1930s.
therefore, the majority of infected individuals who were vaccinated with the who recommended seasonal flu vaccine did not produce neutralizing antibodies against the new influenza strain.
however, elderly and individuals born before  <dig> were less affected than expected.
the lower infection rate of these age groups has been interpreted as the results of cross-reactive t cells  <cit>  and antibody  <cit>  responses to the pandemic 1918-h1n <dig> and partially cross-reactive t cell response to seasonal flu strains of the 1930s.
a study by boon et al.
<cit>  on cd8+ t cell recognition of heterosubtypic h1n <dig> variants indicated that repeated infection with heterologous viruses may increase cross-reactive cytotoxic t lymphocytes  and thus confer protection against newly emerging strains in absence of a cross-reactive antibody response.
further support for this concept comes from a study of subjects who were vaccinated against seasonal influenza and showed in vitro cross-reactive t cell responses against ha of the pandemic 2009-h1n <dig>  <cit> .
in growing recognition of the role of t cell responses to h1n <dig>  several groups conducted large-scale human leukocyte antigen  binding motif scanning analyses of pandemic and seasonal strains to predict and identify conserved peptides that elicit cross-reactive hla class i and/or class ii restricted t cell responses  <cit> .
while the affinity-based approach allows a broad coverage of hla supertypes and epitope bindings  <cit> , structural approach gives better insight view onto t cell recognition of the hla-restricted t cell epitopes  <cit> .
in our study, we are interested in immunogenicity that depends on the quality of t-cell receptor  interaction with the hla/peptide complexes rather than hla-binding peptide affinity only.
we, therefore, combined affinity-based epitope prediction with molecular docking to generate conserved high confidence ha t cell epitope candidates of current and past pandemic strains, and consequently analyzed the potential tcr cross-recognition of 2009-h1n <dig> and 2004-h5n <dig>
according to archbold et al.
complex of dm1-tcr and hla-b*4405/peptide showed significant enhancement in t cell-mediated responses among micropolymorphisms in the hla-b* <dig> family, and as such they are key factors in controlling persistent viral infections  <cit> .
thus, to perform the experiments we used hla-b* <dig> and dm1-tcr as models.
results of structural models of tcr cross-recognition between 2009-h1n <dig> and 2004-h5n <dig> revealed steric and topological effects of tcr contact residue mutations on tcr binding affinity.
while these results are novel with respect to hla-b*4405-restricted h1n <dig> ha epitopes and dm1-tcr, yet with limited available structural data upon the tcr repertoire, more investigations and experimental analyses are still recommended for further broad perspective of their utility in vaccine development against the emerging virus strains.
RESULTS
conserved ha t cell epitope candidates generated for hla-b* <dig> and dm1-tcr
examining various ha sequences among the pandemic 2009-h1n <dig>  1918-h1n <dig>  and who recommended vaccine strains , we predicted potential 9-mer t cell epitopes using the tool netctl v <dig>  from immune epitope database  .
nineteen candidates, which scored greater than  <dig> , are more likely well presented by hla-b <dig> family .
we then docked these  <dig> epitopes to hla-b* <dig>  and subsequently the hla-b*4405/epitope complex as ligand to dm1-tcr.
the  <dig> predicted epitope candidates differ in their physico-chemical properties.
eight candidates starting at positions  <dig>   <dig>   <dig>   <dig>   <dig>   <dig>   <dig>  and  <dig> contain mostly hydrophobic and polar residues, whereas other  <dig> candidates  are composed of predominantly hydrophilic residues  which result in higher hla-b* <dig> binding energies .
as expected, all the  <dig> epitopes bound to the helical antigen-presenting groove of the hla-b* <dig>  <cit> .
eleven epitopes  bound in similar orientations to hla-b* <dig> with glu at position  <dig> and residues at the c-terminus binding to the b and f pockets of the hla-b* <dig>  respectively  <cit> .
residues which occupy the centre of the binding groove are solvent-exposed and likely to bind to tcr  <cit> .
in contrast, most residues of epitopes at positions  <dig>   <dig>   <dig>   <dig>   <dig>  and  <dig> interacted with the hla-b* <dig> peptide binding pockets.
in our model, the deeply embedded residues were not exposed to the solvent.
therefore tcr recognition of hla-b*4405/epitope complexes is expected to be conformationally restrained.
dm1-tcr was docked to the hla-b*4405/epitope complexes to assess their binding conformation.
in the models with minimum binding energies, dm1-tcr vα and vβ domains interacted with hla-b* <dig> α <dig> and α <dig> domain residues and solvent exposed residues of the epitopes.
epitope candidates  <dig> and  <dig> were embedded in the binding groove of hla-b* <dig>  and interacted with dm1-tcr via tyr <dig> and tyr <dig>  and lys <dig>  as shown in table  <dig>  these interactions appeared to be mediated by a change of the tcr binding position to hla-b* <dig> α1- and α2-domain residues, resulting in contacts with polar and charged residues asn <dig>  glu <dig>  and gln <dig> of the hla-b* <dig>  hydrogen bond lengths  and dihedrals around these h-bonds made by dm1-tcr and hla-b* <dig> domains in cases of exposed and embedded epitope types were calculated.
in case of epitope  <dig>  residues at positions  <dig>   <dig>  and  <dig> were exposed while the tcr vα domain interacted with asn <dig>  and glu <dig> .
in contrast, for the embedded-type epitope  <dig>  we observed binding of tcr vβ domain to asn <dig> and glu <dig> at  <dig>  Å h-bond lengths.
epitope candidates  <dig>  and  <dig>  also showed similar noticeable h-bond length changes.
distances of the tcr to the residues gln <dig>  decreased when the contacts with the hla domains shifted from the tcr vβ to tcr vα.
meanwhile, the dihedrals between residues that made the h-bonds also showed decreasing trend when the tcr changed its binding positions to the hla-b* <dig> from vβ to vα domain  .
it could suggest that the changes in h-bond lengths and dihedral angles indicate an attempt of the tcr to adjust its binding access to the hla-b*4405/epitope complexes when the epitopes change from exposed to embedded type.
epitope candidates at positions  <dig> and  <dig> in  <dig> and who vaccine sequences  yielded rather low hla-b* <dig> binding scores  and could not be docked to dm1-tcr.
therefore it is unlikely that the two candidate epitopes were antigenic to the  <dig> and who strains.
mutations at positions  <dig> and/or  <dig> in ha sequences of the  <dig> viral strains increased the hla-b* <dig> binding scores above the threshold, but did not facilitate tcr recognition in our model.
recognition of computationally inferred optimal epitope kekmntefw by hla-b <dig> and dm1-tcr
we computationally designed the mosaic epitope candidate kekmntefw from five epitope sequences, which were in the top  <dig> ranks of dm1-tcr binding energy .
these epitopes are at positions  <dig>   <dig>   <dig>   <dig>  and  <dig>  whose corresponding residue positions were favourably bound by the dm1-tcr model.
we selected the epitope iekmntqft at position  <dig> as the starting point because most of its residues made direct contacts with dm1-tcr, i.e.
-ekmnt---.
also, archbold et al.
<cit>  suggested that the second positioned residue glu  be required for preferential binding to hla-b <dig>  according to our top  <dig> dm1-tcr docking results,  <dig> out of  <dig> epitopes  contain residue lys  at the first position, and lysepitope <dig> directly interacted with the dm1-tcr.
therefore, we used lys  for the first position of the mosaic epitope.
similarly, we chose glu  for the 7th position since it was a tcr-interacting residue of the epitope  <dig>  finally, we used bulky side-chains of f <dig>  and w <dig>  serving as anchors for hla-b* <dig> binding.
thus, using deep-view  <cit> , we substituted residues i <dig>  q <dig>  and t <dig> with k, e, and w respectively.
docking of the mosaic epitope kekmntefw to hla-b* <dig> and dm1-tcr showed that it bound favourably to both hla-b* <dig>  and dm1-tcr  with asn <dig> and thr <dig> exposed to the solvent and directly interacting with dm1-tcr.
although the ha peptide appears to be a good candidate for inclusion in multivalent peptide vaccine against the h1n <dig> influenza a, its efficacy as a protective epitope on population level depends on the tcr repertoire which could be only tested experimentally.
cross-recognition of 2009-h1n <dig> and 2004-h5n <dig> ha t cell epitope candidates
a study by kreijtz et al.
<cit>  showed that t cell responses to seasonal h1n <dig> and h3n <dig> strains are largely cross-reactive to avian h5n <dig>  according to who global influenza program  <cit> , h <dig> ha viral strain a/vietnam/1194/ <dig> of the avian flu outbreak in vietnam was one of the h5n <dig> prototype vaccine strains in  <dig> and recommended candidate of pre-pandemic h5n <dig> vaccine.
therefore, we used ha protein of this strain as a model to test if our 2009-h1n <dig> t cell epitope candidates would be cross-reactive for 2004-h5n <dig>
netctl v <dig>  was used to extract the 2004-h5n <dig> hla-b* <dig> restricted t cell epitopes candidates from iedb.
of all candidates with predicted scores greater than  <dig> , seven were highly similar  to the 2009-h1n <dig> t cell epitope candidates  and likely to be recognized by dm1-tcr.
2009_h1n1
*different residues are underlined.
the residues that interacted with dm1-tcr are highlighted in bold.
two significant changes in tcr binding energy are marked in bold.
docking of the seven hla-b*4405/2004-h5n <dig> epitope complexes to dm1-tcr revealed that the dm1-tcr predominantly interacted with the 2004-h5n <dig> epitopes at conserved positions  <dig>   <dig>   <dig>  and  <dig>  dm1-tcr binding energies of the 2004-h5n <dig> epitope candidates were lower and thus more favourable than these of the corresponding 2009-h1n <dig> epitope candidates .
most mutations that occurred between these two influenza outbreaks did not appear to affect dm1-tcr recognition of hla-b* <dig> presented epitope candidates.
however, we observed a significant decrease in tcr binding energy of the epitope candidate 2004-h5n <dig> complex at position  <dig> .
the mutation k4t changed the structural conformation of the epitope's exposed region.
the side chain of the mutated thr <dig> pointed toward the hla-α <dig> domain and is embedded in the helical binding groove of the hla-b* <dig>  it might therefore induce the interactions of lys <dig> and leu <dig> at its c-terminal with the dm1-tcr .
this could consequently suggest a more favourable binding of dm1-tcr to the hla-b*4405/epitope <dig> in 2004-h5n <dig> than in 2009-h1n <dig> viral strain.
in addition, we noticed that the binding affinity of dm1-tcr to the 2004-h5n <dig> epitope candidates considerably decreased when the tcr interactions occurred directly at mutated residues of the epitope candidates at position  <dig>  and  <dig> .
substitution of a positively charged his with a smaller-sized neutral asn reduced the contact surface of the epitope candidate's exposed region , resulting in a conformationally constrained contact of dm1-tcr with 2004-h5n <dig> candidate epitope  <dig> and a higher binding energy  compared to the 2009-h1n <dig> candidate epitope  <dig>  in a future pandemic we expect that apart from a few mutated epitopes, heterologous immunity  <cit>  mediated by pre-existing cross-reactive t cell responses to seasonal influenza virus will limit its severity and extent.
CONCLUSIONS
the hla-b* <dig> and dm1-tcr docking models showed differential recognition of the 2009-h1n <dig> ha t cell epitope candidates, reflecting the topological constraints of the epitopes.
this information was used to derive the synthetic h1n <dig> epitope kekmntefw with optimal recognition of both hla-b* <dig> and dm1-tcr models and to identify likely cross-reactive 2004-h5n <dig> epitopes.
while the results are novel with regard to hla-b*4405-restricted h1n <dig> ha epitopes, their utility in vaccination strategies against influenza viruses is limited by the fact that the t cell responses to viruses depend on the tcr repertoire, and in particular on the nature of tcr alpha chain and their conformation as shown in a study by zhong et al.
<cit> .
to simulate a t cell response to h1n <dig> epitopes on population level as it is desirable for vaccine design, a large number of crystal structure data on tcr vα and vβ chains and their heterodimers would be necessary to computationally assess epitope candidates for their potential to induce a broad t cell response.

 in the outbreak of a new swine-origin strain of influenza a h1n caused widespread human infection. one of the most important surface proteins, hemagglutinin permits the virus to bind to cell membrane and infect the cells. since mutations enable the virus to escape from either t cell or antibody recognition, current flu vaccines were not effective against the emerging virus. sequence analyses showed that the ha sequence of the pandemic 2009-h1n underwent an antigenic shift that altered its antigenicity in context of the seasonal flu vaccine. the antigenicity of ha 2009-h1n remained highly conserved to pandemic 1918-h1n and partially conserved to seasonal flu strains of the 1930s. therefore, the majority of infected individuals who were vaccinated with the who recommended seasonal flu vaccine did not produce neutralizing antibodies against the new influenza strain. however, elderly and individuals born before were less affected than expected. the lower infection rate of these age groups has been interpreted as the results of cross-reactive t cells and antibody responses to the pandemic 1918-h1n and partially cross-reactive t cell response to seasonal flu strains of the 1930s. a study by boon et al. on cd8+ t cell recognition of heterosubtypic h1n variants indicated that repeated infection with heterologous viruses may increase cross-reactive cytotoxic t lymphocytes and thus confer protection against newly emerging strains in absence of a cross-reactive antibody response. further support for this concept comes from a study of subjects who were vaccinated against seasonal influenza and showed in vitro cross-reactive t cell responses against ha of the pandemic 2009-h1n. in growing recognition of the role of t cell responses to h1n several groups conducted large-scale human leukocyte antigen binding motif scanning analyses of pandemic and seasonal strains to predict and identify conserved peptides that elicit cross-reactive hla class i and/or class ii restricted t cell responses. while the affinity-based approach allows a broad coverage of hla supertypes and epitope bindings, structural approach gives better insight view onto t cell recognition of the hla-restricted t cell epitopes. in our study, we are interested in immunogenicity that depends on the quality of t-cell receptor interaction with the hla/peptide complexes rather than hla-binding peptide affinity only. we, therefore, combined affinity-based epitope prediction with molecular docking to generate conserved high confidence ha t cell epitope candidates of current and past pandemic strains, and consequently analyzed the potential tcr cross-recognition of 2009-h1n and 2004-h5n according to archbold et al. complex of dm1-tcr and hla-b*4405/peptide showed significant enhancement in t cell-mediated responses among micropolymorphisms in the hla-b* family, and as such they are key factors in controlling persistent viral infections. thus, to perform the experiments we used hla-b* and dm1-tcr as models. results of structural models of tcr cross-recognition between 2009-h1n and 2004-h5n revealed steric and topological effects of tcr contact residue mutations on tcr binding affinity. while these results are novel with respect to hla-b*4405-restricted h1n ha epitopes and dm1-tcr, yet with limited available structural data upon the tcr repertoire, more investigations and experimental analyses are still recommended for further broad perspective of their utility in vaccine development against the emerging virus strains.  conserved ha t cell epitope candidates generated for hla-b* and dm1-tcr examining various ha sequences among the pandemic 2009-h1n 1918-h1n and who recommended vaccine strains, we predicted potential 9-mer t cell epitopes using the tool netctl v from immune epitope database. nineteen candidates, which scored greater than, are more likely well presented by hla-b family. we then docked these epitopes to hla-b* and subsequently the hla-b*4405/epitope complex as ligand to dm1-tcr. the predicted epitope candidates differ in their physico-chemical properties. eight candidates starting at positions and contain mostly hydrophobic and polar residues, whereas other candidates are composed of predominantly hydrophilic residues which result in higher hla-b* binding energies. as expected, all the epitopes bound to the helical antigen-presenting groove of the hla-b*. eleven epitopes bound in similar orientations to hla-b* with glu at position and residues at the c-terminus binding to the b and f pockets of the hla-b* respectively. residues which occupy the centre of the binding groove are solvent-exposed and likely to bind to tcr. in contrast, most residues of epitopes at positions and interacted with the hla-b* peptide binding pockets. in our model, the deeply embedded residues were not exposed to the solvent. therefore tcr recognition of hla-b*4405/epitope complexes is expected to be conformationally restrained. dm1-tcr was docked to the hla-b*4405/epitope complexes to assess their binding conformation. in the models with minimum binding energies, dm1-tcr vα and vβ domains interacted with hla-b* α and α domain residues and solvent exposed residues of the epitopes. epitope candidates and were embedded in the binding groove of hla-b* and interacted with dm1-tcr via tyr and tyr and lys as shown in table these interactions appeared to be mediated by a change of the tcr binding position to hla-b* α1- and α2-domain residues, resulting in contacts with polar and charged residues asn glu and gln of the hla-b* hydrogen bond lengths and dihedrals around these h-bonds made by dm1-tcr and hla-b* domains in cases of exposed and embedded epitope types were calculated. in case of epitope residues at positions and were exposed while the tcr vα domain interacted with asn and glu. in contrast, for the embedded-type epitope we observed binding of tcr vβ domain to asn and glu at Å h-bond lengths. epitope candidates and also showed similar noticeable h-bond length changes. distances of the tcr to the residues gln decreased when the contacts with the hla domains shifted from the tcr vβ to tcr vα. meanwhile, the dihedrals between residues that made the h-bonds also showed decreasing trend when the tcr changed its binding positions to the hla-b* from vβ to vα domain. it could suggest that the changes in h-bond lengths and dihedral angles indicate an attempt of the tcr to adjust its binding access to the hla-b*4405/epitope complexes when the epitopes change from exposed to embedded type. epitope candidates at positions and in and who vaccine sequences yielded rather low hla-b* binding scores and could not be docked to dm1-tcr. therefore it is unlikely that the two candidate epitopes were antigenic to the and who strains. mutations at positions and/or in ha sequences of the viral strains increased the hla-b* binding scores above the threshold, but did not facilitate tcr recognition in our model. recognition of computationally inferred optimal epitope kekmntefw by hla-b and dm1-tcr we computationally designed the mosaic epitope candidate kekmntefw from five epitope sequences, which were in the top ranks of dm1-tcr binding energy. these epitopes are at positions and whose corresponding residue positions were favourably bound by the dm1-tcr model. we selected the epitope iekmntqft at position as the starting point because most of its residues made direct contacts with dm1-tcr, i.e. -ekmnt---. also, archbold et al. suggested that the second positioned residue glu be required for preferential binding to hla-b according to our top dm1-tcr docking results, out of epitopes contain residue lys at the first position, and lysepitope directly interacted with the dm1-tcr. therefore, we used lys for the first position of the mosaic epitope. similarly, we chose glu for the 7th position since it was a tcr-interacting residue of the epitope finally, we used bulky side-chains of f and w serving as anchors for hla-b* binding. thus, using deep-view, we substituted residues i q and t with k, e, and w respectively. docking of the mosaic epitope kekmntefw to hla-b* and dm1-tcr showed that it bound favourably to both hla-b* and dm1-tcr with asn and thr exposed to the solvent and directly interacting with dm1-tcr. although the ha peptide appears to be a good candidate for inclusion in multivalent peptide vaccine against the h1n influenza a, its efficacy as a protective epitope on population level depends on the tcr repertoire which could be only tested experimentally. cross-recognition of 2009-h1n and 2004-h5n ha t cell epitope candidates a study by kreijtz et al. showed that t cell responses to seasonal h1n and h3n strains are largely cross-reactive to avian h5n according to who global influenza program, h ha viral strain a/vietnam/1194/ of the avian flu outbreak in vietnam was one of the h5n prototype vaccine strains in and recommended candidate of pre-pandemic h5n vaccine. therefore, we used ha protein of this strain as a model to test if our 2009-h1n t cell epitope candidates would be cross-reactive for 2004-h5n netctl v was used to extract the 2004-h5n hla-b* restricted t cell epitopes candidates from iedb. of all candidates with predicted scores greater than, seven were highly similar to the 2009-h1n t cell epitope candidates and likely to be recognized by dm1-tcr. 2009_h1n1 *different residues are underlined. the residues that interacted with dm1-tcr are highlighted in bold. two significant changes in tcr binding energy are marked in bold. docking of the seven hla-b*4405/2004-h5n epitope complexes to dm1-tcr revealed that the dm1-tcr predominantly interacted with the 2004-h5n epitopes at conserved positions and dm1-tcr binding energies of the 2004-h5n epitope candidates were lower and thus more favourable than these of the corresponding 2009-h1n epitope candidates. most mutations that occurred between these two influenza outbreaks did not appear to affect dm1-tcr recognition of hla-b* presented epitope candidates. however, we observed a significant decrease in tcr binding energy of the epitope candidate 2004-h5n complex at position. the mutation k4t changed the structural conformation of the epitope's exposed region. the side chain of the mutated thr pointed toward the hla-α domain and is embedded in the helical binding groove of the hla-b* it might therefore induce the interactions of lys and leu at its c-terminal with the dm1-tcr. this could consequently suggest a more favourable binding of dm1-tcr to the hla-b*4405/epitope in 2004-h5n than in 2009-h1n viral strain. in addition, we noticed that the binding affinity of dm1-tcr to the 2004-h5n epitope candidates considerably decreased when the tcr interactions occurred directly at mutated residues of the epitope candidates at position and. substitution of a positively charged his with a smaller-sized neutral asn reduced the contact surface of the epitope candidate's exposed region, resulting in a conformationally constrained contact of dm1-tcr with 2004-h5n candidate epitope and a higher binding energy compared to the 2009-h1n candidate epitope in a future pandemic we expect that apart from a few mutated epitopes, heterologous immunity mediated by pre-existing cross-reactive t cell responses to seasonal influenza virus will limit its severity and extent.  the hla-b* and dm1-tcr docking models showed differential recognition of the 2009-h1n ha t cell epitope candidates, reflecting the topological constraints of the epitopes. this information was used to derive the synthetic h1n epitope kekmntefw with optimal recognition of both hla-b* and dm1-tcr models and to identify likely cross-reactive 2004-h5n epitopes. while the results are novel with regard to hla-b*4405-restricted h1n ha epitopes, their utility in vaccination strategies against influenza viruses is limited by the fact that the t cell responses to viruses depend on the tcr repertoire, and in particular on the nature of tcr alpha chain and their conformation as shown in a study by zhong et al.. to simulate a t cell response to h1n epitopes on population level as it is desirable for vaccine design, a large number of crystal structure data on tcr vα and vβ chains and their heterodimers would be necessary to computationally assess epitope candidates for their potential to induce a broad t cell response. 
studies on pandemic influenza vaccines have shown that t cell recognition to conserved epitopes and cross-reactive t cell responses are important when new strains emerge, especially in the absence of antibody cross-reactivity. the results are novel with regard to ha epitopes and useful for developing possible vaccination strategies against the rapidly changing influenza viruses. molecular docking analysis of differential dm1-tcr recognition of the 2009-h1n epitope candidates yielded a mosaic epitope and potential h5n ha cross-reactive epitopes that could be applied as multivalent peptide towards influenza a vaccine development. in this work, using hla-b* and dm1-tcr structure model, we systematically generated high confidence conserved 2009-h1n t cell epitope candidates and investigated their potential cross-reactivity against h5n avian flu virus. yet, the challenge of identifying epitope candidates that result in heterologous t cell immunity under natural influenza infection conditions can only be overcome if more structural data on the tcr repertoire become available. structural models of tcr cross-recognition between 2009-h1n and 2004-h5n revealed steric and topological effects of tcr contact residue mutations on tcr binding affinity.
 the pandemic 2009-h1n influenza virus circulated in the human population and caused thousands deaths worldwide. studies on pandemic influenza vaccines have shown that t cell recognition to conserved epitopes and cross-reactive t cell responses are important when new strains emerge, especially in the absence of antibody cross-reactivity. in this work, using hla-b* and dm1-tcr structure model, we systematically generated high confidence conserved 2009-h1n t cell epitope candidates and investigated their potential cross-reactivity against h5n avian flu virus.  molecular docking analysis of differential dm1-tcr recognition of the 2009-h1n epitope candidates yielded a mosaic epitope and potential h5n ha cross-reactive epitopes that could be applied as multivalent peptide towards influenza a vaccine development. structural models of tcr cross-recognition between 2009-h1n and 2004-h5n revealed steric and topological effects of tcr contact residue mutations on tcr binding affinity.  the results are novel with regard to ha epitopes and useful for developing possible vaccination strategies against the rapidly changing influenza viruses. yet, the challenge of identifying epitope candidates that result in heterologous t cell immunity under natural influenza infection conditions can only be overcome if more structural data on the tcr repertoire become available. 21- january the eleventh asia pacific bioinformatics conference vancouver, canada 