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Sequence and phylogenetic analysis of highly pathogenic avian influenza H5N1 viruses isolated during 2006–2008 outbreaks in Pakistan reveals genetic diversity

Naila Siddique12, Khalid Naeem1*, Muhammad A Abbas1, Zaheer Ahmed1 and Salman A Malik2

Author Affiliations

1 National Reference Lab for Poultry Diseases, Animal Sciences Institute, National Agricultural Research Centre, Islamabad, 45500, Pakistan

2 Department of Biochemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan

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Virology Journal 2012, 9:300  doi:10.1186/1743-422X-9-300

Published: 3 December 2012

Additional files

Additional file 1:

Percentage nucleotides homology of the all genes of Pakistani H5N1 AIVs among them with other closely related AIV strains.

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Open Data

Additional file 2:

Evolutionary relationship of M gene of Pakistani HP H5N1 viruses compared with other representative Eurasian H5N1 viruses. The nucleotide coding regions tree was generated by neighbour joining method (with Maximum Composite Likelihood) as implemented in MEGA version 4. Numbers at the nodes indicate confidence level of a bootstrap analysis with 1000 replications as a percentage value. Scale bar indicates 0.005 nucleotide substitutions per site. The Pakistani isolates are marked in dark circles. Tree is midpoint rooted.

Format: PDF Size: 576KB Download file

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Open Data

Additional file 3:

Evolutionary relationship of NP gene of Pakistani HP H5N1 viruses compared with other representative Eurasian H5N1 viruses. The nucleotide coding regions tree was generated by neighbour joining method (with Maximum Composite Likelihood) as implemented in MEGA version 4. Numbers at the nodes indicate confidence level of a bootstrap analysis with 1000 replications as a percentage value. Scale bar indicates 0.01 nucleotide substitutions per site. The Pakistani isolates are marked in dark circles. Tree is midpoint rooted.

Format: PDF Size: 614KB Download file

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Open Data

Additional file 4:

Evolutionary relationship of PA gene of Pakistani HP H5N1 viruses compared with other representative Eurasian H5N1 viruses. The nucleotide coding regions tree was generated by neighbour joining method (with Maximum Composite Likelihood) as implemented in MEGA version 4. Numbers at the nodes indicate confidence level of a bootstrap analysis with 1000 replications as a percentage value. Scale bar indicates 0.01 nucleotide substitutions per site. The Pakistani isolates are marked in dark circles. Tree is midpoint rooted.

Format: PDF Size: 582KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Evolutionary relationship of PB1 gene of Pakistani HP H5N1 viruses compared with other representative Eurasian H5N1 viruses. The nucleotide coding regions tree was generated by neighbour joining method (with Maximum Composite Likelihood) as implemented in MEGA version 4. Numbers at the nodes indicate confidence level of a bootstrap analysis with 1000 replications as a percentage value. Scale bar indicates 0.005 nucleotide substitutions per site. The Pakistani isolates are marked in dark circles. Tree is midpoint rooted.

Format: PDF Size: 577KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6:

Evolutionary relationship of PB2 gene of Pakistani HP H5N1 viruses compared with other representative Eurasian H5N1 viruses. The nucleotide coding regions tree was generated by neighbour joining method (with Maximum Composite Likelihood) as implemented in MEGA version 4. Numbers at the nodes indicate confidence level of a bootstrap analysis with 1000 replications as a percentage value. Scale bar indicates 0.02 nucleotide substitutions per site. The Pakistani isolates are marked in dark circles. Tree is midpoint rooted.

Format: PDF Size: 749KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data