Protein T cell epitopes Amino acid position Predicted binding to HLA Class II alleles 
 
Hemagglutinin		 LKGVAPLHL 
 
 60-68 DRB1_0101, 0102,0701,0703,1104,1106,1128,1305,1311,1321,1501,1506, DRB5_0101, DRB5_0105
VVLLYTFTT 
 
 5-13 DRB1_0101, 0102,0301, 0305, 0306, 0307, 0308,0309, 0311 0401,0402,0404, 0405,0408,0410,0421,0423,0426,0801,0804,0806, 0813, 0817, 1101,1102, 1104,1106,1107,1114, 1120,1121, 1128, 1301,1302, 1304, 1305,1307, 1311,1321, 1322,1327,1328,1501,1502,1506 
 
Neuraminidase		 FVIREPFIS 114-122 DRB1_0305,0309,0801,0802,0804,0813, 0817, 1101,1102, 1104,1106, 1107, 1114, 1120,1121, 1128,1302,1304, 1305,1311,1321,1322,1323,1327,1328,1502,DRB5_0101, DRB5_0105
VNISNTNFA 
 
 66-74 DRB1_0306, 0307, 0308,0311, 0401,0402, 0404,0405,0408,0410,0421,0423,0426,1102,1107,1121,1301, 1322,1327,1328 
 
Polymerase PA		 FLLMDALKL 
 
 281-289 DRB1_0101,0102,0405,0408,0421,0701,0703, 0817,1101,1114, 1128,1305,1307,1321,1323,1501,1502,1506, DRB5_0101, DRB5_0105
VVNFVSMEF 
 
 516-524 DRB1_0102, 0301,0402,0404,0405,0408,0410, 0423,0701, 0703,1102, 1104,1106,1121,1128,1301,1305,1311, 1321, 1327, 1328,1501,1502,1506
Polymerase PB1 VRKMMTNSQ 
 
 280-288 DRB1_0306, 0307, 0308, 0311, 0401,0402, 0404,0405, 0408, 0410,0421, 0423,0426,0804, 0801, 0802,0806, 0813,1102,1104, 1106,1114, 1121,1301,1304,1307,1311, 1322,1323,1327,1328
MITYITRNQ 
 
 315-323 DRB1_ 0402, 0801, 0802, 0804, 0806, 1102, 1114, 1121, 1301,1304, 1322,1323,1327,1328 
 
Polymerase PB2
 LRILVRGNS 
 
 639-647 DRB1_0301,0305,0306,0307,0308,0309,0311,0801,0802,0804,0806, 0813,0817, 1101,1102,1104,1106,1107, 1114,1121, 1128,1301,1305,1307,1311,1321, 1322,1323,1327,1328,1501,1502,1506
LRISSSFSF 
 
 316-324 DRB1_0101,0102,0301,0309,0421,0701,0703,1501,1502,1506, DRB5_0101, DRB5_0105 
 
Matrix protein		 FVFTLTVPS 
 
 61-69 DRB1_0101,0301,0308,0401,0402, 0404,0405,0408,0410,0421,0423,0426,0701,0703, 0802,0813,1101,1114,1120,1128,1302, 1305,1307,1321,1323
MRAIGTHPS 
 
 215-223 DRB1_0102,0301,0305,0306, 0307, 0308, 0309,0311,0401,0402,0404,0405,0408,0410,0421, 0423,0426,0802,0804,0806, 0813,1101,1102,1104,1106,1107,1114,1121, 1128,1301,1305,1307,1311,1321, 1322,1323,1327,1328,DRB5_0101, DRB5_0105
Nucleocapsid protein LVWMACHSA 
 
 327-335 DRB1_0101, 0102,0402, 0404,0423,1102, 1104,1106, 1114,1121,1311, 1322,1323, DRB5_0101, DRB5_0105
IRMMESAKP 
 
 444-452 DRB1_ 0102,0401,0402, 0404,0405,0408,0410,0421,0423,0426,0802,0804, 1101,1102, 1104,1106,1114,1121,1301, 1307,1311,1322,1323,1327,1328
Table 3: Selected peptides of H1N1 proteome and their allele coverage (The given peptides are predicted to bind to the depicted HLA class II molecules, PROPRED~4%).