ABSTRACT
Detailed genetic analysis was carried out of the VP4/VP2 coding region in human rhinovirus species C (HRV-C) strains detected in patients with acute respiratory infection in Japan. Phylogenetic trees were constructed by the neighbour-joining (NJ) and maximum-likelihood (ML) methods. The NJ phylogenetic tree assigned 11 genotypes to the present strains, whilst the ML tree showed that the strains diversified sometime in the early 1870 s. Moreover, the pairwise distance among the present strains was relatively long, and the rate of molecular evolution of the coding region was rapid (3.07 × 10(-3) substitutions per site per year). The results suggest that the present HRV-C strains have a wide genetic divergence and a unique evolutionary timescale.
Subject(s)
Genetic Variation , Picornaviridae Infections/virology , Respiratory Tract Infections/virology , Rhinovirus/classification , Rhinovirus/genetics , Viral Proteins/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Child , Child, Preschool , Cluster Analysis , Evolution, Molecular , Female , Genotype , Humans , Infant , Japan , Male , Middle Aged , Molecular Epidemiology , Molecular Sequence Data , Phylogeny , RNA, Viral/genetics , Rhinovirus/isolation & purification , Sequence Analysis, DNA , Young AdultABSTRACT
Recent studies suggest that human rhinovirus species A, B and C (HRV-ABCs) may be associated with both the common cold and severe acute respiratory illnesses (ARIs) such as bronchiolitis, wheezy bronchiolitis and pneumonia. However, the state and molecular epidemiology of these viruses in Japan is not fully understood. This study detected the genomes of HRV-ABCs from Japanese patients (92 cases, 0-36 years old, mean±sd 3.5±5.0 years) with various ARIs including upper respiratory infection, bronchiolitis, wheezy bronchiolitis, croup and pneumonia between January and December 2010. HRV-ABCs were provisionally type assigned from the pairwise distances among the strains. On phylogenetic trees based on the nucleotide sequences of the VP4/VP2 coding region, HRV-A, -B and -C were provisionally assigned to 14, 2 and 12 types, respectively. The present HRV-A and -C strains had a wide genetic diversity (>30â% divergence). The interspecies distances were 0.230±0.063 (mean±sd, HRV-A), 0.218±0.048 (HRV-B) and 0.281±0.105 (HRV-C), based on nucleotide sequences, and 0.075±0.036 (HRV-A), 0.049±0.022 (HRV-B) and 0.141±0.064 (HRV-C) at the deduced amino acid level. Furthermore, HRV-A and -C were the predominant species and were detected throughout the seasons. The results suggested that HRV-A and -C strains have a wide genetic divergence and are associated with various ARIs in Japan.
Subject(s)
Picornaviridae Infections/epidemiology , Picornaviridae Infections/virology , RNA, Viral/genetics , Respiratory Tract Diseases/epidemiology , Respiratory Tract Diseases/virology , Rhinovirus/classification , Rhinovirus/isolation & purification , Adolescent , Adult , Child , Child, Preschool , Cluster Analysis , Female , Genetic Variation , Genotype , Humans , Infant , Japan/epidemiology , Male , Molecular Sequence Data , Phylogeny , Rhinovirus/genetics , Sequence Analysis, DNA , Young AdultABSTRACT
BACKGROUND: Recent studies strongly suggest that some respiratory viruses are associated with the induction of acute wheezing and/or exacerbation of bronchial asthma. However, molecular epidemiology of these viruses is not exactly known. METHODS: Using PCR technology, we attempted to detect various respiratory viruses from 115 Japanese children. Furthermore, the detected viruses were subjected to homology, pairwise distance, and phylogenetic analysis. RESULTS: Viruses were detected from 99 (86.1%) patients. Respiratory syncytial virus (RSV) alone and human rhinovirus (HRV) alone were detected in 47 (40.9%) and 36 (31.3%) patients, respectively. Both RSV and HRV were detected in 14 (12.2%) patients. Human metapneumovirus (HMPV) alone and human parainfluenza virus (HPIV) alone were detected in 1 (0.9%) patient each, respectively. Homology and phylogenetic analyses showed that the RSV and HRV strains were classified into genetically diverse species or subgroups. In addition, RSV was the dominant virus detected in patients with no history of wheezing, whereas HRV was dominant in patients with a history of wheezing. CONCLUSIONS: The results suggested that these genetically diverse respiratory viruses, especially RSV and HRV, might be associated with wheezing in Japanese children.
