Molecular Evolution of the Capsid Gene in Norovirus Genogroup I

Kobayashi, Miho; Yoshizumi, Shima; Kogawa, Sayaka; Takahashi, Tomoko; Ueki, Yo; Shinohara, Michiyo; Mizukoshi, Fuminori; Tsukagoshi, Hiroyuki; Sasaki, Yoshiko; Suzuki, Riéko; Shimizu, Hideaki; Iwakiri, Akira; Okabe, Nobuhiko; Shirabe, Komei; Shinomiya, Hiroto; Kozawa, Kunihisa; Kusunoki, Hideki; Ryo, Akihide; Kuroda, Makoto; Katayama, Kazuhiko; Kimura, Hirokazu

doi:10.1038/srep13806

Cited by 21 publications

(28 citation statements)

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“…We attempted to identify positive and negative selection sites using all methods described in previous reports (Botosso et al, 2009;Kobayashi et al, 2015;Nagasawa et al, 2015). No…”

Section: Positive and Negative Selection Site Analysesmentioning

confidence: 99%

“…Four different methods were used: the single likelihood ancestor (SLAC) method, the fixed effects likelihood (FEL) method, the internal fixed effects likelihood (IFEL) method, and the mixed effects model of evolution (MEME; Kobayashi et al, 2015).…”

Section: Positive and Negative Selection Site Analysesmentioning

confidence: 99%

“…We tested for positive selection using four methods: IFL, IFEL, SLAC, and MEME (Botosso et al, 2009;Kushibuchi et al, 2013;Kobayashi et al, 2015). Each method has revealed different numbers of sites produced by positive selection in other virus genomes Kobayashi et al, 2015).…”

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confidence: 99%

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Molecular evolution of the fusion protein gene in human respiratory syncytial virus subgroup A

Kimura

Nagasawa

Tsukagoshi

et al. 2016

Infection, Genetics and Evolution

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“…We attempted to identify positive and negative selection sites using all methods described in previous reports (Botosso et al, 2009;Kobayashi et al, 2015;Nagasawa et al, 2015). No…”

Section: Positive and Negative Selection Site Analysesmentioning

confidence: 99%

Section: Positive and Negative Selection Site Analysesmentioning

confidence: 99%

See 1 more Smart Citation

Molecular evolution of the fusion protein gene in human respiratory syncytial virus subgroup A

Kimura

Nagasawa

Tsukagoshi

et al. 2016

Infection, Genetics and Evolution

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“…Amino acid substitutions within the G gene 3rd hypervariable region under positive and negative selection pressure for central Vietnam RSV-A NA1 and ON1 strains were estimated by calculating synonymous (dS) and non-synonymous (dN) substitution rates at every codon with Datamonkey (http://www.datamonkey.org/) (Pond and Frost, 2005 (Kobayashi et al, 2015). In the selection pressure analyses, p-values less than 0.05 were considered to be statistically significant (Kimura et al, 2015;Kobayashi et al, 2015).…”

Section: Positive and Negative Selection Pressure Analysesmentioning

confidence: 99%

Molecular evolution of respiratory syncytial virus subgroup A genotype NA1 and ON1 attachment glycoprotein ( G ) gene in central Vietnam

Yoshihara

Nagasawa

et al. 2016

Infection, Genetics and Evolution

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We performed molecular evolutionary analyses of the G gene C-terminal 3rd hypervariable region of RSV-A genotypes NA1 and ON1 strains from the paediatric acute respiratory infection patients in central Vietnam during the 2010-2012 study period. Time-scaled phylogenetic analyses were performed using Bayesian Markov Chain Monte Carlo (MCMC) method, and pairwise distances (p-distances) were calculated. Bayesian Skyline Plot (BSP) was constructed to analyze the time-trend relative genetic diversity of central Vietnam RSV-A strains. We also estimated the N-glycosylation sites within G gene hypervariable region. Amino acid substitutions under positive and negative selection pressure were examined using Conservative Single Likelihood Ancestor Counting (SLAC), Fixed Effects Likelihood (FEL), Internal Fixed Effects Likelihood (IFEL) and Mixed Effects Model for Episodic Diversifying Selection (MEME) models. The majority of central Vietnam ON1 strains detected in 2012 were classified into lineage 1 with few positively selected substitutions. As for the Vietnamese NA1 strains, four lineages were circulating during the study period with a few positive selection sites. Shifting patterns of the predominantly circulating NA1 lineage were observed in each year during the investigation period. Median p-distance of central Vietnam NA1 strains was wider (p-distance = 0.028) than that of ON1 (p-distance = 0.012). The molecular evolutionary rate of central Vietnam ON1 strains was estimated to be 2.55 × 10-2 (substitutions/site/year) and was faster than NA1 (7.12 × 10-3 (substitutions/site/year)). Interestingly, the evolutionary rates of both genotypes ON1 and NA1 strains from central Vietnam were faster than the global strains respectively. Furthermore, the shifts of N-glycosylation pattern within the G gene 3rd hypervariable region of Vietnamese NA1 strains were observed in each year. BSP analysis indicated the rapid growth of RSV-A effective population size in early 2012. These results suggested that the molecular evolution of RSV-A G gene detected in central Vietnam was fast with unique evolutionary dynamics.

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“…1/1000 (Jünemann et al, 2013), it is extremely improbable to find multiple mutations in a single read. The natural genetic diversity of NoVs has been studied previously within individual patients (Nilsson et al, 2003;Obara et al, 2008;Vega et al, 2014), within defined outbreaks (Dingle, 2004;Holzknecht et al, 2015;Sasaki et al, 2006), or at larger geographic and temporal scales (Bodhidatta et al, 2015;Carlsson et al, 2009;Cotten et al, 2014;Kobayashi et al, 2015;Vega et al, 2014). However, this diversity depends on multiple factors other than spontaneous mutation rates, including natural selection, the number of replication rounds elapsed and random genetic drift, among others.…”

Section: Introductionmentioning

confidence: 99%

Human norovirus hyper-mutation revealed by ultra-deep sequencing

Cuevas

Combe

Torres-Puente

et al. 2016

Infection, Genetics and Evolution

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Human norovirus hyper-mutation revealed by ultra-deep sequencing, (2016), doi: 10.1016/j.meegid.2016.04.017 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT 2 AbstractHuman noroviruses (NoVs) are a major cause of gastroenteritis worldwide. It is thought that, similar to other RNA viruses, high mutation rates allow NoVs to evolve fast and to undergo rapid immune escape at the population level. However, the rate and spectrum of spontaneous mutations of human NoVs has not been quantified previously. Here, we analysed the intrapatient diversity of the NoV capsid by carrying out RT-PCR and ultra-deep sequencing with 100,000-fold coverage of 16 stool samples from symptomatic patients. This revealed the presence of low-frequency sequences carrying large numbers of U-to-C or A-to-G base transitions, suggesting a role for hyper-mutation in NoV diversity. To more directly test for hyper-mutation, we performed transfection assays in which the production of mutations was restricted to a single cell infection cycle. This confirmed the presence of sequences with multiple U-to-C/A-to-G transitions, and suggested that hyper-mutation contributed a large fraction of the total NoV spontaneous mutation rate. The type of changes produced and their sequence context are compatible with ADAR-mediated editing of the viral RNA.Graphical abstract: this optional item will be prepared and submitted upon manuscript acceptance.

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Molecular Evolution of the Capsid Gene in Norovirus Genogroup I

Cited by 21 publications

References 50 publications

Molecular evolution of the fusion protein gene in human respiratory syncytial virus subgroup A

Molecular evolution of the fusion protein gene in human respiratory syncytial virus subgroup A

Molecular evolution of respiratory syncytial virus subgroup A genotype NA1 and ON1 attachment glycoprotein ( G ) gene in central Vietnam

Human norovirus hyper-mutation revealed by ultra-deep sequencing

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