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.

Findings: 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.

Figure 1

Phylogenetic analysis based on the complete HN gene nucleotide sequence of the different HPIV-2 strains circulating globally. Tree was constructed using Megalign program of Lasergene software (DNASTAR) with 1000 bootstraps. HPIV-2 strains included in the analysis were grouped in four clusters (G1-4). Each of clusters G1 and G4 were split into two subclusters (a and b). Riyadh 105/2009 strain was indicated by a red frame, and was grouped with Oklahoma-94-2009 strain in cluster G3. Scale bar indicates number of nucleotide substitution per site.