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Comparing the structures of H3, H5 and H9 subtype haemagglutinins, we deduced a structural basis for including all 15 influenza subtypes in four clades. H3, H5 and H9 represent three of these clades; we now report the structure of an H7 HA as a representative of the fourth clade. We confirm the structure of the turn at the N-terminus of the conserved central alpha-helix of HA2, and the combination of ionisable residues near the "fusion peptide" as clade-specific features. We compare the structures of three H1 HAs with H5 HA in the same clade, to refine our previous classification and we confirm the division of the clades into two groups of two. We also show the roles of carbohydrate side chains in the esterase-fusion domain boundaries in the formation of clade-specific structural markers.

The 1918 influenza pandemic resulted in about 20 million deaths. This enormous impact, coupled with renewed interest in emerging infections, makes characterization of the virus involved a priority. Receptor binding, the initial event in virus infection, is a major determinant of virus transmissibility that, for influenza viruses, is mediated by the hemagglutinin (HA) membrane glycoprotein. We have determined the crystal structures of the HA from the 1918 virus and two closely related HAs in complex with receptor analogs. They explain how the 1918 HA, while retaining receptor binding site amino acids characteristic of an avian precursor HA, is able to bind human receptors and how, as a consequence, the virus was able to spread in the human population.

The three-dimensional structures of avian H5 and swine H9 influenza hemagglutinins (HAs) from viruses closely related to those that caused outbreaks of human disease in Hong Kong in 1997 and 1999 were determined bound to avian and human cell receptor analogs. Emerging influenza pandemics have been accompanied by the evolution of receptor-binding specificity from the preference of avian viruses for sialic acid receptors in alpha2,3 linkage to the preference of human viruses for alpha2,6 linkages. The four new structures show that HA binding sites specific for human receptors appear to be wider than those preferring avian receptors and how avian and human receptors are distinguished by atomic contacts at the glycosidic linkage. alpha2,3-Linked sialosides bind the avian HA in a trans conformation to form an alpha2,3 linkage-specific motif, made by the glycosidic oxygen and 4-OH of the penultimate galactose, that is complementary to the hydrogen-bonding capacity of Gln-226, an avian-specific residue. alpha2,6-Linked sialosides bind in a cis conformation, exposing the glycosidic oxygen to solution and nonpolar atoms of the receptor to Leu-226, a human-specific residue. The new structures are compared with previously reported crystal structures of HA/sialoside complexes of the H3 subtype that caused the 1968 Hong Kong Influenza virus pandemic and analyzed in relation to HA sequences of all 15 subtypes and to receptor affinity data to make clearer how receptor-binding sites of HAs from avian viruses evolve as the virus adapts to humans.

A single amino acid substitution, Asp-63 to Asn-63, was detected in the hemagglutinin of an antigenic variant of the 1968 Hong Kong (H3) influenza virus that was selected by growth of the wild-type virus in the presence of a monoclonal antibody. The mutation generates an oligosaccharide attachment site, Asn-Cys-Thr at residues 63-65, that is glycosylated. Immunoprecipitation experiments with extracts from variant virus-infected cells prepared in the presence or absence of tunicamycin, which inhibits glycosylation, demonstrate that addition of the new oligosaccharide side chain is required to prevent reaction with the monoclonal antibody. Similar experiments with the virus of the 1969 Hong Kong influenza epidemic, A/England/878/69, which also contains a hemagglutinin glycosylated at residue 63, support this conclusion and provide evidence for the epidemiological significance of carbohydrate-mediated modifications of hemagglutinin antigenicity.

Since their reintroduction to human populations in 1977, influenza A viruses of the H1N1 subtype have undergone antigenic drift. Recently a distinct antigenic variant, A/Singapore/6/86, has been almost exclusively isolated internationally, and the antigenic properties and amino acid sequence of its haemagglutinin have been determined and compared with those of the haemagglutinins of other H1N1 viruses, in particular A/Chile/1/83. Fourteen amino acid sequence differences are detected between the HA1 components of these two viruses, ten of which are different from equivalent residues in the haemagglutinins of all H1N1 viruses isolated between 1982 and 1983, and seven of which are novel in the haemagglutinins of all H1N1 viruses sequenced to date. The results are discussed in relation to the three-dimensional structure of the haemagglutinin and the location of the previously defined antigenically important regions.