title: Multiple introductions of a reassortant H5N1 avian influenza virus of clade 2.3.2.1c with PB2 gene of H9N2 subtype into Indian poultry.
abstract: Highly pathogenic avian influenza (HPAI) H5N1 viruses are a threat to poultry in Asia, Europe, Africa and North America. Here, we report isolation and characterization of H5N1 viruses isolated from ducks and turkeys in Kerala, Chandigarh and Uttar Pradesh, India between November 2014 and March 2015. Genetic and phylogenetic analyses of haemagglutinin gene identified that the virus belonged to a new clade 2.3.2.1c which has not been detected earlier in Indian poultry. The virus possessed molecular signature for high pathogenicity to chickens, which was corroborated by intravenous pathogenicity index of 2.96. The virus was a reassortant which derives its PB2 gene from H9N2 virus isolated in China during 2007-2013. However, the neuraminidase and internal genes are of H5N1 subtype. Phylogenetic and network analysis revealed that after detection in China in 2013/2014, the virus moved to Europe, West Africa and other Asian countries including India. The analyses further indicated multiple introductions of H5N1 virus in Indian poultry and internal spread in Kerala. One of the outbreaks in ducks in Kerala is linked to the H5N1 virus isolated from wild birds in Dubai suggesting movement of virus probably through migration of wild birds. However, the outbreaks in ducks in Chandigarh and Uttar Pradesh were from an unknown source in Asia which also contributed gene pools to the outbreaks in Europe and West Africa. The widespread incidence of the novel H5N1 HPAI is similar to the spread of clade 2.2 ("Qinghai-like") virus in 2005, and should be monitored to avoid threat to animal and public health.
authors.affiliation: ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India. Electronic address: chakradhar.tosh@gmail.com.
authors.forename: Chakradhar
authors.initials: C
authors.lastname: Tosh
authors.affiliation: ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India.
authors.forename: Shanmugasundaram
authors.initials: S
authors.lastname: Nagarajan
authors.affiliation: ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India.
authors.forename: Manoj
authors.initials: M
authors.lastname: Kumar
authors.affiliation: ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India.
authors.forename: Harshad V
authors.initials: HV
authors.lastname: Murugkar
authors.affiliation: ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India.
authors.forename: Govindarajulu
authors.initials: G
authors.lastname: Venkatesh
authors.affiliation: ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India.
authors.forename: Shweta
authors.initials: S
authors.lastname: Shukla
authors.affiliation: ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India.
authors.forename: Amit
authors.initials: A
authors.lastname: Mishra
authors.affiliation: ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India.
authors.forename: Pranav
authors.initials: P
authors.lastname: Mishra
authors.affiliation: ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India.
authors.forename: Sonam
authors.initials: S
authors.lastname: Agarwal
authors.affiliation: ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India.
authors.forename: Bharati
authors.initials: B
authors.lastname: Singh
authors.affiliation: ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India.
authors.forename: Prashant
authors.initials: P
authors.lastname: Dubey
authors.affiliation: ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India.
authors.forename: Sushil
authors.initials: S
authors.lastname: Tripathi
authors.affiliation: ICAR-National Institute of High Security Animal Diseases, Bhopal 462 022, India.
authors.forename: Diwakar D
authors.initials: DD
authors.lastname: Kulkarni
mesh_terms: D000349:Africa / Q000453:epidemiology; D000818:Animals; D002645:Chickens / Q000821:virology; D004196:Disease Outbreaks; D004372:Ducks / Q000821:virology; D062665:Epidemiological Monitoring; D005060:Europe / Q000453:epidemiology; D015870:Gene Expression; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics; D007194:India / Q000453:epidemiology; D053124:Influenza A Virus, H5N1 Subtype / Q000145:classification / Q000235:genetics*; D053127:Influenza A Virus, H9N2 Subtype / Q000145:classification / Q000235:genetics*; D005585:Influenza in Birds / Q000453:epidemiology* / Q000635:transmission / Q000821:virology; D009439:Neuraminidase / Q000235:genetics; D010802:Phylogeny; D058974:Phylogeography; D011200:Poultry / Q000821:virology; D016865:Reassortant Viruses / Q000145:classification / Q000235:genetics*; D014422:Turkeys / Q000821:virology
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus; C109963:hemagglutinin, avian influenza A virus; D009439:Neuraminidase
keywords: Duck; H5N1 subtype; Highly pathogenic avian influenza; India; Reassortment; Turkey