Comparative phylogenetic analyses of recombinant noroviruses based on different protein-encoding regions show the recombination-associated evolution pattern

Abstract Noroviruses are the major cause of acute gastroenteritis worldwide, and recombination is recognized as the important mechanism for its continuous emergence. In this study, for the common GII.P12 and GII.3 recombinants, phylogenetic relationships based on different proteins in three ORFs wer...

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Autores principales:	Liang Xue, Qingping Wu, Ruimin Dong, Weicheng Cai, Haoming Wu, Moutong Chen, Gang Chen, Juan Wang, Jumei Zhang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/32417f489f914029a34ae625f91fcbe6
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spelling	oai:doaj.org-article:32417f489f914029a34ae625f91fcbe62021-12-02T12:32:05ZComparative phylogenetic analyses of recombinant noroviruses based on different protein-encoding regions show the recombination-associated evolution pattern10.1038/s41598-017-01640-42045-2322https://doaj.org/article/32417f489f914029a34ae625f91fcbe62017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-01640-4https://doaj.org/toc/2045-2322Abstract Noroviruses are the major cause of acute gastroenteritis worldwide, and recombination is recognized as the important mechanism for its continuous emergence. In this study, for the common GII.P12 and GII.3 recombinants, phylogenetic relationships based on different proteins in three ORFs were comparatively analyzed, focusing on the influence of intergenic recombination. By using newly designed primers, genomes of two GII.P12/GII.3 Guangzhou recombinants were firstly amplified. Combined with other reported sequences of GII.P12_ORF1 (n = 20), GII.3_ORF2 (n = 131), GII.3_ORF3 (n = 36), all GII.P12 and GII.3 strains could be divided into 6, 8, and 7 clusters based on different ORFs, which showed an obvious recombination-associated and temporally sequential evolution pattern (with the exception of GII.P12/GII.13 recombinants). Based on multiple alignments, 126 informative sites were identified in three ORFs (44, 54, and 28), and four proteins (p48, p22, VP1, and VP2) were found under positive selection. Furthermore, by using homology modeling, predicted epitopes were mapped on the P proteins of seven GII.3 representative strains, without one (Epi: 353–361) specific to the GII.4 VA387 strain. In summary, via the genome analyses, phylogenetic relationships of GII.P12 and GII.3 recombinants based on the different proteins presented a special temporally sequential evolution process associated with their recombinant types.Liang XueQingping WuRuimin DongWeicheng CaiHaoming WuMoutong ChenGang ChenJuan WangJumei ZhangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Liang Xue Qingping Wu Ruimin Dong Weicheng Cai Haoming Wu Moutong Chen Gang Chen Juan Wang Jumei Zhang Comparative phylogenetic analyses of recombinant noroviruses based on different protein-encoding regions show the recombination-associated evolution pattern
description	Abstract Noroviruses are the major cause of acute gastroenteritis worldwide, and recombination is recognized as the important mechanism for its continuous emergence. In this study, for the common GII.P12 and GII.3 recombinants, phylogenetic relationships based on different proteins in three ORFs were comparatively analyzed, focusing on the influence of intergenic recombination. By using newly designed primers, genomes of two GII.P12/GII.3 Guangzhou recombinants were firstly amplified. Combined with other reported sequences of GII.P12_ORF1 (n = 20), GII.3_ORF2 (n = 131), GII.3_ORF3 (n = 36), all GII.P12 and GII.3 strains could be divided into 6, 8, and 7 clusters based on different ORFs, which showed an obvious recombination-associated and temporally sequential evolution pattern (with the exception of GII.P12/GII.13 recombinants). Based on multiple alignments, 126 informative sites were identified in three ORFs (44, 54, and 28), and four proteins (p48, p22, VP1, and VP2) were found under positive selection. Furthermore, by using homology modeling, predicted epitopes were mapped on the P proteins of seven GII.3 representative strains, without one (Epi: 353–361) specific to the GII.4 VA387 strain. In summary, via the genome analyses, phylogenetic relationships of GII.P12 and GII.3 recombinants based on the different proteins presented a special temporally sequential evolution process associated with their recombinant types.
format	article
author	Liang Xue Qingping Wu Ruimin Dong Weicheng Cai Haoming Wu Moutong Chen Gang Chen Juan Wang Jumei Zhang
author_facet	Liang Xue Qingping Wu Ruimin Dong Weicheng Cai Haoming Wu Moutong Chen Gang Chen Juan Wang Jumei Zhang
author_sort	Liang Xue
title	Comparative phylogenetic analyses of recombinant noroviruses based on different protein-encoding regions show the recombination-associated evolution pattern
title_short	Comparative phylogenetic analyses of recombinant noroviruses based on different protein-encoding regions show the recombination-associated evolution pattern
title_full	Comparative phylogenetic analyses of recombinant noroviruses based on different protein-encoding regions show the recombination-associated evolution pattern
title_fullStr	Comparative phylogenetic analyses of recombinant noroviruses based on different protein-encoding regions show the recombination-associated evolution pattern
title_full_unstemmed	Comparative phylogenetic analyses of recombinant noroviruses based on different protein-encoding regions show the recombination-associated evolution pattern
title_sort	comparative phylogenetic analyses of recombinant noroviruses based on different protein-encoding regions show the recombination-associated evolution pattern
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/32417f489f914029a34ae625f91fcbe6
work_keys_str_mv	AT liangxue comparativephylogeneticanalysesofrecombinantnorovirusesbasedondifferentproteinencodingregionsshowtherecombinationassociatedevolutionpattern AT qingpingwu comparativephylogeneticanalysesofrecombinantnorovirusesbasedondifferentproteinencodingregionsshowtherecombinationassociatedevolutionpattern AT ruimindong comparativephylogeneticanalysesofrecombinantnorovirusesbasedondifferentproteinencodingregionsshowtherecombinationassociatedevolutionpattern AT weichengcai comparativephylogeneticanalysesofrecombinantnorovirusesbasedondifferentproteinencodingregionsshowtherecombinationassociatedevolutionpattern AT haomingwu comparativephylogeneticanalysesofrecombinantnorovirusesbasedondifferentproteinencodingregionsshowtherecombinationassociatedevolutionpattern AT moutongchen comparativephylogeneticanalysesofrecombinantnorovirusesbasedondifferentproteinencodingregionsshowtherecombinationassociatedevolutionpattern AT gangchen comparativephylogeneticanalysesofrecombinantnorovirusesbasedondifferentproteinencodingregionsshowtherecombinationassociatedevolutionpattern AT juanwang comparativephylogeneticanalysesofrecombinantnorovirusesbasedondifferentproteinencodingregionsshowtherecombinationassociatedevolutionpattern AT jumeizhang comparativephylogeneticanalysesofrecombinantnorovirusesbasedondifferentproteinencodingregionsshowtherecombinationassociatedevolutionpattern
_version_	1718394147664035840

Comparative phylogenetic analyses of recombinant noroviruses based on different protein-encoding regions show the recombination-associated evolution pattern

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