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Table S1: Summary map of influenza A(H1N1)-HA gene antigenic sites by study Region Region Position as reported by different authors Caton Brownlee Stray Huang Liao All_PR34 Caton Brownlee Stray Huang Liao All_PR34 Sa Ca1 121 121 35 35 124 124 36 36 125 125 125 43 43 43 127 127 127 169 169 169 128 128 128 128 128 170 170 170 129 129 129 129 171 171 155 155 172 172 172 156 156 156 156 173 173 173 173 157 157 157 157 179 179 158 158 158 204 204 159 159 159 205 205 205 160 160 160 160 206 206 162 162 162 162 207 207 207 207 163 163 163 163 163 208 208 208 164 164 164 209 209 165 165 165 165 212 212 166 166 166 166 166 216 216 216 167 167 167 238 247 247 239 239 248 248 240 240 240 240 241 241 242 242 Sb 244 244 153 153 153 245 245 183 183 183 271 271 186 186 186 187 187 Ca2 188 188 130 130 130 189 189 189 189 189 132 132 190 190 190 190 190 133 133 133 133 191 191 191 191 137 137 192 192 192 192 139 139 193 193 193 193 193 193 140 140 140 140 194 194 194 194 141 141 141 141 195 195 195 142 142 142 142 142 196 196 196 143 143 143 197 197 197 144 144 144 144 198 198 198 145 145 145 146 146 Cb 149 149 47 47 221 221 51 51 222 222 54 54 54 224 224 224 224 57 57 225 225 225 225 69 69 69 237 237 70 70 71 71 71 H1c 73 73 86 86 74 74 74 94 94 75 75 271 271 76 272 272 77 77 273 273 273
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Table S1: Summary map of influenza A(H1N1)-HA gene antigenic sites by study
Region Region Position as reported by different authors
Caton Brownlee Stray Huang Liao
All_PR34 Caton Brownlee Stray Huang Liao All_PR34
Sa Ca1121 121 35 35
124 124 36 36
125 125 125 43 43 43
127 127 127 169 169 169
128 128 128 128 128 170 170 170
129 129 129 129 171 171
155 155 172 172 172
156 156 156 156 173 173 173 173
157 157 157 157 179 179
158 158 158 204 204
159 159 159 205 205 205
160 160 160 160 206 206
162 162 162 162 207 207 207 207
163 163 163 163 163 208 208 208
164 164 164 209 209
165 165 165 165 212 212
166 166 166 166 166 216 216 216
167 167 167 238
247 247 239 239
248 248 240 240 240 240
241 241
242 242
Sb 244 244
153 153 153 245 245
183 183 183 271 271
186 186 186
187 187 Ca2188 188 130 130 130
189 189 189 189 189 132 132
190 190 190 190 190 133 133 133 133
191 191 191 191 137 137
192 192 192 192 139 139
193 193 193 193 193 193 140 140 140 140
194 194 194 194 141 141 141 141
195 195 195 142 142 142 142 142
196 196 196 143 143 143
197 197 197 144 144 144 144
198 198 198 145 145 145
146 146
Cb 149 149
47 47 221 221
51 51 222 222
54 54 54 224 224 224 224
57 57 225 225 225 225
69 69 69 237 237
70 70
71 71 71 H1c73 73 86 86
74 74 74 94 94
75 75 271 271
76 272 272
77 77 273 273 273
78 78 78 274 274 274
79 79 79 275 275
80 80 80 80 276 276
81 81 81 277 277 277 277
82 82 82 82 279 279
83 83 83 280 280
85 85 281 281
115 115 282 282
149 149 286 286
252 252 295 295
253 253 310 310 310
255 255
256 256
259 259
260 260
261 261
262 262
263 263
264 264
265 265
266 266
267 267
Notes: Antigenic sites as reported by Caton et al., [30], Brownlee et al., [33], Huang et al., [35], Liao et al., [11]. The other authors numbering was based on influenza A/PR/8/1934 virus. A number of methods are used to identify positively selected sites on the HA gene including: a serological method, the haemagglutination inhibition assay (HI); genetic methods such as: pairwise analysis of the genome and determination of positively selected codons by comparing differences between non-synonymous (non-silent) vs. synonymous (silent) codon substitutions (ω=dN/dS), mapping amino acid changes using maximum parsimony tree, Shannon entropy (amino acid variation) and likelihood ratio (for a given antigenic site - LR), or use of the hamming distance to determine the percentage difference between vaccine strains (Pepitope), and determination of amino or 3D crystal structure of HA constructed using homology modelling [10,11,35,36,142,144,149–152]. The HI and 3D genetic comparison the 3D being the most commonly used. The studies here used one or more of these methods to determine that these sites are antigenic sites
