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Genetic Analysis of Human Norovirus Strains in Japan in 2016–2017
In the 2016/2017 winter season in Japan, HuNoV GII.P16-GII.2 strains (2016 strains) emerged and caused large outbreaks of acute gastroenteritis. To better understand the outbreaks, we examined the molecular evolution of the VP1 gene and RdRp region in 2016 strains from patients by studying their tim...
Autores principales: | , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5778136/ https://www.ncbi.nlm.nih.gov/pubmed/29403456 http://dx.doi.org/10.3389/fmicb.2018.00001 |
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author | Nagasawa, Koo Matsushima, Yuki Motoya, Takumi Mizukoshi, Fuminori Ueki, Yo Sakon, Naomi Murakami, Koichi Shimizu, Tomomi Okabe, Nobuhiko Nagata, Noriko Shirabe, Komei Shinomiya, Hiroto Suzuki, Wataru Kuroda, Makoto Sekizuka, Tsuyoshi Suzuki, Yoshiyuki Ryo, Akihide Fujita, Kiyotaka Oishi, Kazunori Katayama, Kazuhiko Kimura, Hirokazu |
author_facet | Nagasawa, Koo Matsushima, Yuki Motoya, Takumi Mizukoshi, Fuminori Ueki, Yo Sakon, Naomi Murakami, Koichi Shimizu, Tomomi Okabe, Nobuhiko Nagata, Noriko Shirabe, Komei Shinomiya, Hiroto Suzuki, Wataru Kuroda, Makoto Sekizuka, Tsuyoshi Suzuki, Yoshiyuki Ryo, Akihide Fujita, Kiyotaka Oishi, Kazunori Katayama, Kazuhiko Kimura, Hirokazu |
author_sort | Nagasawa, Koo |
collection | PubMed |
description | In the 2016/2017 winter season in Japan, HuNoV GII.P16-GII.2 strains (2016 strains) emerged and caused large outbreaks of acute gastroenteritis. To better understand the outbreaks, we examined the molecular evolution of the VP1 gene and RdRp region in 2016 strains from patients by studying their time-scale evolutionary phylogeny, positive/negative selection, conformational epitopes, and phylodynamics. The time-scale phylogeny suggested that the common ancestors of the 2016 strains VP1 gene and RdRp region diverged in 2006 and 1999, respectively, and that the 2016 strain was the progeny of a pre-2016 GII.2. The evolutionary rates of the VP1 gene and RdRp region were around 10(-3) substitutions/site/year. Amino acid substitutions (position 341) in an epitope in the P2 domain of 2016 strains were not found in pre-2016 GII.2 strains. Bayesian skyline plot analyses showed that the effective population size of the VP1 gene in GII.2 strains was almost constant for those 50 years, although the number of patients with NoV GII.2 increased in 2016. The 2016 strain may be involved in future outbreaks in Japan and elsewhere. |
format | Online Article Text |
id | pubmed-5778136 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-57781362018-02-05 Genetic Analysis of Human Norovirus Strains in Japan in 2016–2017 Nagasawa, Koo Matsushima, Yuki Motoya, Takumi Mizukoshi, Fuminori Ueki, Yo Sakon, Naomi Murakami, Koichi Shimizu, Tomomi Okabe, Nobuhiko Nagata, Noriko Shirabe, Komei Shinomiya, Hiroto Suzuki, Wataru Kuroda, Makoto Sekizuka, Tsuyoshi Suzuki, Yoshiyuki Ryo, Akihide Fujita, Kiyotaka Oishi, Kazunori Katayama, Kazuhiko Kimura, Hirokazu Front Microbiol Microbiology In the 2016/2017 winter season in Japan, HuNoV GII.P16-GII.2 strains (2016 strains) emerged and caused large outbreaks of acute gastroenteritis. To better understand the outbreaks, we examined the molecular evolution of the VP1 gene and RdRp region in 2016 strains from patients by studying their time-scale evolutionary phylogeny, positive/negative selection, conformational epitopes, and phylodynamics. The time-scale phylogeny suggested that the common ancestors of the 2016 strains VP1 gene and RdRp region diverged in 2006 and 1999, respectively, and that the 2016 strain was the progeny of a pre-2016 GII.2. The evolutionary rates of the VP1 gene and RdRp region were around 10(-3) substitutions/site/year. Amino acid substitutions (position 341) in an epitope in the P2 domain of 2016 strains were not found in pre-2016 GII.2 strains. Bayesian skyline plot analyses showed that the effective population size of the VP1 gene in GII.2 strains was almost constant for those 50 years, although the number of patients with NoV GII.2 increased in 2016. The 2016 strain may be involved in future outbreaks in Japan and elsewhere. Frontiers Media S.A. 2018-01-18 /pmc/articles/PMC5778136/ /pubmed/29403456 http://dx.doi.org/10.3389/fmicb.2018.00001 Text en Copyright © 2018 Nagasawa, Matsushima, Motoya, Mizukoshi, Ueki, Sakon, Murakami, Shimizu, Okabe, Nagata, Shirabe, Shinomiya, Suzuki, Kuroda, Sekizuka, Suzuki, Ryo, Fujita, Oishi, Katayama and Kimura. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Nagasawa, Koo Matsushima, Yuki Motoya, Takumi Mizukoshi, Fuminori Ueki, Yo Sakon, Naomi Murakami, Koichi Shimizu, Tomomi Okabe, Nobuhiko Nagata, Noriko Shirabe, Komei Shinomiya, Hiroto Suzuki, Wataru Kuroda, Makoto Sekizuka, Tsuyoshi Suzuki, Yoshiyuki Ryo, Akihide Fujita, Kiyotaka Oishi, Kazunori Katayama, Kazuhiko Kimura, Hirokazu Genetic Analysis of Human Norovirus Strains in Japan in 2016–2017 |
title | Genetic Analysis of Human Norovirus Strains in Japan in 2016–2017 |
title_full | Genetic Analysis of Human Norovirus Strains in Japan in 2016–2017 |
title_fullStr | Genetic Analysis of Human Norovirus Strains in Japan in 2016–2017 |
title_full_unstemmed | Genetic Analysis of Human Norovirus Strains in Japan in 2016–2017 |
title_short | Genetic Analysis of Human Norovirus Strains in Japan in 2016–2017 |
title_sort | genetic analysis of human norovirus strains in japan in 2016–2017 |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5778136/ https://www.ncbi.nlm.nih.gov/pubmed/29403456 http://dx.doi.org/10.3389/fmicb.2018.00001 |
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