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.

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.