title: Human parainfluenza virus type 2 hemagglutinin-neuramindase gene: sequence and phylogenetic analysis of the Saudi strain Riyadh 105/2009.
abstract: BACKGROUND
  Although human parainfluenza type 2 (HPIV-2) virus is an important respiratory pathogen, a little is known about strains circulating in Saudi Arabia.
  
  
  RESULTS
  Among 180 nasopharyngeal aspirates collected from suspected cases in Riyadh, only one sample (0.56%) was confirmed HPIV-2 positive by nested RT-PCR. The sample that was designated Riyadh 105/2009 was used for sequencing and phylogenetic analysis of the most variable virus gene; the haemagglutinin-neuramindase (HN). Comparison of HN gene of Riyadh 105/2009 strain and the relevant sequences available in GenBank revealed a strong relationship with Oklahoma-94-2009 strain. Phylogenetic analysis indicated four different clusters of HPIV-2 strains (G1-4). Twenty-three amino acid substitutions were recorded for Riyadh 105/2009, from which four are unique. The majority of substitutions (n=18) had changed their amino acids characteristics. By analyzing the effect of the recorded substitutions on the protein function using SIFT program, only two located at positions 360 and 571 were predicted to be deleterious.
  
  
  CONCLUSIONS
  The presented changes of Riyadh 105/2009 strain may possess potential effect on the protein structure and/or function level. This is the first report that describes partial characterization of Saudi HPIV-2 strain.
authors.affiliation: Department of Botany and Microbiology, College of Science, King Saud University, P,O, Box, 2455, Riyadh, 11451, Kingdom of Saudi Arabia. majhdi@ksu.edu.sa
authors.forename: Fahad N
authors.initials: FN
authors.lastname: Almajhdi
authors.forename: Mohamed S
authors.initials: MS
authors.lastname: Alshaman
authors.forename: Haitham M
authors.initials: HM
authors.lastname: Amer
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D002675:Child, Preschool; D030561:Databases, Nucleic Acid; D005260:Female; D005814:Genes, Viral; D015707:HN Protein / Q000235:genetics*; D006801:Humans; D010223:Parainfluenza Virus 2, Human / Q000145:classification / Q000201:enzymology / Q000235:genetics*; D010802:Phylogeny; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012529:Saudi Arabia; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012984:Software; D013045:Species Specificity
chemical_list: D015707:HN Protein