A recommended numbering scheme for influenza A HA subtypes

PLoS One. 2014 Nov 12;9(11):e112302. doi: 10.1371/journal.pone.0112302. eCollection 2014.


Comparisons of residues between sub-types of influenza virus is increasingly used to assess the zoonotic potential of a circulating strain and for comparative studies across subtypes. An analysis of N-terminal cleavage sites for thirteen subtypes of influenza A hemagglutinin (HA) sequences, has previously been described by Nobusawa and colleagues. We have expanded this analysis for the eighteen known subtypes of influenza. Due to differences in the length of HA, we have included strains from multiple clades of H1 and H5, as well as strains of H5 and H7 subtypes with both high and low pathogenicity. Analysis of known structures of influenza A HA enables us to define amino acids which are structurally and functionally equivalent across all HA subtypes using a numbering system based on the mature HA sequence. We provide a list of equivalences for amino acids which are known to affect the phenotype of the virus.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Hemagglutinins / chemistry
  • Hemagglutinins / classification*
  • Hemagglutinins / metabolism
  • Humans
  • Influenza A virus / metabolism*
  • Influenza, Human / pathology
  • Influenza, Human / virology
  • Molecular Sequence Data
  • Phenotype
  • Sequence Alignment


  • Hemagglutinins