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

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.

Figure 1

Phylogenetic tree of HN region by NJ method. Phylogenetic tree based on the nucleotide sequence of the HN coding region (1233nt), including the present strains (182) and representative reference strains (3). HPIV3 was used as an outgroup. Distance was calculated according to Kimura's 2-parameter method, and the tree was plotted with the neighbor-joining method. Reference strains are shown in italic type. The larger tree was simply expanded for HPIV1 strains, to clarify the distance of each of the minor clusters in the trees. The tree was constructed by neighbor-joining analysis with labeling of the branches showing at least 70% bootstrap support. The representation of the strain was changed from Yamagata/20XX/ZZZZ to YXX/ZZZZ.

Figure 2

Phylogenetic tree of HN region by ML method. Phylogenetic tree based on the nucleotide sequence of the HN coding region (1233 nt), including the present strains (43) and representative reference strains (3), with branch lengths scaled under the SRDT model. Reference strains are shown in italic type.

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.