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Influenza virus contains two highly variable envelope glycoproteins,hemagglutinin (HA) and neuraminidase (NA). The structure and properties of HA,which is responsible for binding the virus to the cell that is being infected,change significantly when the virus is transmitted from avian or swine speciesto humans. Previously we identified much smaller human individual evolutionaryamino acid mutational changes in NA, which cleaves sialic acid groups and isrequired for influenza virus replication. We showed that these smaller changescan be monitored very accurately across many Uniprot and NCBI strains usinghydropathicity scales to quantify the roughness of water film packages, whichincreases gradually due to migration, but decreases abruptly under large-scalevaccination pressures. Here we show that, while HA evolution is much morecomplex, it still shows abrupt punctuation changes linked to those of NA. HAexhibits proteinquakes, which resemble earthquakes and are related tohydropathic shifting of sialic acid binding regions. HA proteinquakes based onsialic acid interactions are required for optimal balance between thereceptor-binding and receptor-destroying activities of HA and NA for efficientvirus replication. Our comprehensive results present an historical (1945-2011)panorama of HA evolution over thousands of strains, and are consistent withmany studies of HA and NA interactions based on a few mutations of a fewstrains. While the common influenza virus discussed here has been renderedalmost harmless by decades of vaccination programs, the sequential decodinglessons learned here are applicable to other viruses that are emerging aspowerful weapons for controlling and even curing common organ cancers. Thoseengineered oncolytic drugs will be discussed in future papers.

Punctuated evolution of influenza virus hemagglutinin (A/H1N1) under opposing migration and vaccination pressures