Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus

Abstract

The 2009 H1N1 swine flu is the first influenza pandemic in decades. The crystal structure of the hemagglutinin from the A/California/04/2009 H1N1 virus shows that its antigenic structure, particularly within the Sa antigenic site, is extremely similar to those of human H1N1 viruses circulating early in the 20th century. The cocrystal structure of the 1918 hemagglutinin with 2D1, an antibody from a survivor of the 1918 Spanish flu that neutralizes both 1918 and 2009 H1N1 viruses, reveals an epitope that is conserved in both pandemic viruses. Thus, antigenic similarity between the 2009 and 1918-like viruses provides an explanation for the age-related immunity to the current influenza pandemic.

Fig. 1

Crystal structure, phylogeny and antigenic variation in influenza A 2009 H1N1 HA. (A) Phylogenetic tree of selected H1 HAs in swine and human. (B) Antigenic structure of CA04 HA from the 2009 H1N1 pandemic virus. A trimer complex is shown in surface representation with the antigenic sites highlighted: Sa site in magenta; Sb site in cyan; Ca site in orange; and Cb site in blue. Sa and Sb sites are located near the receptor-binding site. The Ca site straddles the subunit interface in the trimer. (C) Sequence alignment of membrane-distal domains from representative H1 HAs. Antigenic epitopes are color-coded as in B.

Fig. 2

Antigenic sites and antigenic variation in H1N1 HAs. (A) Localization of H1 antigenic sites in the HA1 membrane-distal domain in close view. Antigenic sites are color-coded as in Fig. 1. (B–D) Antigenic variation of seasonal flu H1N1 HAs compared to CA04. Antigenic sites of three H1 HAs are displayed in molecular surface [(B) SC1918; (C) PR8/34; (D) Brisbane2007 (current seasonal flu vaccine strain)]. Residual differences between CA04 and selected H1 HAs are highlighted based on antigenic regions (Sa, magenta; Sb, cyan; Ca, orange; Cb, blue). The SC1918 HA antigenic surface is highly conserved in CA04. In later years (1930 –2007), the H1N1 HA antigenic surface has become more variable through mutations and importantly, acquired additional N-glycosylation sites (shown as a cartoon with branched sticks in green) that mask the surface from recognition by neutralizing antibodies. (E) Increased variation over these time periods is shown in the plot of residual differences between CA04 and selected human H1 HAs in the antigenic sites over time. Sequences of H1 HA in the early half of 20^th century are selected from the NCBI Influenza Virus Resource (http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html). After 1977, only the nine H1N1 vaccine strains are shown. The sequences and antigenic site variation of the HAs analyzed in panels E and F are listed in table S2. (F) Similar plot for the Sa site color-coded by the number of potential N-glycosylation sites in the Sa antigenic region (green, 0 glycans; blue, 1 glycan; orange, 2 glycans; red, 3 glycans).

Fig. 3

Crystal structure of cross-neutralizing antibody 2D1 in complex with SC1918. (A) Antibody 2D1, with the light and heavy chains of the Fab in yellow and red, respectively, recognizes the Sa site of SC1918 HA, where HA1 is shown in magenta and HA2 in cyan. (B) Footprint of antibody 2D1 on the SC1918 HA shows the central role of the Sa site residues for 2D1 binding. The interacting surface contributed by residues from the Sa site is colored in magenta, whereas residues that contribute to the epitope, but are outside of the ‘canonical’ Sa site, are colored in yellow. Sa site residues not in contact with 2D1 are shown in pink. SC1918 and CA04 do not have N-glycosylation sites in the Sa region, whereas the vaccine strain Brisbane07, like many other seasonal H1 HAs, have acquired potential glycosylation sites at positions 129 and 163 (italics on surface). (C) Antibody 2D1 exhibits strong binding to both 1918 HA and CA04 HA, but not to PR8 and HAs of other influenza subtypes, as tested in ELISA assay.