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Phylogenetic and cluster analysis of human rhinovirus species A (HRV-A) isolated from children with acute respiratory infections in Yamagata, Japan

Phylogenetic and cluster analysis of human rhinovirus species A (HRV-A) isolated from children with acute respiratory infections in Yamagata, Japan,10

Phylogenetic and cluster analysis of human rhinovirus species A (HRV-A) isolated from children with acute respiratory infections in Yamagata, Japan   (Citations: 1)
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Katsumi Mizuta, Asumi Hirata, Asuka Suto, Yoko Aoki, Tadayuki Ahiko, Tsutomu Itagaki, Hiroyuki Tsukagoshi, Yukio Morita, Masatsugu Obuchi, Miho Akiyama, Nobuhiko Okabe, Masahiro Nodahttp://academic.research.microsoft.com/io.ashx?type=5&id=35839880&selfId1=0&selfId2=0&maxNumber=12&query=
We performed phylogenetic and cluster analysis of human rhinovirus species A (HRV-A) isolated from 76 children with acute respiratory infection in Yamagata prefecture, Japan during the period 2003–2007. Phylogenetic trees based on the nucleotide and amino acid sequences of the VP4/VP2 coding region showed that the present strains could be classified into 11 and 8 clusters, respectively. The homology among the present strains ranged from 66.6% to 100% at the nucleotide level and 84.7% to 100% at the amino acid level. The interspecies distance (mean±standard deviation) was calculated to be 0.235±0.048 at the nucleotide level and 0.076±0.033 at the amino acid level. In addition, the phylogenetic trees created based on the nucleotide and amino acid sequences showed that HRV-A strains belonging to some clusters were associated with both upper respiratory infection and wheezy bronchiolitis, while other strains were associated with upper respiratory infection alone. These results suggest that the present HRV-A isolates had a wide nucleotide divergence and were associated with acute respiratory infection, including upper respiratory infection and wheezy bronchiolitis, in Yamagata prefecture, Japan during the investigation period.
Journal: Virus Research - VIRUS RES , vol. 147, no. 2, pp. 265-274, 2010
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    • ...DNA/RNA extraction, PCR, and sequencing For viral DNA/RNA extraction, RT-PCR, and sequence analysis, nasopharyngeal swab samples were centrifuged at 3000 × g at 4°C for 15 min, and the supernatants were used for RT-PCR and sequence analysis as described previously [17]...
    • ...Purification of DNA fragments and nucleotide sequence determination procedures were performed as described previously [17]...
    • ...[17,27]. Moreover, we calculated subgroup or species frequency distributions using pairwise genetic distances for each strain, as previously described [17]...
    • ...[17,27]. Moreover, we calculated subgroup or species frequency distributions using pairwise genetic distances for each strain, as previously described [17]...
    • ...that HRV-A isolates showed wide genetic diversity, and some viruses belonging to specific clusters of the phylogenetic tree of HRV-A isolates might be associated with bronchiolitis [17]...

    Asako Fujitsukaet al. A molecular epidemiological study of respiratory viruses detected in J...

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