title: Phylogenetic and nucleotide sequence analysis of influenza A (H1N1) HA and NA genes of strains isolated from Saudi Arabia.
abstract: BACKGROUND
  In early 2009, a novel influenza A (H1N1) virus appeared in Mexico and rapidly disseminated worldwide. Little is known about the phylogeny and evolutionary dynamics of the H1N1 strain found in Saudi Arabia.
  
  
  METHODS
  Nucleotide sequencing and bioinformatics analyses were used to study molecular variation between the virus isolates.
  
  
  RESULTS
  In this report, 72 hemagglutinin (HA) and 45 neuraminidase (NA) H1N1 virus gene sequences, isolated in 2009 from various regions of Saudi Arabia, were analyzed. Genetic characterization indicated that viruses from two different clades, 6 and 7, were circulating in the region, with clade 7, the most widely circulating H1N1 clade globally in 2009, being predominant. Sequence analysis of the HA and NA genes revealed a high degree of sequence identity with the corresponding genes from viruses circulating in the South East Asia region and with the A/California/7/2009 strain. New mutations in the HA gene of pandemic H1N1 (pH1N1) viruses, that could alter viral fitness, were identified. Relaxed-clock and Bayesian Skyline Plot analyses, based on the isolates used in this study and closely related globally representative strains, indicated marginally higher substitution rates than the type strain (5.14×10-3 and 4.18×10-3 substitutions/nucleotide/year in the HA and NA genes, respectively).
  
  
  CONCLUSIONS
  The Saudi isolates were antigenically homogeneous and closely related to the prototype vaccine strain A/California/7/2009. The antigenic site of the HA gene had acquired novel mutations in some isolates, making continued monitoring of these viruses vital for the identification of potentially highly virulent and drug resistant variants.
authors.affiliation: 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: Damian M
authors.initials: DM
authors.lastname: Dela Cruz
authors.forename: Sahar Isa
authors.initials: SI
authors.lastname: Althawadi
authors.forename: Muhammad Shah Nawaz
authors.initials: MS
authors.lastname: Ul Rehman
authors.forename: Marie Fe F
authors.initials: MF
authors.lastname: Bohol
authors.forename: Mohammed N
authors.initials: MN
authors.lastname: Al-Ahdal
mesh_terms: D000293:Adolescent; D000328:Adult; D002648:Child; D002675:Child, Preschool; D000939:Epitopes / Q000235:genetics; D005260:Female; D014644:Genetic Variation; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics*; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D053118:Influenza A Virus, H1N1 Subtype / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D007251:Influenza, Human / Q000453:epidemiology / Q000821:virology*; D008297:Male; D017720:Molecular Epidemiology; D009154:Mutation; D009439:Neuraminidase / Q000235:genetics*; D010802:Phylogeny; D012529:Saudi Arabia / Q000453:epidemiology; D017422:Sequence Analysis, DNA; D014764:Viral Proteins / Q000235:genetics*; D055815:Young Adult
chemical_list: D000939:Epitopes; D019267:Hemagglutinin Glycoproteins, Influenza Virus; D014764:Viral Proteins; C487630:NA protein, influenza A virus; D009439:Neuraminidase