Rapid pathotyping of recent H5N1 highly pathogenic avian influenza viruses and of H5 viruses with low pathogenicity by RT-PCR and restriction enzyme cleavage pattern (RECP)

J Virol Methods. 2008 Dec;154(1-2):14-9. doi: 10.1016/j.jviromet.2008.09.011. Epub 2008 Oct 30.


Rapid and accurate diagnosis of avian influenza virus infections of poultry and humans comprises detection, subtyping, and, in case of subtypes H5 and H7, pathotyping of such viruses. Reliable methods for pathotyping of H5 avian influenza viruses (AIV) are based on determination of the intravenous pathogenicity index (IVPI) in specific pathogen free (SPF) chickens and on characterization of the hemagglutinin (HA) gene cleavage site by sequencing. The number of basic amino acids (arginine and lysine) at the cleavage site is an important indicator of pathogenicity. In this paper, a new rapid method for pathotyping of H5 subtype avian influenza viruses is described which is based on RT-PCR and restriction enzyme cleavage pattern (RECP) assay using the MboII restriction enzyme. Validation of the method using 28 H5 subtype reference isolates from different animal species revealed good performance characteristics regarding sensitivity and specificity, especially when targeting recent highly pathogenic AIV (HPAIV) of subtype H5N1 and Asian origin. In addition, RECP results were validated by testing 47 field samples from different sources and by sequencing of their RT-PCR products. This approach for H5 AIV pathotyping proved to be fast, reliable, and comparatively sensitive and is suitable especially for laboratories lacking sequencing or in vivo pathotyping facilities.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Deoxyribonucleases, Type II Site-Specific / metabolism
  • Influenza A Virus, H5N1 Subtype / genetics
  • Influenza A Virus, H5N1 Subtype / pathogenicity
  • Influenza A virus / genetics*
  • Influenza A virus / isolation & purification
  • Influenza A virus / pathogenicity*
  • Influenza in Birds / virology*
  • Polymorphism, Restriction Fragment Length*
  • Poultry
  • RNA, Viral / genetics*
  • Reverse Transcriptase Polymerase Chain Reaction / methods*
  • Sensitivity and Specificity


  • RNA, Viral
  • endodeoxyribonuclease MboII
  • Deoxyribonucleases, Type II Site-Specific