Evolutionary characterization of the six internal genes of H5N1 human influenza A virus

J Gen Virol. 2000 May;81(Pt 5):1293-303. doi: 10.1099/0022-1317-81-5-1293.


The entire nucleotide sequences of all six internal genes of six human H5N1 influenza A viruses isolated in Hong Kong in 1997 were analysed in detail from a phylogenetic point of view and compared with the evolutionary patterns of the haemagglutinin and neuraminidase genes. Despite being isolated within a single year in the same geographical location, human H5N1 viruses were characterized by a variety of amino acid substitutions in the ribonucleoprotein complex [PB2, PB1, PA and nucleoprotein (NP)] as well as the matrix (M) proteins 1 and 2 and nonstructural (NS) proteins 1 and 2. The presence of previously reported amino acid sequences specific for human strains was confirmed in the PB2, PA, NP and M2 proteins. Nucleotide and amino acid sequence identities of the six internal genes of H5N1 viruses examined here were separated into at least two variant groups. In agreement with the above result, phylogenetic trees of the six internal genes of human H5N1 viruses were generally composed of two minor clades. Additionally, variable dendrogram topologies suggested that reassortment among viruses contributed further to the genetic variability of these viruses. As a result, it became clear that human H5N1 viruses are characterized by divergent gene constellations, suggesting the possible occurrence of genetic reassortment between viruses of the two evolutionary lineages.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA-Directed RNA Polymerases / chemistry
  • DNA-Directed RNA Polymerases / genetics
  • Evolution, Molecular*
  • Genes, Viral*
  • Genetic Variation*
  • Humans
  • Influenza A Virus, H5N1 Subtype*
  • Influenza A virus / genetics*
  • Molecular Sequence Data
  • Nucleocapsid Proteins
  • Nucleoproteins*
  • Phylogeny
  • RNA Replicase*
  • Sequence Analysis, DNA
  • Viral Core Proteins / chemistry
  • Viral Core Proteins / genetics
  • Viral Matrix Proteins / chemistry
  • Viral Matrix Proteins / genetics
  • Viral Nonstructural Proteins / chemistry
  • Viral Nonstructural Proteins / genetics
  • Viral Proteins / chemistry
  • Viral Proteins / genetics*


  • M-protein, influenza virus
  • M2 protein, Influenza A virus
  • NS protein, influenza virus
  • Nucleocapsid Proteins
  • Nucleoproteins
  • PA protein, influenza viruses
  • PB2 protein, Influenzavirus A
  • Viral Core Proteins
  • Viral Matrix Proteins
  • Viral Nonstructural Proteins
  • Viral Proteins
  • influenza virus polymerase basic protein 1
  • RNA Replicase
  • DNA-Directed RNA Polymerases

Associated data

  • GENBANK/AF036358
  • GENBANK/AF036359
  • GENBANK/AF036360
  • GENBANK/AF036362
  • GENBANK/AF036363
  • GENBANK/AF084261
  • GENBANK/AF084262
  • GENBANK/AF084263
  • GENBANK/AF084264
  • GENBANK/AF084265
  • GENBANK/AF084266
  • GENBANK/AF084267
  • GENBANK/AF084268
  • GENBANK/AF084269
  • GENBANK/AF084270
  • GENBANK/AF084276
  • GENBANK/AF084277
  • GENBANK/AF084278
  • GENBANK/AF084282
  • GENBANK/AF084283
  • GENBANK/AF084284
  • GENBANK/AF084285
  • GENBANK/AF084286
  • GENBANK/AF084287
  • GENBANK/AF115284
  • GENBANK/AF115285
  • GENBANK/AF115286
  • GENBANK/AF115287
  • GENBANK/AF115288
  • GENBANK/AF115289