Punctuated evolution of influenza virus neuraminidase (A/H1N1) under   migration and vaccination pressures
  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 species to humans. Here we focus on much smaller human individual evolutionary amino acid mutational changes in NA, which cleaves sialic acid groups and is required for influenza virus replication. We show that very small amino acid changes can be monitored very accurately across many Uniprot and NCBI strains using hydropathicity scales to quantify the roughness of water film packages. Quantitative sequential analysis is most effective with the differential hydropathicity scale based on protein self-organized criticality (SOC). NA exhibits punctuated evolution at the molecular scale, millions of times smaller than the more familiar species scale, and thousands of times smaller than the genomic scale. Our analysis shows that large-scale vaccination programs have been responsible for a very large convergent reduction in influenza severity in the last century, a reduction which is hidden from short-term studies of vaccine effectiveness. Hydropathic analysis is capable of interpreting and even predicting trends of functional changes in mutation prolific viruses. 
J. C. Phillips
q-bio.BM