title: Molecular evolution of the VP1, VP2, and VP3 genes in human rhinovirus species C.
abstract: Human rhinovirus species C (HRV-C) was recently discovered, and this virus has been associated with various acute respiratory illnesses (ARI). However, the molecular evolution of the major antigens of this virus, including VP1, VP2, and VP3, is unknown. Thus, we performed complete VP1, VP2, and VP3 gene analyses of 139 clinical HRV-C strains using RT-PCR with newly designed primer sets and next-generation sequencing. We assessed the time-scale evolution and evolutionary rate of these genes using the Bayesian Markov chain Monte Carlo method. In addition, we calculated the pairwise distance and confirmed the positive/negative selection sites in these genes. The phylogenetic trees showed that the HRV-C strains analyzed using these genes could be dated back approximately 400 to 900 years, and these strains exhibited high evolutionary rates (1.35 to 3.74 × 10(-3) substitutions/site/year). Many genotypes (>40) were confirmed in the phylogenetic trees. Furthermore, no positively selected site was found in the VP1, VP2, and VP3 protein. Molecular modeling analysis combined with variation analysis suggested that the exterior surfaces of the VP1, VP2 and VP3 proteins are rich in loops and are highly variable. These results suggested that HRV-C may have an old history and unique antigenicity as an agent of various ARI.
authors: Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
authors: Makoto
authors: M
authors: Kuroda
authors: Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan.
authors: Shoichi
authors: S
authors: Niwa
authors: Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
authors: Tsuyoshi
authors: T
authors: Sekizuka
authors: Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan.
authors: Hiroyuki
authors: H
authors: Tsukagoshi
authors: Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
authors: Masaru
authors: M
authors: Yokoyama
authors: Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan.
authors: Akihide
authors: A
authors: Ryo
authors: Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
authors: Hironori
authors: H
authors: Sato
authors: Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1, Kurisaki-machi, Uto-shi, Kumamoto 869-0425, Japan.
authors: Naoko
authors: N
authors: Kiyota
authors: Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan.
authors: Masahiro
authors: M
authors: Noda
authors: Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan.
authors: Kunihisa
authors: K
authors: Kozawa
authors: Yamaguchi Prefectural Institute of Public Health and Environment, 2-57-6 Aoi, Yamaguchi-shi, Yamaguchi 753-082, Japan.
authors: Komei
authors: K
authors: Shirabe
authors: Maternal Perinatal Center, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan.
authors: Takashi
authors: T
authors: Kusaka
authors: Department of Pediatrics, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8670, Japan.
authors: Naoki
authors: N
authors: Shimojo
authors: Department of Pediatrics, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube-shi, Yamaguchi 755-8505, Japan.
authors: Shunji
authors: S
authors: Hasegawa
authors: Department of Pediatrics, National Hospital Organization Yokohama Medical Center, 3-60-2 Harajuku, Totsuka-ku, Yokohama, Kanagawa 245-8575, Japan.
authors: Kazuko
authors: K
authors: Sugai
authors: Toyama Institute of Health, 17-1 Nakataikoyama, Imizu-shi, Toyama 939-0363, Japan.
authors: Masatsugu
authors: M
authors: Obuchi
authors: Influenza virus Research Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan.
authors: Masato
authors: M
authors: Tashiro
authors: Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan.
authors: Kazunori
authors: K
authors: Oishi
authors: Department of Respiratory Medicine, Kyorin University, School of Medicine, 6-20-2 Shinkawa, Mitaka-shi, Tokyo 181-8611, Japan.
authors: Haruyuki
authors: H
authors: Ishii
authors: 1] Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan [2] Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan [3] Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan.
authors: Hirokazu
authors: H
authors: Kimura
mesh_terms: D001483:Base Sequence; D001499:Bayes Theorem; D036022:Capsid Proteins / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D005838:Genotype; D008390:Markov Chains; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D010802:Phylogeny; D012229:Rhinovirus / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D014764:Viral Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: D036022:Capsid Proteins; C442544:VP2 protein, Rhinovirus; D014764:Viral Proteins; C074995:viral protein 1, rhinovirus
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