Subgenotyping of genotype C hepatitis B virus: correcting misclassifications and identifying a novel subgenotype.

<h4>Background</h4>More than ten subgenotypes of genotype C Hepatitis B virus (HBV) have been reported, including C1 to C16 and two C/D recombinant subgenotypes (CD1 and CD2), however, inconsistent designations of these subgenotypes still exist.<h4>Methodology/principal findings<...

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Autores principales:	Weifeng Shi, Chaodong Zhu, Weimin Zheng, Wei Zheng, Cheng Ling, Michael J Carr, Desmond G Higgins, Zhong Zhang
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fc5958cba9f54f82a4562ce6bc5d03ac
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spelling	oai:doaj.org-article:fc5958cba9f54f82a4562ce6bc5d03ac2021-11-18T08:12:01ZSubgenotyping of genotype C hepatitis B virus: correcting misclassifications and identifying a novel subgenotype.1932-620310.1371/journal.pone.0047271https://doaj.org/article/fc5958cba9f54f82a4562ce6bc5d03ac2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23077582/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>More than ten subgenotypes of genotype C Hepatitis B virus (HBV) have been reported, including C1 to C16 and two C/D recombinant subgenotypes (CD1 and CD2), however, inconsistent designations of these subgenotypes still exist.<h4>Methodology/principal findings</h4>We performed a phylogenetic analysis of all full-length genotype C HBV genome sequences to correct the misclassifications of HBV subgenotypes and to study the influence of recombination on HBV subgenotyping. Our results showed that although inclusion of the recombinant sequences changed the topology of the phylogenetic tree, it did not affect the subgenotyping of the non-recombinant sequences, except subgenotype C2. In addition, most of the subgenotypes have been properly designated. However, several misclassifications of HBV subgenotypes have been identified and corrected. For example, C11 proposed by Utsumi and colleagues in 2011 was found to be grouped with C12 proposed by Mulyanto and colleagues. Two sequences, GQ358157 and GU721029, previously designated as C6 have been re-designated as C12 and C7, respectively. Moreover, a quasi-subgenotype C2 was proposed, which included the old C2, several previously unclassified sequences and previously designated C14. In particular, we identified a novel subgenotype, tentative C14, which was well supported by phylogenetic analysis and sequence divergence of >4%.<h4>Conclusions/significance</h4>A number of misclassifications in the subgenotyping of genotype C HBV have been identified in this study. After correcting the misclassifications, we proposed a better classification for the subgenotyping of genotype C HBV, in which a novel quasi-subgenotype C2 and a novel subgenotype, tentative C14, were described. Based on this large-scale analysis, we propose that a novel subgenotype should only be reported after a complete comparison of all relevant sequences rather than a few representative sequences only.Weifeng ShiChaodong ZhuWeimin ZhengWei ZhengCheng LingMichael J CarrDesmond G HigginsZhong ZhangPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 10, p e47271 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Weifeng Shi Chaodong Zhu Weimin Zheng Wei Zheng Cheng Ling Michael J Carr Desmond G Higgins Zhong Zhang Subgenotyping of genotype C hepatitis B virus: correcting misclassifications and identifying a novel subgenotype.
description	<h4>Background</h4>More than ten subgenotypes of genotype C Hepatitis B virus (HBV) have been reported, including C1 to C16 and two C/D recombinant subgenotypes (CD1 and CD2), however, inconsistent designations of these subgenotypes still exist.<h4>Methodology/principal findings</h4>We performed a phylogenetic analysis of all full-length genotype C HBV genome sequences to correct the misclassifications of HBV subgenotypes and to study the influence of recombination on HBV subgenotyping. Our results showed that although inclusion of the recombinant sequences changed the topology of the phylogenetic tree, it did not affect the subgenotyping of the non-recombinant sequences, except subgenotype C2. In addition, most of the subgenotypes have been properly designated. However, several misclassifications of HBV subgenotypes have been identified and corrected. For example, C11 proposed by Utsumi and colleagues in 2011 was found to be grouped with C12 proposed by Mulyanto and colleagues. Two sequences, GQ358157 and GU721029, previously designated as C6 have been re-designated as C12 and C7, respectively. Moreover, a quasi-subgenotype C2 was proposed, which included the old C2, several previously unclassified sequences and previously designated C14. In particular, we identified a novel subgenotype, tentative C14, which was well supported by phylogenetic analysis and sequence divergence of >4%.<h4>Conclusions/significance</h4>A number of misclassifications in the subgenotyping of genotype C HBV have been identified in this study. After correcting the misclassifications, we proposed a better classification for the subgenotyping of genotype C HBV, in which a novel quasi-subgenotype C2 and a novel subgenotype, tentative C14, were described. Based on this large-scale analysis, we propose that a novel subgenotype should only be reported after a complete comparison of all relevant sequences rather than a few representative sequences only.
format	article
author	Weifeng Shi Chaodong Zhu Weimin Zheng Wei Zheng Cheng Ling Michael J Carr Desmond G Higgins Zhong Zhang
author_facet	Weifeng Shi Chaodong Zhu Weimin Zheng Wei Zheng Cheng Ling Michael J Carr Desmond G Higgins Zhong Zhang
author_sort	Weifeng Shi
title	Subgenotyping of genotype C hepatitis B virus: correcting misclassifications and identifying a novel subgenotype.
title_short	Subgenotyping of genotype C hepatitis B virus: correcting misclassifications and identifying a novel subgenotype.
title_full	Subgenotyping of genotype C hepatitis B virus: correcting misclassifications and identifying a novel subgenotype.
title_fullStr	Subgenotyping of genotype C hepatitis B virus: correcting misclassifications and identifying a novel subgenotype.
title_full_unstemmed	Subgenotyping of genotype C hepatitis B virus: correcting misclassifications and identifying a novel subgenotype.
title_sort	subgenotyping of genotype c hepatitis b virus: correcting misclassifications and identifying a novel subgenotype.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/fc5958cba9f54f82a4562ce6bc5d03ac
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Subgenotyping of genotype C hepatitis B virus: correcting misclassifications and identifying a novel subgenotype.

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