Literature detail

Characterization of the influenza A H5N1 viruses of the 2008-09 outbreaks in India reveals a third introduction and possible endemicity.

Alok K Chakrabarti¹ Shailesh D Pawar Sarah S Cherian Santosh S Koratkar Santosh M Jadhav Biswajoy Pal Satish Raut Vishal Thite Sadhana S Kode Sachin S Keng Bestin J Payyapilly Jayati Mullick Akhilesh C Mishra

Affiliations 1 institutions

Microbial Containment Complex, National Institute of Virology, Pune, India.

PMID 19924254 2009 PLoS One eng epublish

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Article

Publication summary

Widespread infection of highly pathogenic avian influenza A H5N1 was reported from backyard and commercial poultry in West Bengal (WB), an eastern state of India in early 2008. Infection gradually spread to Tripura, Assam and Sikkim, the northeastern states, with 70 outbreaks reported between January 2008 and May 2009. Whole genome sequence analysis of three isolates from WB, one isolate from Tripura along with the analysis of hemagglutinin (HA) and neuraminidase (NA) genes of 17 other isolates was performed during this study. In the HA gene phylogenetic tree, all the 2008-09 Indian isolates belonged to EMA3 sublineage of clade 2.2. The closest phylogenetic relationship was found to be with the 2007-09 isolates from Bangladesh and not with the earlier 2006 and 2007 Indian isolates implying a third introduction into the country. The receptor-binding pocket of HA1 of two isolates from WB showed S221P mutation, one of the markers predicted to be associated with human receptor specificity. Two substitutions E119A (2 isolates of WB) and N294S (2 other isolates of WB) known to confer resistance to NA inhibitors were observed in the active site of neuraminidase. Several additional mutations were observed within the 2008-09 Indian isolates indicating genetic diversification. Overall, the study is indicative of a possible endemicity in the eastern and northeastern parts of the country, demanding active surveillance specifically in view of the critical mutations that have been observed in the influenza A H5N1 viruses.

Animals Bayes Theorem Birds Catalytic Domain Communicable Disease Control Disease Outbreaks Geography Hemagglutinins Humans India Influenza A Virus, H5N1 Subtype Influenza in Birds Influenza, Human Mutation Neuraminidase Phylogeny Sequence Analysis, DNA

Structured evidence records

Evidence records

6 total

Molecular Adaptation 2 records

Molecular Adaptation Extraction confidence 0.90

Key finding

H5N1 viruses from West Bengal contained HA1 S221P mutation associated with human receptor specificity, indicating adaptation toward human-type receptors.

Virus

Host

Location

Supporting text

The receptor-binding pocket of HA1 of two isolates from WB showed S221P mutation, one of the markers predicted to be associated with human receptor specificity.

Genes or proteins: HA1
Mutations: S221P
Mechanism types: receptor_binding

Molecular Adaptation Extraction confidence 0.90

Key finding

H5N1 viruses from West Bengal exhibited NA mutations E119A and N294S that confer resistance to neuraminidase inhibitors, indicating antiviral adaptation.

Virus

Host

Location

Supporting text

Two substitutions E119A (2 isolates of WB) and N294S (2 other isolates of WB) known to confer resistance to NA inhibitors were observed in the active site of neuraminidase.

Genes or proteins: neuraminidase
Mutations: E119A; N294S
Mechanism types: immune_escape

Genomic Evolution 1 records

Genomic Evolution Extraction confidence 0.95

Key finding

Phylogenetic and whole-genome analyses showed that 2008–09 Indian influenza A H5N1 isolates clustered in EMA3 sublineage of clade 2.2, closely related to Bangladesh isolates, indicating a third independent introduction into India.

Virus

Host

Location

Supporting text

Whole genome sequence analysis of three isolates from WB, one isolate from Tripura along with the analysis of hemagglutinin (HA) and neuraminidase (NA) genes of 17 other isolates was performed during this study. In the HA gene phylogenetic tree, all the 2008-09 Indian isolates belonged to EMA3 sublineage of clade 2.2. The closest phylogenetic relationship was found to be with the 2007-09 isolates from Bangladesh and not with the earlier 2006 and 2007 Indian isolates implying a third introduction into the country.

Genes or proteins: hemagglutinin (HA); neuraminidase (NA); whole genome
Analysis methods: whole genome sequence analysis; phylogenetic analysis

Outbreak Investigation 1 records

Outbreak Investigation Extraction confidence 0.80

Key finding

Highly pathogenic avian influenza A H5N1 caused 70 outbreaks among poultry in multiple Indian states during 2008–2009.

Virus

Host

Location

Supporting text

Widespread infection of highly pathogenic avian influenza A H5N1 was reported from backyard and commercial poultry in West Bengal, India in early 2008, spreading to Tripura, Assam and Sikkim with 70 outbreaks reported between January 2008 and May 2009.

Method: whole genome sequence analysis; phylogenetic analysis
Transmission direction: animal-to-animal
Geographic raw: West Bengal, Tripura, Assam and Sikkim, India
Country inferred: India
Outbreak setting: backyard and commercial poultry
Outbreak time: January 2008 to May 2009
Outbreak scale: 70 outbreaks

Receptor Usage 1 records

Receptor Usage Extraction confidence 0.85

Key finding

Influenza A H5N1 isolates from West Bengal displayed an HA1 S221P mutation linked to human receptor specificity.

Virus

Host

Location

Supporting text

The receptor-binding pocket of HA1 of two isolates from WB showed S221P mutation, one of the markers predicted to be associated with human receptor specificity.

Method: sequence analysis
Receptors: human receptor

Zoonotic Surveillance 1 records

Zoonotic Surveillance Extraction confidence 0.90

Key finding

Genomic surveillance of influenza A H5N1 outbreaks in Indian poultry during 2008–09 revealed widespread infection and genetic diversification, highlighting the need for continued active monitoring.

Virus

Host

Location

Supporting text

Method: whole genome sequence analysis; HA and NA gene analysis; phylogenetic analysis
Geographic raw: West Bengal, Tripura, Assam and Sikkim
Country inferred: India

Citation context

References

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-	Cumulative Number of Confirmed Human Cases of Avian Influenza A/(H5N1) Reported to WHO	World Health Organization	2009
PMID 16318689	Emerg Infect Dis	The World Health Organization Global Inf	2005
PMID 17622635	Molecular and antigenic evolution and geographical spread of H5N1 highly pathogenic avian influenza viruses in western Africa	Ducatez	2007
PMID 18837987	Molecular characterization of highly pathogenic H5N1 avian influenza viruses isolated in Sweden in 2006	Kiss	2008
PMID 18031958	Phylogenetic analyses of highly pathogenic avian influenza virus isolates from Germany in 2006 and 2007 suggest at least three separate introductions of H5N1 virus	Starick	2008
PMID 17553249	Genome analysis linking recent European and African influenza (H5N1) viruses	Salzberg	2007
-	Update on highly pathogenic avian influenza in animals (Type H5 and H7)	OIE	2009
PMID 18214665 In OmniVira	Characterization of the complete genome of influenza A (H5N1) virus isolated during the 2006 outbreak in poultry in India.	Ray	2008
PMID 19236725	A unique influenza A (H5N1) virus causing a focal poultry outbreak in 2007 in Manipur, India. Virology J Feb 24. 2009;6:26	Mishra	2009
-	Update on highly pathogenic avian influenza in animals (Type H5 and H7)	OIE	2009
-	Update on highly pathogenic avian influenza in animals (Type H5 and H7)	OIE	2009
PMID 19751601	Avian Influenza Virus A (H5N1). Detected through Routine Surveillance, in Child, Bangladesh	Brooks	2009
PMID 17428885	Avian influenza virus (H5N1): a threat to human health	Peiris	2007
PMID 15331729	Molecular determinants within the surface proteins involved in the pathogenicity of H5N1 influenza viruses in chickens	Hulse	2004
PMID 16318689	Evolution of H5N1 avian influenza viruses in Asia	The World Health Organization Global Inf	2005
PMID 14764887	Structure of the uncleaved human H1 hemagglutinin from the extinct 1918 influenza virus	Stevens	2004
PMID 16543414 In OmniVira	Structure and receptor specificity of the hemagglutinin from an H5N1 influenza virus.	Stevens	2006
PMID 16915235	The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design	Russell	2006
-	Role of NA mutations conferring Resistance to NA inhibitors on viral fitness and pathogenicity in A/Turkey/15/06 (H5N1) Influenza Virus	Ilyushina	2009
PMID 17855542	Neuraminidase inhibitor-resistant recombinant A/Vietnam/1203/04 (H5N1) influenza viruses retain their replication efficiency and pathogenicity in vitro and in vivo	Yen	2007
PMID 14513385	Emergence of amantadine-resistant influenza A viruses: epidemiological study	Suzuki	2003
PMID 11748666	Molecular changes associated with the transmission of avian influenza a H5N1 and H9N2 viruses to humans	Shaw	2002
PMID 15016548	PB2 amino acid at position 627 affects replicative efficiency, but not cell tropism, of Hong Kong H5N1 influenza A viruses in mice	Shinya	2004
PMID 16339318	The viral polymerase mediates adaptation of an avian influenza virus to a mammalian host	Gabriel	2005
PMID 12195436	Lethal H5N1 influenza virus escape host antiviral cytokine responses	Seosh	2007
PMID 16439620	Large-scale sequence analysis of avian influenza isolates	Obenauer	2006
PMID 19496842	2009	Continuing progress towards a unified no	2009
-	Accessed 14 July 2008	World Health Organization: H5N1 avian in	2008
PMID 19046518	Avian influenza outbreaks in chickens, Bangladesh	Biswas	2008
-	2008. Molecular characterization and phylogenetic analysis of highly pathogenic H5N1 avian influenza virus of chickens of Bangladesh Poster presented at the Bangkok International Conference on Avian Influenza 2008: integration from knowledge to control; Jan 23–25; Bangkok, Thailand	Islam	2008
PMID 14671105	Structural Differences among Hemagglutinins of Influenza A Virus Subtypes Are Reflected in Their Antigenic Architecture: Analysis of H9 Escape Mutants	Kaverin	2004
PMID 16801417	Detection of Influenza Viruses Resistant to Neuraminidase Inhibitors in Global Surveillance during the First 3 Years of Their Use	Arnold	2006
PMID 16940075	Natural variation can significantly alter the sensitivity of influenza A (H5N1) viruses to oseltamivir	Rameix-Welti	2006
PMID 18252107	Reduced sensitivity of influenza A to oseltamivir	McKimm-Breschkin	2007
PMID 19124660	Detection of molecular markers of antiviral resistance in Influenza A (H5N1) viruses using a pyrosequencing method	Deyde	2009
PMID 16371632	Oseltamivir resistance during treatment of influenza A(H5N1) infection	de Jong	2005
PMID 16228009	Avian flu: isolation of drug-resistant H5N1 virus	Le	2005
PMID 12821478	Neuraminidase sequence analysis and susceptibilities of Influenza virus clinical isolates to Zanamivir and Oseltamivir	McKimm-Breschkin	2003
PMID 19290041	Highly pathogenic avian influenza virus subtype H5N1 in Africa: A comprehensive phylogenetic analysis and molecular characterization of isolates	Cattoli	2009
PMID 16801417	Detection of influenza viruses resistant to neuraminidase inhibitors in global surveillance during the first 3 years of their use. Antimicrob Agents Chemother 2006. 50:2395–402	Monto	2006
-	Kendal AP, Pereira MS, Skehe JJ, editors. Hemagglutinin inhibition in Concepts and Procedures for Laboratory-Based Influenza Surveillance, ed	Kendal	1982
-	WHO June Available:	Recommended laboratory tests to identify	2009
PMID 11811679	Universal primer set for the full-length amplification of all influenza A viruses	Hoffmann	2001
PMID 8743695	Using CLUSTAL for multiple sequence alignments	Higgins	1996
PMID 15260895	MEGA3.1: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment	Kumar	2004
PMID 12912839	Mr Bayes 3: Bayesian phylogenetic inference under mixed models	Ronquist	2003

Evidence overview

Evidence 6

Types 5

Virus 1

Host 1

Evidence types

Molecular Adaptation 2 Genomic Evolution 1 Outbreak Investigation 1 Receptor Usage 1 Zoonotic Surveillance 1

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Publication metadata

Journal: PloS one
Volume / Issue / Pages: 4 / 11 / e7846
ISSN: 1932-6203
Journal country: United States
DOI: 10.1371/journal.pone.0007846