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

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.