Virus Genes

, Volume 36, Issue 2, pp 345–353 | Cite as

Characterization of the complete genome of influenza A (H5N1) virus isolated during the 2006 outbreak in poultry in India

  • Koninika Ray
  • Varsha A. Potdar
  • Sarah S. Cherian
  • Shailesh D. Pawar
  • Santosh M. Jadhav
  • Shamal R. Waregaonkar
  • Anshu A. Joshi
  • Akhilesh C. Mishra


An outbreak of highly pathogenic avian influenza A (H5N1) virus in poultry was reported from Nandurbar and Jalgaon districts of Maharashtra and adjoining areas of Uchhal in Gujarat and Burhanpur in Madhya Pradesh in India from January to April, 2006. In the present study, the full genome of two previously uncharacterized strains of H5N1 viruses isolated at the National Institute of Virology (NIV), Pune, from post-mortem tissues of chicken collected from Navapur, Nandurbar district during the outbreak, has been presented. All the genes belong to clade 2.2 of the Z genotype and are close to the 2006 isolates from Iran, Afghanistan, Mongolia, Italy, and Krasnodar. In a study reported earlier, based on the partial gene sequences of HA, the authors (Pattnaik et al.) hypothesized that the viruses in Jalgaon and Navapur, causing outbreaks 12 days apart, were introduced at different times from different sources. However, our Navapur isolates are closer to the isolate reported from Jalgaon than that from Navapur. Molecular markers suggest that the isolates are sensitive to both drugs Oseltamivir and Amantadine. Amino acid residues responsible for pathogenesis, glycosylation, and receptor binding have also been discussed. The relationship between the Indian viruses and those in the East Africa/West-Asia flyway of migratory birds and the position of Nandurbar in this route suggests that the viruses in India may have been introduced through migratory birds although the role of trade as a possible route of introduction of the virus cannot be ruled out.


Highly Pathogenic Avian Influenza (HPAI) H5N1 India Clade 2.2 Poultry 



The work described was supported by the Intramural Grant of the National Institute of Virology, Pune (Indian Council of Medical Research, Government of India). The authors wish to thank Dr. A. Chakrabarty, Mr. A. Walimbe, Mr. G. Prabhakar, Mr. N. Mishra, and Mr. S. Ranawade for scientific discussions, bioinformatics analyses and help in the laboratory. We are grateful to Drs. M. Chadhha and D. Mourya for their support.


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Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Koninika Ray
    • 1
  • Varsha A. Potdar
    • 2
  • Sarah S. Cherian
    • 2
  • Shailesh D. Pawar
    • 1
  • Santosh M. Jadhav
    • 2
  • Shamal R. Waregaonkar
    • 2
  • Anshu A. Joshi
    • 2
  • Akhilesh C. Mishra
    • 2
  1. 1.Microbial Containment ComplexNational Institute of VirologyPuneIndia
  2. 2.National Institute of VirologyPuneIndia

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