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A unique influenza A (H5N1) virus causing a focal poultry outbreak in 2007 in Manipur, India.

Mishra AC, Cherian SS, Chakrabarti AK, Pawar SD, Jadhav SM, Pal B, Raut S, Koratkar S, Kode SS - Virol. J. (2009)

Bottom Line: A focal H5N1 outbreak in poultry was reported from Manipur, a north-eastern state, of India, in 2007.The HA gene, had the cleavage site GERRRRKR, earlier reported in whooper swan isolates from Mongolia in 2005.A stop codon at position 29 in the PB1-F2 protein could have implications on the replication efficiency.

View Article: PubMed Central - HTML - PubMed

Affiliation: Microbial Containment Complex, National Institute of Virology, Pashan, Pune 411021, Maharashtra, India. acm1750@rediffmail.com

ABSTRACT

Background: A focal H5N1 outbreak in poultry was reported from Manipur, a north-eastern state, of India, in 2007. The aim of this study was to genetically characterize the Manipur isolate to understand the relationship with other H5N1 isolates and to trace the possible source of introduction of the virus into the country.

Results: Characterization of the complete genome revealed that the virus belonged to clade 2.2. It was distinctly different from viruses of the three EMA sublineages of clade 2.2 but related to isolates from wild migratory waterfowl from Russia, China and Mongolia. The HA gene, had the cleavage site GERRRRKR, earlier reported in whooper swan isolates from Mongolia in 2005. A stop codon at position 29 in the PB1-F2 protein could have implications on the replication efficiency. The acquisition of polymorphisms as seen in recent isolates of 2005-07 from distinct geographical regions suggests the possibility of transportation of H5N1 viruses through migratory birds.

Conclusion: Considering that all eight genes of the earlier Indian isolates belonged to the EMA3 sublineage and similar strains have not been reported from neighbouring countries of the subcontinent, it appears that the virus may have been introduced independently.

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Phylogenetic tree of whole genome (all genes concatenated as PB2, PB1, PA, HA, NP, NA, M, NS). Phylogenetic trees were constructed by using the Bayesian, Markov Chain Monto Carlo approach as implemented in Mr Bayes. Coding region of all genes was used for analysis. The lengths of the horizontal lines are proportional to the number of nucleotide differences per site. Scale bar indicates number of nucleotide substitutions per site. Gs/Guangdong/1/96 was used as out group sequence. Abbreviations: BHGs – Bar headed goose, Ck – Chicken, Dk – Duck, Gs – Goose, Ws – Whooper swan, Md – Mallard, Tk – Turkey, Co – Cygnus olor, Gf – Guinea fowl, Pg – Peregrine, PgFc – Peregrine falcon,
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Figure 2: Phylogenetic tree of whole genome (all genes concatenated as PB2, PB1, PA, HA, NP, NA, M, NS). Phylogenetic trees were constructed by using the Bayesian, Markov Chain Monto Carlo approach as implemented in Mr Bayes. Coding region of all genes was used for analysis. The lengths of the horizontal lines are proportional to the number of nucleotide differences per site. Scale bar indicates number of nucleotide substitutions per site. Gs/Guangdong/1/96 was used as out group sequence. Abbreviations: BHGs – Bar headed goose, Ck – Chicken, Dk – Duck, Gs – Goose, Ws – Whooper swan, Md – Mallard, Tk – Turkey, Co – Cygnus olor, Gf – Guinea fowl, Pg – Peregrine, PgFc – Peregrine falcon,

Mentions: The GenBank accession numbers for the PB2, PB1, PA, HA, NP, M and NS gene segments of the isolate, A/Ck/India/NIV9743/07, herein referred to as the Manipur isolate, is from FJ719831–FJ719838. The percent nucleotide identity (PNI) and percent amino acid identity (PAI) values were calculated as pairwise p-distances, for a dataset of about 80 representative sequences in each gene. For clarity, limited representative sequences are shown in the phylogenetic trees (Figures 2, 3 and 4).


A unique influenza A (H5N1) virus causing a focal poultry outbreak in 2007 in Manipur, India.

Mishra AC, Cherian SS, Chakrabarti AK, Pawar SD, Jadhav SM, Pal B, Raut S, Koratkar S, Kode SS - Virol. J. (2009)

Phylogenetic tree of whole genome (all genes concatenated as PB2, PB1, PA, HA, NP, NA, M, NS). Phylogenetic trees were constructed by using the Bayesian, Markov Chain Monto Carlo approach as implemented in Mr Bayes. Coding region of all genes was used for analysis. The lengths of the horizontal lines are proportional to the number of nucleotide differences per site. Scale bar indicates number of nucleotide substitutions per site. Gs/Guangdong/1/96 was used as out group sequence. Abbreviations: BHGs – Bar headed goose, Ck – Chicken, Dk – Duck, Gs – Goose, Ws – Whooper swan, Md – Mallard, Tk – Turkey, Co – Cygnus olor, Gf – Guinea fowl, Pg – Peregrine, PgFc – Peregrine falcon,
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2654876&req=5

Figure 2: Phylogenetic tree of whole genome (all genes concatenated as PB2, PB1, PA, HA, NP, NA, M, NS). Phylogenetic trees were constructed by using the Bayesian, Markov Chain Monto Carlo approach as implemented in Mr Bayes. Coding region of all genes was used for analysis. The lengths of the horizontal lines are proportional to the number of nucleotide differences per site. Scale bar indicates number of nucleotide substitutions per site. Gs/Guangdong/1/96 was used as out group sequence. Abbreviations: BHGs – Bar headed goose, Ck – Chicken, Dk – Duck, Gs – Goose, Ws – Whooper swan, Md – Mallard, Tk – Turkey, Co – Cygnus olor, Gf – Guinea fowl, Pg – Peregrine, PgFc – Peregrine falcon,
Mentions: The GenBank accession numbers for the PB2, PB1, PA, HA, NP, M and NS gene segments of the isolate, A/Ck/India/NIV9743/07, herein referred to as the Manipur isolate, is from FJ719831–FJ719838. The percent nucleotide identity (PNI) and percent amino acid identity (PAI) values were calculated as pairwise p-distances, for a dataset of about 80 representative sequences in each gene. For clarity, limited representative sequences are shown in the phylogenetic trees (Figures 2, 3 and 4).

Bottom Line: A focal H5N1 outbreak in poultry was reported from Manipur, a north-eastern state, of India, in 2007.The HA gene, had the cleavage site GERRRRKR, earlier reported in whooper swan isolates from Mongolia in 2005.A stop codon at position 29 in the PB1-F2 protein could have implications on the replication efficiency.

View Article: PubMed Central - HTML - PubMed

Affiliation: Microbial Containment Complex, National Institute of Virology, Pashan, Pune 411021, Maharashtra, India. acm1750@rediffmail.com

ABSTRACT

Background: A focal H5N1 outbreak in poultry was reported from Manipur, a north-eastern state, of India, in 2007. The aim of this study was to genetically characterize the Manipur isolate to understand the relationship with other H5N1 isolates and to trace the possible source of introduction of the virus into the country.

Results: Characterization of the complete genome revealed that the virus belonged to clade 2.2. It was distinctly different from viruses of the three EMA sublineages of clade 2.2 but related to isolates from wild migratory waterfowl from Russia, China and Mongolia. The HA gene, had the cleavage site GERRRRKR, earlier reported in whooper swan isolates from Mongolia in 2005. A stop codon at position 29 in the PB1-F2 protein could have implications on the replication efficiency. The acquisition of polymorphisms as seen in recent isolates of 2005-07 from distinct geographical regions suggests the possibility of transportation of H5N1 viruses through migratory birds.

Conclusion: Considering that all eight genes of the earlier Indian isolates belonged to the EMA3 sublineage and similar strains have not been reported from neighbouring countries of the subcontinent, it appears that the virus may have been introduced independently.

Show MeSH
Related in: MedlinePlus