title: Molecular epidemiology of novel swine origin influenza virus (S-OIV) from Gwalior, India, 2009.
abstract: BACKGROUND
  The H1N1pandemic virus is a newly emergent human influenza A virus that is closely related to a number of currently circulating pig viruses in the 'classic North American' and 'Eurasian' swine influenza virus lineages and thus referred as S-OIV. Since the first reports of the virus in humans in April 2009, H1N1 virus has spread to 168 countries and overseas territories. India also witnessed severe H1N1 pandemic virus epidemic with considerable morbidity and mortality in different parts starting from May 2009.
  
  
  RESULTS
  The suspected swine flu outbreak from Gwalior India during October- December 2009 was confirmed through S-OIV HA gene specific RT-LAMP and real time RT-PCR. Positive samples through CDC real time and Lamp assay were further processed for isolation of the virus. Full HA gene sequencing of the H1N1 isolates of Gwalior, India revealed 99% homology with California and other circulating novel swine flu viruses. Three major changes were observed at nucleotide level, while two major amino acid shifts were observed at the position C9W and I30M corresponding to the ORF with prototype strain. The HA gene sequence phylogeny revealed the circulation of two genetically distinct lineages belonging to Clade VII and Clade I of S-OIV.
  
  
  CONCLUSIONS
  Our findings also supported the earlier report about circulation of mixed genogroups of S-OIV in India. Therefore continuous monitoring of the genetic makeup of this newly emergent virus is essential to understand its evolution within the country.
authors.affiliation: Division of Virology, Defence Research & Development Establishment, Gwalior- 474002, India.
authors.forename: Shashi
authors.initials: S
authors.lastname: Sharma
authors.forename: Manmohan
authors.initials: M
authors.lastname: Parida
authors.forename: Jyoti
authors.initials: J
authors.lastname: Shukla
authors.forename: P V L
authors.initials: PV
authors.lastname: Rao
mesh_terms: D016000:Cluster Analysis; D005838:Genotype; D006801:Humans; D007194:India / Q000453:epidemiology; D053118:Influenza A Virus, H1N1 Subtype / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D007251:Influenza, Human / Q000453:epidemiology* / Q000821:virology*; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D012367:RNA, Viral