title: Characterization of the influenza A H5N1 viruses of the 2008-09 outbreaks in India reveals a third introduction and possible endemicity.
abstract: 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.
authors.affiliation: Microbial Containment Complex, National Institute of Virology, Pune, India.
authors.forename: Alok K
authors.initials: AK
authors.lastname: Chakrabarti
authors.forename: Shailesh D
authors.initials: SD
authors.lastname: Pawar
authors.forename: Sarah S
authors.initials: SS
authors.lastname: Cherian
authors.forename: Santosh S
authors.initials: SS
authors.lastname: Koratkar
authors.forename: Santosh M
authors.initials: SM
authors.lastname: Jadhav
authors.forename: Biswajoy
authors.initials: B
authors.lastname: Pal
authors.forename: Satish
authors.initials: S
authors.lastname: Raut
authors.forename: Vishal
authors.initials: V
authors.lastname: Thite
authors.forename: Sadhana S
authors.initials: SS
authors.lastname: Kode
authors.forename: Sachin S
authors.initials: SS
authors.lastname: Keng
authors.forename: Bestin J
authors.initials: BJ
authors.lastname: Payyapilly
authors.forename: Jayati
authors.initials: J
authors.lastname: Mullick
authors.forename: Akhilesh C
authors.initials: AC
authors.lastname: Mishra
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D001717:Birds; D020134:Catalytic Domain; D003140:Communicable Disease Control; D004196:Disease Outbreaks; D005843:Geography; D006388:Hemagglutinins / Q000235:genetics; D006801:Humans; D007194:India; D053124:Influenza A Virus, H5N1 Subtype / Q000378:metabolism*; D005585:Influenza in Birds / Q000175:diagnosis* / Q000453:epidemiology* / Q000235:genetics / Q000821:virology*; D007251:Influenza, Human / Q000235:genetics / Q000821:virology; D009154:Mutation; D009439:Neuraminidase / Q000235:genetics; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D006388:Hemagglutinins; D009439:Neuraminidase