A maximum likelihood phylogenetic tree for nucleotide sequences of the HA gene of influenza viruses selected to be representative of HA gene segments in relevant hosts. Phylogenetic trees of a larger number of representative HA gene segments, and of all H1 HA swine gene segments are shown in Figs. S1D and S2D respectively. Tree was inferred using PAUP* (version 4.0b10) (39), using GTR+I+Γ₄ (the general time-reversible model with the proportion of invariant sites and the gamma distribution of among-site rate variation with four categories estimated from the empirical data) as determined by ModelTest (40). Global optimization of the tree topology was performed by tree bisection-reconnection branch swapping. The robustness of individual nodes of the tree was assessed using a bootstrap resampling analysis (1000 replicates, with topologies inferred using the neighbor-joining method under the GTR+I+Γ₄ substitution model).

Host and lineage origins for the gene segments of the 2009 A(H1N1) virus: PB2 polymerase basic 2, PB1 polymerase basic 1, PA polymerase acidic, HA hemagglutinin, NP nucleoprotein, NA neuraminidase, M matrix gene, NS nonstructural gene. Color of gene segment in circle indicates host. Determination of lineage explained in main text.

Antigenic map of 71 early swine-origin 2009 A(H1N1) influenza viruses and 11 antisera. An antigenic map is a geometric representation of binding assay data, in this case the HI assay data in Tables S3 and S4. In such a map, the relative positions of strains (colored circles) and antisera (uncolored squares) are adjusted such that the distances between strains and antisera in the map represent the corresponding HI measurements with the least error. Distance in the map thus represents antigenic distance and the closer antigens are to each other in the map the more similar they are antigenically (37). The color of a circle in the map indicates whether the strain is a 2009 A(H1N1) influenza virus (blue) or an A(H1) swine influenza virus isolated between 1998 and 2007 from either a swine or a human infected with a swine influenza virus (green). The vertical and horizontal axes both represent antigenic distance, and because only the relative positions of antigens and antisera can be determined, the orientation of the map within these axes is free (thus an antigenic map can be rotated in the same way that a geographic map can be rotated). The spacing between grid lines is one unit of antigenic distance--corresponding to a 2-fold dilution of antiserum in the HI assay. Two units correspond to 4-fold dilution, three units to 8- fold dilution, etc. A difference higher than 4-fold in HI titer is usually considered to be sufficient to necessitate an update of the human seasonal influenza virus vaccine. Antigenic clusters of human seasonal influenza viruses typically have a radius of 2 antigenic units (4-fold in HI) (37). (see Fig. S3 for a zoomable PDF that includes the names of each strain and antiserum).