title: Comparative sequence, antigenic and phylogenetic analysis of avian influenza (H9N2) surface proteins isolated in Pakistan between 1999 and 2008.
abstract: BACKGROUND
  Influenza A viruses possess a unique genomic structure which leads to genetic instability, especially in products of neuraminidase and hemagglutinin genes. These surface proteins play major roles in viral entry and release, and in the activation of the host immune system.
  
  
  METHODS
  This study involved an in silico sequence, phylogenetic and antigenic analyses of hemagglutinin and neuraminidase proteins of avian influenza A (H9N2) strains that circulated in Pakistan's poultry flocks from 1999 to 2008 and determined variations among these sequences at different levels.
  
  
  RESULTS
  Sequence and phylogenetic analysis revealed a large number of similar substitution mutations and close evolutionary relation among sequences of both proteins. Changes were observed in the N-glycosylation sites of both surface proteins, along with the appearance of a new glycosylation site in the neuraminidase sequence isolated in 2007. Epitopes for hemagglutinin remained conserved, whereas for neuraminidase, epitopes from older strains reappeared in present sequences.
  
  
  CONCLUSIONS
  Because of the rapid mutating nature of avian influenza subtype H9N2, constant surveillance of annual sequence variations is important. Preventive measures and vaccine products can be evaluated by keeping track of changes that may lead to reassortment among different circulating strains in Pakistan's commercial poultry flocks or in humans.
authors: National Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan. azeem@cemb.edu.pk
authors: Azeem Mehmood
authors: AM
authors: Butt
authors: Samerene
authors: S
authors: Siddique
authors: Shifa
authors: S
authors: Tahir
authors: Izza
authors: I
authors: Nasrullah
authors: Mureed
authors: M
authors: Hussain
authors: Muhammad
authors: M
authors: Idrees
authors: Jun
authors: J
authors: Lu
authors: Yigang
authors: Y
authors: Tong
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution / Q000235:genetics; D000818:Animals; D016000:Cluster Analysis; D000939:Epitopes / Q000235:genetics / Q000276:immunology; D019143:Evolution, Molecular; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics* / Q000276:immunology*; D053127:Influenza A Virus, H9N2 Subtype / Q000145:classification* / Q000235:genetics / Q000276:immunology / Q000302:isolation & purification*; D005585:Influenza in Birds / Q000821:virology*; D008969:Molecular Sequence Data; D009439:Neuraminidase / Q000235:genetics* / Q000276:immunology*; D010154:Pakistan; D010802:Phylogeny; D011200:Poultry; D017422:Sequence Analysis, DNA; D014764:Viral Proteins / Q000235:genetics* / Q000276:immunology*
chemical_list: D000939:Epitopes; D019267:Hemagglutinin Glycoproteins, Influenza Virus; D014764:Viral Proteins; C487630:NA protein, influenza A virus; D009439:Neuraminidase