Virus Genes

, Volume 45, Issue 2, pp 283–294 | Cite as

Complete genome characterization of avian influenza virus subtype H9N2 from a commercial quail flock in Egypt

  • Abdel-Satar Arafa
  • Naglaa Hagag
  • Ahmed Erfan
  • Wessam Mady
  • Mohamed El-Husseiny
  • Amany Adel
  • Soad Nasef


The suspected presence of avian influenza virus subtype H9N2 in poultry in Egypt is a major concern since this subtype is widely distributed in different countries in the Middle East, here we describe the full genetic characterization of an avian influenza A virus (Qa/Egypt/11; H9N2) of subtype H9N2 that was previously isolated from a clinically normal quail flock in Giza, Egypt in May 2011. The nucleotide sequence analysis of the hemagglutinin gene of the isolated Egyptian virus showed the highest similarity with one group of recent Israeli strains (97 %) circulating from 2006–2010. Sequence homology and phylogenetic analysis indicated that the Qa/Egypt/11 isolate belonged to the A/quail/Hong Kong/G1/1997-like lineage with new mutations identified in all viral proteins. The phylogenetic analysis for the eight genes indicated placement of the Egyptian virus within the same lineage of H9N2 viruses that circulated in the region from 2006, especially with one group of recent Israeli strains. However, phylogenetic analysis of the internal genes like PB2, NP, and PA genes identified possible reassortment events for these genes with singular Israeli strains. This study indicates progressive evolution of this subtype in the Middle East region and possible mechanism of virus adaptation in land-based poultry like in quails.


Low pathogenic avian influenza H9N2 subtype Genetic characterization Full gene sequencing Phylogenetic analysis of Egyptian H9N2 virus Commercial quails 

Supplementary material

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Supplementary material 1 (DOCX 60 kb)
11262_2012_775_MOESM2_ESM.docx (20 kb)
Supplementary material 2 (DOCX 20 kb)
11262_2012_775_MOESM3_ESM.docx (17 kb)
Supplementary material 3 (DOCX 16 kb)


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Abdel-Satar Arafa
    • 1
  • Naglaa Hagag
    • 1
  • Ahmed Erfan
    • 1
  • Wessam Mady
    • 1
  • Mohamed El-Husseiny
    • 1
  • Amany Adel
    • 1
  • Soad Nasef
    • 1
  1. 1.National Laboratory for Veterinary Quality Control on Poultry ProductionAnimal Health Research InstituteDokki, GizaEgypt

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