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During protein evolution the amino acid substitutions accumulate with time. However, the effect of accumulation of the amino acid substitutions to structural changes has not been estimated well. We will propose that the discordance of amino acid substitution on the HA protein of influenza A virus is useful for the assessment of structural changes during evolution. Discordance value can be obtained from the experimental data of tolerance or intolerance by introducing site directed mutagenesis at the homologous positions of two HA proteins holding the same amino acid residues. The value of discordance correlated to the number of amino acid differences among proteins. In the H3HA discordance rate was calculated to be 0.45% per one amino acid change. Furthermore, discordance of amino acid substitutions suggests that tolerable amino acid substitutions in different order have a probability of promoting irreversible divergence of the HA protein to different subtypes.

Cleavage of the hemagglutinin (HA) molecule by proteases is a prerequisite for the pathogenicity and even for the neurovirulence of influenza A viruses. WSN, a neurovirulent virus, adapted to mouse brain, grew in vitro in several types of cells including neuroblastoma cells in the absence of trypsin. When mice were intracerebrally inoculated with WSN, the viral antigen was found in the substantia nigra zona compacta and hippocampus. The mice inoculated with viruses isolated from children with acute encephalopathy associated with an influenza virus infection, on the other hand, showed no neurological symptoms. Furthermore, these viruses did not grow in the human neuroblastoma and glioblastoma cells. Since 1991, most of the human influenza A viruses have not agglutinated chicken erythrocytes. Whether this altered receptor binding specificity is related to the occurrence of influenza encephalitis and encephalopathy is now under investigation.

Influenza A virus is unique among human viruses in its capacity to alter the antigenic phenotype with relative ease and evade neutralizing antibodies. This property is ascribed to the accumulation of a series of amino acid changes in the antigenic regions of hemagglutinin (HA) molecule. Neutralizing antibodies against HA prevent the early stage of infection, whereas neuraminidase (NA) antibodies mediate the antiviral effect by restricting spread of viruses in the host cells after infection. Thus the understanding of antigenic structure on those protective antigen is significant. Sequence analysis of natural variants and escape mutants selected by monoclonal antibodies allowed us to assign each antigenic sites and epitopes to a particular region on the three dimensional structure of HA and NA molecules.

The hemagglutinin(HA) of influenza virus is a major glycoprotein and plays a crucial role in the early stage of virus infection: HA is responsible for binding of the virus to cell surface receptors, and it mediates liberation of the viral genome into the cytoplasm through membrane fusion. The essential component of the receptor for influenza viruses has been considered to be the sialic acid. Influenza A and B viruses recognize N-acetylneuraminic acid, whereas influenza C virus specifically recognizes N-acetyl-9-O-acetylneuraminic acid as the receptor. Influenza A viruses are subdivided into 15 subtypes by their antigenic differences, but several amino acid residues composing functional domains (receptor binding site and fusion peptide) are shown to be conserved among HAs.

Influenza A viruses are suitable for the analysis of virus evolution because the genes of the viruses are well analyzed. The origin of the present human influenza A viruses are deduced to be direct descendent of the viruses which caused Spanish flu in 1918. The analysis of NS gene shows the branching point between avian and human viruses are early 1900. By comparison of the amino acid sequences, HA serotypes could be divided into two groups, i.e., an H1 and an H3 groups. The branching between subtypes H1 and H2 occurred fairly recently. The HA genes of influenza A viruses evolve causing two kinds of antigenic variation, saift and drift, which are caused by different mechanisms.