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. 2008 Aug 22;4(8):e1000133. doi: 10.1371/journal.ppat.1000133

Table 3. Number of amino acid differences in the HA gene segment between clades A–H of A/H1N1 influenza virus sampled from the 2006–2007 US season.

A B C D E NC99 ‘01 ‘02/03 ‘05 F G H SI06
A - 2 23 34 3 35 2 2 3 1136 1536 131223 12123
B 2 - 43 34 3 35 2 2 3 1136 1536 111223 12123
C 23 43 - 534 53 535 43 43 53 96 156 13122 1212
D 34 34 534 - 44 445 34 34 44 12346 15346 1412234 131234
E 3 3 53 44 - 45 3 3 4 1236 1636 141223 13123
NC99 35 35 535 445 45 - 15 15 45 10356 14356 1212235 111235
‘01 2 2 43 34 3 15 - 0 3 936 1336 111223 10123
‘02/03 2 2 43 34 3 15 0 - 3 936 1336 111223 10123
‘05 3 3 53 44 4 45 3 3 - 1236 1636 141223 13123
F 1136 1136 96 12346 1236 10356 936 936 1236 - 96 81226 7126
G 1536 1536 156 15346 1636 14356 1336 1336 1636 96 - 101226 7126
H 131223 111223 131223 1412234 141223 1212235 111223 111223 141223 81226 101226 - 32
SI06 12123 12123 12123 131234 13123 111235 10123 10123 13123 7126 7126 32 -

As a comparison, isolates used as the A/H1N1 component of the influenza vaccine in 2006–2007 (A/New Caledonia/20/1999(H1N1) (NC99)) and 2007–2008 (A/Solomon Islands/3/2006(H1N1) (SI06)) are included, as well as representative isolates from the 2001 (‘01), 2002–2003 (‘02/03) and 2005 (‘05) seasons. Amino acid differences between clades in set 1 (clades A, B, C, D, E, NC99, ‘01, ‘02/03, and ‘05) and clades in set 2 (clades F, G, H, and SI06) are in bold. Amino acid changes in antigenic sites are denoted by superscripts as follows: 1–Cb antigenic site; 2–potential glycosylation site; 3–Ca2 antigenic site; 4–Sa antigenic site; 5–Ca1 antigenic site; 6–Sb antigenic site. For a complete list of amino acid changes at specific sites, see Table S1.