Genetic analysis of human rhinovirus species A to C detected in patients with acute respiratory infection in Kumamoto prefecture, Japan 2011-2012
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- 作者：Naoko Kiyota ; Miho Kobayashi ; Hiroyuki Tsukagoshi ; Akihide Ryo ; Seiya Harada ; Takashi Kusaka ; Masatsugu Obuchi ; Naoki Shimojo ; Masahiro Noda ; Hirokazu Kimura
- 关键词：AdV ; adenovirus ; ARI ; acute respiratory infection ; ESS ; effective sample size ; EV ; enterovirus ; FEL ; fixed effects likelihood ; GTR ; general time reversible ; HA ; hemagglutinin ; HBoV ; human bocavirus ; HMPV ; human metapneumovirus ; HPD ; highest posterior density ; HPIV ; human parainfluenza virus ; HRV ; human rhinovirus ; IFEL ; internal fixed effects likelihood ; LRI ; lower respiratory infection ; MCMC ; Markov chain Monte Carlo ; NJ ; neighbor joining ; NPS ; nasopharyngeal swabs ; PCR ; polymerase chain reacti
- 刊名：Infection, Genetics and Evolution
- 出版年：January, 2014
- 年：2014
- 卷：21
- 期：Complete
- 页码：90-102
- 全文大小：633 K
文摘
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 脳 10鈭? to 4 脳 10鈭? 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.