Sequence alignment of HA for known sub-types.

<p>Alignment of mature HA sequence for all known HA sub-types. Additional strains have been included for sub-types which show variation in the length of HA. Sequences are ordered according to their phylogenetic classification as group 1 (magenta bar) or group 2 (orange bar) HA. The protein secondary structure elements, α-helices and β-strands, are highlighted with red bars and cyan arrows, respectively. A blue box highlights regions which have high structural variation across all subtypes. Amino acids within these regions should not be defined as equivalent between all sub-types. Each amino acid is coloured according to clustalx2 rules <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112302#pone.0112302-Larkin1" target="_blank">[11]</a>. Briefly, glycine and proline are coloured orange and yellow, respectively. Conserved positively charged residues and negatively charged residues are coloured red and magenta, respectively. Conserved cysteines are coloured pink while conserved serine or threonine residues are in green. The remaining amino acids, if conserved are coloured blue. The sequences representative of each subtype are as follows: H1(A/United Kingdom/1/1933); H1pdm(A/California/04/2009); H2(A/Singapore/1/1957); H3(A/Aichi/2/1968); H4(A/swine/Ontario/01911/2/1999); H5(A/Vietnam/1203/2004); H5c221(A/chicken/Egypt/0915-NLQP/2009); H6(A/chicken/Taiwan/0705/1999); H7(A/Netherlands/219/2003); H8(A/turkey/Ontario/6118/1968); H9(A/swine/HongKong/9/1998); H10(A/mallard/bavaria/3/2006); H11(A/duck/England/1/1956); H12(A/duck/Alberta/60/1976); H13(A/gull/Maryland/704/1977); H14(A/mallard/Astrakhan/263/1982); H15(A/duck/Australia/341/1983); H16(A/black-headed-gull/Turkmenistan/13/1976); H17(A/little-yellow-shouldered-bat/Guatemala/060/2010); H18(A/flat-facedbat/Peru/033/2010).</p

Equivalent amino acid numbering for subtypes currently circulating in humans or have pandemic potential.

<p>Residue numbering is based on the mature sequence of HA1 across all subtypes for a set mutations shown to cause phenotypic differences. Positions where there is a deletion relative to other subtypes are represented by a “Δ”.</p><p>Equivalent amino acid numbering for subtypes currently circulating in humans or have pandemic potential.</p

Selective advantages when the substitution is absent at the start of infection.

<p>A) The selective advantage required to achieve 50% (black) prevalence of the adaptive substitution within the host after a certain number of days of infection in a situation where the substitution is not present in the infecting virus population (results for 10% and 90% shown in grey). B) The proportion of mutant observed after 3 (dark blue), 6 (blue), 9 (pink), 12 (red) and 15 (dark red) days of infection for a range of selective advantages. The grey bar indicates 50% prevalence.</p

Quantifying the selective advantage as a function of substitution prevalence at the start of infection and infection duration.

<p>The minimum selective advantage necessary to reach 50% prevalence in the human host is displayed in color as a function of days of infection (y-axis) and mutant proportion at start of infection (x-axis). Selective advantages of 2.5 and 1 represent the upper and lower bounds of the color bar. The selective advantage exceeds 2.5 for early time points (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0076047#pone-0076047-g001" target="_blank">Figure 1A</a>), but for clarity, a threshold was used here. For starting prevalences of >50% no selective advantage is required.</p

Figure 1A

gif files for rotational views of 3D antigenic maps in Figure

Figure 1B

gif files for rotational views of 3D antigenic maps in Figure

Figure 1D

gif files for rotational views of 3D antigenic maps in Figure

Figure 2. Source data 2

Figure 2. Source data 2 - Input and output text files used to calculate H1 and H3 comparative rates of antigenic evolution and diversity shown in Figure 2 and Supplementary File 3_ Table

Supplemental Table 2. Source data

Supplemental Table 2.Source data Text infiles, phylogenetic trees and source script for antigenic distance analyse

Supplemental Table 1. Source Data

Supplemental Table 1. Source Data - Text files and plots of summary statistics of testing in 1, 2, 3, 4 and 5 dimension