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Detailed genetic analysis of hemagglutinin-neuraminidase glycoprotein gene in human parainfluenza virus type 1 isolates from patients with acute respiratory infection between 2002 and 2009 in Yamagata prefecture, Japan.

Mizuta K, Saitoh M, Kobayashi M, Tsukagoshi H, Aoki Y, Ikeda T, Abiko C, Katsushima N, Itagaki T, Noda M, Kozawa K, Ahiko T, Kimura H - Virol. J. (2011)

Bottom Line: No positively selected sites were found in the present strains.Moreover, the pairwise distance among the present isolates was relatively short.The evolution of HN gene in the present HPIV1 isolates was relatively slow.

View Article: PubMed Central - HTML - PubMed

Affiliation: Yamagata Prefectural Institute of Public Health, 1-6-6 Toka-machi, Yamagata-shi, Yamagata 990-0031, Japan.

ABSTRACT

Background: Human parainfluenza virus type 1 (HPIV1) causes various acute respiratory infections (ARI). Hemagglutinin-neuraminidase (HN) glycoprotein of HPIV1 is a major antigen. However, the molecular epidemiology and genetic characteristics of such ARI are not exactly known. Recent studies suggested that a phylogenetic analysis tool, namely the maximum likelihood (ML) method, may be applied to estimate the evolutionary time scale of various viruses. Thus, we conducted detailed genetic analyses including homology analysis, phylogenetic analysis (using both the neighbor joining (NJ) and ML methods), and analysis of the pairwise distances of HN gene in HPIV1 isolated from patients with ARI in Yamagata prefecture, Japan.

Results: A few substitutions of nucleotides in the second binding site of HN gene were observed among the present isolates. The strains were classified into two major clusters in the phylogenetic tree by the NJ method. Another phylogenetic tree constructed by the ML method showed that the strains diversified in the late 1980s. No positively selected sites were found in the present strains. Moreover, the pairwise distance among the present isolates was relatively short.

Conclusions: The evolution of HN gene in the present HPIV1 isolates was relatively slow. The ML method may be a useful phylogenetic method to estimate the evolutionary time scale of HPIV and other viruses.

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Distributions of pairwise distances for HPIV1 of HN region. (a) Distribution of pairwise distances for the 182 present and 3 reference strains. (b) Distribution of pairwise intercluster distances for cluster 1. (c) Distribution of pairwise intercluster distances for cluster 2.
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Figure 3: Distributions of pairwise distances for HPIV1 of HN region. (a) Distribution of pairwise distances for the 182 present and 3 reference strains. (b) Distribution of pairwise intercluster distances for cluster 1. (c) Distribution of pairwise intercluster distances for cluster 2.

Mentions: The nucleotide and amino acid sequence identities among all 182 isolates were high at 92.6-100% and 96.0-100%, respectively. In addition, we calculated the intercluster distances of HPIV1 from the distribution of the pairwise distances. Based on the nucleotide sequences, the pairwise distance was 0.018 ± 0.013 [mean ± SD, Figure 3a] for the 182 present and 3 reference strains. The pairwise intercluster distances were as follows: cluster 1, 0.003 ± 0.002 (Figure 3b); and cluster 2, 0.008 ± 0.005 (Figure 3c). Cluster 2 showed a large pairwise intercluster distance, whereas that for cluster 1 was small. However, irregular peaks of pairwise distance are seen in Figure 3, and we were not able to genotyping the present strains based on the pairwise distance value. Next, amino acid substitutions in the analyzed HN coding region in the present strains were found at 31sites (detailed substitution data not shown). Among these was an essential substitution of the second binding site, N523S. This substitution (N523S) was seen in seven of the present strains (HPIVi/Yamagata/2007/1577, HPIVi/Yamagata/2007/1599, HPIVi/Yamagata/2007/2211, HPIVi/Yamagata/2007/2072, HPIVi/Yamagata/2007/2354, HPIVi/Yamagata/2007/2274, and HPIVi/Yamagata/2008/413). These strains belonged in cluster 2 (Figure 1).


Detailed genetic analysis of hemagglutinin-neuraminidase glycoprotein gene in human parainfluenza virus type 1 isolates from patients with acute respiratory infection between 2002 and 2009 in Yamagata prefecture, Japan.

Mizuta K, Saitoh M, Kobayashi M, Tsukagoshi H, Aoki Y, Ikeda T, Abiko C, Katsushima N, Itagaki T, Noda M, Kozawa K, Ahiko T, Kimura H - Virol. J. (2011)

Distributions of pairwise distances for HPIV1 of HN region. (a) Distribution of pairwise distances for the 182 present and 3 reference strains. (b) Distribution of pairwise intercluster distances for cluster 1. (c) Distribution of pairwise intercluster distances for cluster 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3295729&req=5

Figure 3: Distributions of pairwise distances for HPIV1 of HN region. (a) Distribution of pairwise distances for the 182 present and 3 reference strains. (b) Distribution of pairwise intercluster distances for cluster 1. (c) Distribution of pairwise intercluster distances for cluster 2.
Mentions: The nucleotide and amino acid sequence identities among all 182 isolates were high at 92.6-100% and 96.0-100%, respectively. In addition, we calculated the intercluster distances of HPIV1 from the distribution of the pairwise distances. Based on the nucleotide sequences, the pairwise distance was 0.018 ± 0.013 [mean ± SD, Figure 3a] for the 182 present and 3 reference strains. The pairwise intercluster distances were as follows: cluster 1, 0.003 ± 0.002 (Figure 3b); and cluster 2, 0.008 ± 0.005 (Figure 3c). Cluster 2 showed a large pairwise intercluster distance, whereas that for cluster 1 was small. However, irregular peaks of pairwise distance are seen in Figure 3, and we were not able to genotyping the present strains based on the pairwise distance value. Next, amino acid substitutions in the analyzed HN coding region in the present strains were found at 31sites (detailed substitution data not shown). Among these was an essential substitution of the second binding site, N523S. This substitution (N523S) was seen in seven of the present strains (HPIVi/Yamagata/2007/1577, HPIVi/Yamagata/2007/1599, HPIVi/Yamagata/2007/2211, HPIVi/Yamagata/2007/2072, HPIVi/Yamagata/2007/2354, HPIVi/Yamagata/2007/2274, and HPIVi/Yamagata/2008/413). These strains belonged in cluster 2 (Figure 1).

Bottom Line: No positively selected sites were found in the present strains.Moreover, the pairwise distance among the present isolates was relatively short.The evolution of HN gene in the present HPIV1 isolates was relatively slow.

View Article: PubMed Central - HTML - PubMed

Affiliation: Yamagata Prefectural Institute of Public Health, 1-6-6 Toka-machi, Yamagata-shi, Yamagata 990-0031, Japan.

ABSTRACT

Background: Human parainfluenza virus type 1 (HPIV1) causes various acute respiratory infections (ARI). Hemagglutinin-neuraminidase (HN) glycoprotein of HPIV1 is a major antigen. However, the molecular epidemiology and genetic characteristics of such ARI are not exactly known. Recent studies suggested that a phylogenetic analysis tool, namely the maximum likelihood (ML) method, may be applied to estimate the evolutionary time scale of various viruses. Thus, we conducted detailed genetic analyses including homology analysis, phylogenetic analysis (using both the neighbor joining (NJ) and ML methods), and analysis of the pairwise distances of HN gene in HPIV1 isolated from patients with ARI in Yamagata prefecture, Japan.

Results: A few substitutions of nucleotides in the second binding site of HN gene were observed among the present isolates. The strains were classified into two major clusters in the phylogenetic tree by the NJ method. Another phylogenetic tree constructed by the ML method showed that the strains diversified in the late 1980s. No positively selected sites were found in the present strains. Moreover, the pairwise distance among the present isolates was relatively short.

Conclusions: The evolution of HN gene in the present HPIV1 isolates was relatively slow. The ML method may be a useful phylogenetic method to estimate the evolutionary time scale of HPIV and other viruses.

Show MeSH
Related in: MedlinePlus