title: Genetic analysis of human rhinovirus species A to C detected in patients with acute respiratory infection in Kumamoto prefecture, Japan 2011-2012.
abstract: We performed detailed genetic analysis of the VP4/VP2 coding region in human rhinovirus species A to C (HRV-ABC) strains detected in patients with a variety of acute respiratory infections in Kumamoto, Japan in the period 2011-12. The phylogenetic tree and evolutionary timescale were obtained by the Bayesian Markov chain Monte Carlo method. Phylogenetic analyses showed that the present HRV-A, -B, and -C strains belonged to 25, 4, and 18 genotypes, respectively. Some new genotypes were confirmed as prevalent strains of HRV-C. An ancestor of the present HRV-ABCs could be dated back to about 20,000 years ago. The present HRV-A and -C strains have wide genetic divergence (pairwise distance >0.2) with rapid evolutionary rates (around 7 × 10(-4) to 4 × 10(-3)substitutions/site/year). Over 100 sites were found to be under negative selection, while no positively selected sites were found in the analyzed region. No evidence of recombination events was found in this region of the present strains. Our results indicate that the present HRV strains have rapidly evolved and subsequently diverged over a long period into multiple genotypes.
authors.affiliation: Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1 Uto-shi, Kumamoto 869-0425, Japan.
authors.forename: Naoko
authors.initials: N
authors.lastname: Kiyota
authors.affiliation: Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan.
authors.forename: Miho
authors.initials: M
authors.lastname: Kobayashi
authors.affiliation: Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Tsukagoshi
authors.affiliation: Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan.
authors.forename: Akihide
authors.initials: A
authors.lastname: Ryo
authors.affiliation: Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1 Uto-shi, Kumamoto 869-0425, Japan.
authors.forename: Seiya
authors.initials: S
authors.lastname: Harada
authors.affiliation: Maternal Perinatal Center, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Kusaka
authors.affiliation: Toyama Institute of Health, 17-1 Nakataikoyama, Imizu-shi, Toyama 939-0363, Japan.
authors.forename: Masatsugu
authors.initials: M
authors.lastname: Obuchi
authors.affiliation: Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan.
authors.forename: Naoki
authors.initials: N
authors.lastname: Shimojo
authors.affiliation: Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Noda
authors.affiliation: Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan. Electronic address: kimhiro@nih.go.jp.
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Kimura
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001499:Bayes Theorem; D002675:Child, Preschool; D019143:Evolution, Molecular; D005260:Female; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D007564:Japan / Q000453:epidemiology; D008297:Male; D008875:Middle Aged; D010802:Phylogeny; D010850:Picornaviridae Infections / Q000821:virology*; D012141:Respiratory Tract Infections / Q000821:virology*; D012229:Rhinovirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D012641:Selection, Genetic; D055815:Young Adult
keywords: Acute respiratory infection; Bayesian Markov chain Monte Carlo method; Human rhinovirus; Pairwise distance; VP4/VP2 region