The rapid molecular subtyping and pathotyping of avian influenza viruses

Abstract

Highly conserved nucleotide stretches flanking the cleavage site of the haemagglutinin (HA) gene of influenza type A viruses were utilised for generating PCR amplicons from a broad range of avian influenza viruses (AIV) in a one-step real-time SYBR Green RT-PCR assay. The nucleotide sequencing of the amplified PCR products simultaneously reveals both the HA subtype and the pathotype of the AIV isolates, as we demonstrated in case of H5 subtype viruses. The specificity of the assay was confirmed by investigating 66 strains of AIV and nine heterologous pathogens, including influenza B, C and various avian pathogenic viruses. This assay enables a general HA subtype identification and pathotype determination of AIV isolates providing a useful alternative tool for avian influenza diagnosis

Keywords

Avian influenza; Subtype; Pathotype; Real-time PCR; SYBR Green

Published in

Journal of Virological Methods
2009, volume: 156, number: 1-2, pages: 157-161

SLU Authors

• Zohari, Siamak

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    
  • National Veterinary Institute (SVA)

• Gyarmati, Peter

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    
  • National Veterinary Institute (SVA)

• Belak, Sandor

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    
  • National Veterinary Institute (SVA)

UKÄ Subject classification

Animal and Dairy Science
Veterinary Science

Publication identifier

• DOI: https://doi.org/10.1016/j.jviromet.2008.10.019

Permanent link to this page (URI)

https://res.slu.se/id/publ/27951