Identification and Subtyping of Avian Influenza Viruses by Reverse transcription-PCR

J Virol Methods. 2001 Sep;97(1-2):13-22. doi: 10.1016/s0166-0934(01)00301-9.


Avian influenza viruses have 15 different hemagglutinin (HA) subtypes (H1-H15). We report a procedure for the identification and HA-subtyping of avian influenza virus by reverse transcription-PCR (RT-PCR). The avian influenza virus is identified by RT-PCR using a set of primers specific to the nucleoprotein (NP) gene of avian influenza virus. The HA-subtypes of avian influenza virus were determined by running simultaneously 15 RT-PCR reactions, each using a set of primers specific to one HA-subtype. For a single virus strain or isolate, only one of the 15 RT-PCR reactions will give a product of expected size, and thus the HA-subtype of the virus is determined. The result of HA-subtyping was then confirmed by sequence analysis of the PCR product. A total of 80 strains or isolates of avian influenza viruses were subtyped by this RT-PCR procedure, and the result of RT-PCR gave an excellent (100%) correlation with the result of the conventional serological method. The RT-PCR procedure we developed is rapid and sensitive, and could be used for the identification and HA-subtyping of avian influenza virus in organ homogenates.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Birds / virology*
  • DNA Primers / genetics
  • Hemagglutinin Glycoproteins, Influenza Virus / genetics
  • Humans
  • Influenza A virus / classification*
  • Influenza A virus / genetics*
  • Influenza A virus / isolation & purification
  • Influenza, Human / virology
  • Nucleoproteins / genetics
  • RNA, Viral / genetics
  • RNA, Viral / metabolism
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sensitivity and Specificity


  • DNA Primers
  • Hemagglutinin Glycoproteins, Influenza Virus
  • Nucleoproteins
  • RNA, Viral