Virus Genes

, Volume 44, Issue 3, pp 450–458

Evolution and adaptation of hemagglutinin gene of human H5N1 influenza virus

  • Kaifa Wei
  • Yanfeng Chen
  • Juan Chen
  • Lingjuan Wu
  • Daoxin Xie

DOI: 10.1007/s11262-012-0717-x

Cite this article as:
Wei, K., Chen, Y., Chen, J. et al. Virus Genes (2012) 44: 450. doi:10.1007/s11262-012-0717-x


The H5N1 HPAI virus has brought heavy loss to poultry industry. Although, there exists limited human-to-human transmission, it poses potential serious risks to public health. HA is responsible for receptor-binding and membrane-fusion and contains the host receptor-binding sites and major epitopes for neutralizing antibodies. To investigate molecular adaption of HPAI H5N1 viruses, we performed a phylogenetic analysis of HA sequences with 240 HPAI virus strains isolated from human. The topology of the tree reveals overall clustering of strains in four major clusters based on geographic location, and shows antigenic diversity of HA of human H5N1 isolates co-circulating in Asia, Africa, and Europe. The four clusters possess distinct features within the cleavage site and glycosylation sites, respectively. We identified six sites apparently evolving under positive selection, five of which persist in the population. Three positively selected sites are found to be located either within or flanking the receptor-binding sites, suggesting that selection at these sites may increase the affinity to human-type receptor. Furthermore, some sites are also associated with glycosylation and antigenic changes. In addition, two sites are found to be selected differentially in the two clusters. The analyses provide us deep insight into the adaptive evolution of human H5N1 viruses, show us several candidate mutations that could cause a pandemic, and suggest that efficiency measures should be taken to deal with potential risks.


H5N1HAPI virusHA geneSelective patternAdaptive evolution





Highly pathogenic avian influenza


Maximum likelihood


Akaike information criterion


approximate Likelihood ratio test


Artificial neural networks


Single likelihood ancestor counting


Fixed effects likelihood


Random effects likelihood


Ancestral state reconstruction


Maximum likelihood estimation


Single breakpoint recombination


Bayesian information criteria

RDP test

Recombination detection program test


Internal fixed effects likelihood

Supplementary material

11262_2012_717_MOESM1_ESM.tif (4.4 mb)
Figure S1 Phylogenetic tree of Hemagglutinin genes of 240 human H5N1 viruses and WHO reference sequences. The phylogenetic tree is constructed by neighbor-joining with 1,000 bootstrap replicates. Bootstrap values greater than 60% are placed on the branches. Scale bar represents 0.0005 nucleotide changes. (TIFF 4537 kb)
11262_2012_717_MOESM2_ESM.tif (10.2 mb)
Figure S2 Selective pressure among four clusters. Global rates of HA genes of each cluster. Error bar shows 95% confidence interval. (TIFF 10428 kb)
11262_2012_717_MOESM3_ESM.tif (3.6 mb)
Figure S3 Inferred evolutionary history at sites under positive selection. The trees are rooted to GS/GD/1/96 and ancestral states are inferred by ASR implemented in Datamonkey. Tree branches are color coded by type of substitutions as follows: only non-synonymous substitutions are highlighted in red, only synonymous are in green and both synonymous and non-synonymous substitutions are colored in blue. (TIFF 3640 kb)
11262_2012_717_MOESM4_ESM.doc (362 kb)
Table S1 Strains name, accession number, abbreviation and potential glycosylation sites preidicted in this study. Table S2 Selective pressure among four clusters. Table S3 Sites found to be under differential selection. N/A refer to not available (DOC 362 kb)

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Kaifa Wei
    • 1
  • Yanfeng Chen
    • 1
  • Juan Chen
    • 1
  • Lingjuan Wu
    • 1
  • Daoxin Xie
    • 2
  1. 1.Department of Biological Sciences and BiotechnologyZhangzhou Normal UniversityZhangzhouChina
  2. 2.School of Life SciencesTsinghua UniversityBeijingChina