title: Characterization of H5N1 influenza A virus that caused the first highly pathogenic avian influenza outbreak in Saudi Arabia.
abstract: BACKGROUND
  Saudi Arabia (SA) experienced a highly pathogenic avian influenza (HPAI) H5N1 outbreak in domesticated birds in 2007.
  
  
  METHODS
  Forty-three hemagglutinin (HA) and 41 neuraminidase (NA) genes of HPAI H5N1 viruses were sequenced and phylogenetic analyses of completely sequenced genes were performed to compare with other viral HA and NA gene sequences available in the public databases.
  
  
  RESULTS
  Molecular characterization of the H5N1 viruses revealed two genetically distinct clades, 2.2.2 and 2.3.1, of H5N1 viruses circulating in the area. Amino acid sequence analysis of the HA gene indicated that the virus from 2.2.2 contained the sequence SPQGERRRK-R/G at the cleavage site, while the virus from 2.3.1 contained the sequence SPQRERRRK-R/G. Additionally, a few mutations with amino acid substitutions such as M226I at N-link glycosylation site were identified in two of these isolates. Amino acid sequence of the NA gene showed a 20-amino-acid deletion in the NA stalk region, required for enhanced virulence of influenza viruses and its adaptation from wild birds to domestic chickens. As close contact between humans and birds is unavoidable, there is a need for a thorough understanding of the virus epidemiology, factors affecting the spread of the virus, and molecular characterization such as phylogeny and substitution rates of H5N1 viruses circulating in the region.
  
  
  CONCLUSIONS
  Two genetically distinct clades were found to be circulating in the country, which could likely result in recombination and emergence of more virulent viral strains. These findings could be helpful for the authorities devising control measures against these viruses.
authors.affiliation: Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. aqahtani@kfshrc.edu.sa.
authors.forename: Ahmed Ali
authors.initials: AA
authors.lastname: Al-Qahtani
authors.forename: Muhammad
authors.initials: M
authors.lastname: Mubin
authors.forename: Fahad N
authors.initials: FN
authors.lastname: Almajhdi
authors.forename: Saud
authors.initials: S
authors.lastname: Alarifi
authors.forename: Damian M
authors.initials: DM
authors.lastname: Dela Cruz
authors.forename: Muhammad Shah Nawaz Ul
authors.initials: MS
authors.lastname: Rehman
authors.forename: Mahmoud Moussa
authors.initials: MM
authors.lastname: Ismail
authors.forename: Nisar
authors.initials: N
authors.lastname: Ahmed
authors.forename: Mohamed H
authors.initials: MH
authors.lastname: Al-Blowi
authors.forename: Hanif
authors.initials: H
authors.lastname: Khalak
authors.forename: Mohammed N
authors.initials: MN
authors.lastname: Al-Ahdal
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D004196:Disease Outbreaks; D014644:Genetic Variation; D005838:Genotype; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics; D053124:Influenza A Virus, H5N1 Subtype / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D005585:Influenza in Birds / Q000453:epidemiology* / Q000821:virology*; D017720:Molecular Epidemiology; D009439:Neuraminidase / Q000235:genetics; D010802:Phylogeny; D011200:Poultry; D012529:Saudi Arabia / Q000453:epidemiology; D017422:Sequence Analysis, DNA; D014764:Viral Proteins / Q000235:genetics
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus; D014764:Viral Proteins; C109963:hemagglutinin, avian influenza A virus; C487630:NA protein, influenza A virus; D009439:Neuraminidase