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. 2015 Mar 4;89(10):5427–5440. doi: 10.1128/JVI.03636-14

TABLE 1.

Amino acid sites with annotations of epitopes, diversifying selection, and postpandemic mutations

AA site, H1a AA site, H3b H1 HA1/HA2 coordinate H3 HA1/HA2 coordinate B-cell epitope (IEDB code) Probability of diversified prepandemic P valuec
California, USA New York, USA Texas, USA Louisiana, USA Florida, USA Colorado, USA British Columbia, Canada Czech Republicd Helsinki, Finlandd São Paulo, Brazil Moscow, Russiad Quebec, Canada Taiwan
4 4 Signal peptide Signal peptide 0.83
52 61 35 HA1 45 HA1 150978 0.85
111 117 94 HA1 101 HA1 172565, 181471 0.89
114 120 97 HA1 104 HA1 172565, 181471 1.686E−16 2.529E−12 4.449E−20 4.203E−14 4.332E−15 1.358E−14 2.250E−17 4.504E−15 6.553E−42 1.098E−10 7.488E−14 1.027E−18 1.501E−04
142 145 125 HA1 129 HA1 Sa, Extd Sa, 76963, 164527, 180050, 76962 0.85
158 160 141 HA1 144 HA1 0.91
170 172 153 HA1 156 HA1 Sb, Extd Sb, 72805, 136074, 179938, 76950 0.93
172 174 155 HA1 158 HA1 Sa, Extd Sa, 12284, 72805, 12285, 180309, 164527, 77529, 159269, 194989, 173915, 76950 0.93
177 179 160 HA1 163 HA1 Sa, Extd Sa, 12284, 12285, 164527 0.99
179 181 162 HA1 165 HA1 Sa, Extd Sa, 12284, 12285, 164527, 180050 0.93
180 182 163 HA1 166 HA1 Sa, Extd Sa, 12284, 12285, 133973, 164527, 180050, 190190, 94400 1.177E−12 2.060E−11 4.209E−16 4.838E−13 1.666E−07 1.299E−12 6.855E−09 1.062E−07 1.860E−10 1.217E−03
202 204 185 HA1 188 HA1 180309, 159269 6.160E−19 2.380E−14 6.422E−21 4.203E−14 5.230E−16 1.358E−14 3.149E−17 4.504E−15 2.753E−38 1.098E−10 7.488E−14 1.027E−18 4.561E−13
203 205 186 HA1 189 HA1 76960, 180309, 76961, 159269, 179938, 76959, 76962 0.96
204 206 187 HA1 190 HA1 76960, 180309, 76961, 179938 1.00
220 222 203 HA1 206 HA1 127932, 2136 6.160E−19 2.380E−14 6.422E−21 4.203E−14 5.230E−16 1.358E−14 2.250E−17 4.504E−15 2.436E−19 4.561E−13 7.488E−14 1.027E−18 4.561E−13
239 241 222 HA1 225 HA1 Ca2, Extd Ca2, 177089, 177084, 177087, 177088, 177121, 159269, 179938, 76965 1.00
251 253 234 HA1 237 HA1 8.998E−03 3.146E−02 2.380E−05 3.230E−05 3.617E−13 4.100E−33 1.030E−11 1.331E−04 1.501E−04
273 275 256 HA1 259 HA1 2.957E−11 1.410E−09 1.049E−15 4.838E−13 4.662E−07 1.299E−12 6.855E−09 1.062E−07 1.860E−10
275 Gap 258 HA1 Gap 0.84
278 279 261 HA1 263 HA1 0.95
300 301 283 HA1 285 HA1 1.686E−16 2.529E−12 1.681E−18 4.203E−14 3.285E−14 1.358E−14 1.675E−16 4.228E−14 7.185E−22 1.880E−07 7.488E−14 1.027E−18 1.501E−04
391 392 47 HA2 48 HA2 180911, 190150 6.160E−19 2.380E−14 6.422E−21 4.203E−14 5.230E−16 1.358E−14 2.250E−17 4.504E−15 1.866E−43 4.561E−13 9.248E−13 1.027E−18 4.561E−13
468 469 124 HA2 125 HA2 0.97 6.160E−19 2.380E−14 6.422E−21 4.203E−14 6.327E−16 1.358E−14 2.250E−17 4.504E−15 6.553E−42 1.098E−10 9.248E−13 1.568E−18 4.561E−13
516 517 172 HA2 173 HA2 181381 2.809E−17 2.529E−12 2.841E−19 4.203E−14 4.332E−15 1.358E−14 1.675E−16 4.228E−14 1.303E−35 1.880E−07 7.488E−14 1.027E−18 1.741E−05
537 538 193 HA2 194 HA2 29690 0.85
a

Amino acid (AA) positions based on the reference sequence A/California/04/2009 (H1N1) (GenBank accession number ACP41105.1).

b

Amino acid positions based on the reference sequence A/Aichi/2/1968 (H3N2) (GenBank accession number BAF37221.1).

c

P value based on sequence variation between early versus late pandemic sequences.

d

Notice that the pairwise comparison between the early strain versus strains from the Czech Republic, Helsinki, and Moscow did not find any significant sequence variation at sites 180 and 273. This is because the majority of strains from these three regions are from the 2012-2013 flu season and the mutations present at sites 180 and 273 became dominant in the 2013-2014 flu season.