A new method for next-generation sequencing of the full Hepatitis B virus genome from a clinical specimen: impact for vitus genotyping
Autor(a) principal: | |
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Data de Publicação: | 2020 |
Outros Autores: | , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da FIOCRUZ (ARCA) |
Texto Completo: | https://www.arca.fiocruz.br/handle/icict/45445 |
Resumo: | Universidade do Estado de São Paulo. Escola de Medicina. Botucatu, SP, Brasil / Hospital de Clínicas de Botucatu. Laboratório de Biologia Molecular. Botucatu, SP, Brasil. |
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Barbosa, Flavia HebelerWolf, Ivan RodrigoValente, Guilherme TarginoMello, Francisco Campello do AmaralLampe, ElisabethPardini, Maria Inês de Moura CamposGrotto, Rejane Maria Tommasini2020-12-28T14:54:22Z2020-12-28T14:54:22Z2020BARBOSA, Flavia Hebeler et al. A new method for next-generation sequencing of the full Hepatiti B virus genome from a clinical specimen: impact for virus genotyping. Microorganims, v. 8, n.1291, p. 1-12, Sept. 2020.2076-2607https://www.arca.fiocruz.br/handle/icict/4544510.3390/microorganisms8091391engMDPIVírus da Hepatite BGenotipagemNGSAnálise filogeniaHepatitis B virusNGSGenotypingPhylogeny analysisA new method for next-generation sequencing of the full Hepatitis B virus genome from a clinical specimen: impact for vitus genotypinginfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleUniversidade do Estado de São Paulo. Escola de Medicina. Botucatu, SP, Brasil / Hospital de Clínicas de Botucatu. Laboratório de Biologia Molecular. Botucatu, SP, Brasil.Universidade do Estado de São Paulo. Escola de Agricultura. Botucatu, SP, Brasil.Universidade do Estado de São Paulo. Escola de Agricultura. Botucatu, SP, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Hepatites Virais. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Hepatites Virais. Rio de Janeiro, RJ, Brasil.Universidade do Estado de São Paulo. Escola de Medicina. Botucatu, SP, Brasil / Hospital de Clínicas de Botucatu. Laboratório de Biologia Molecular. Botucatu, SP, Brasil.Universidade do Estado de São Paulo. Escola de Medicina. Botucatu, SP, Brasil / Hospital de Clínicas de Botucatu. Laboratório de Biologia Molecular. Botucatu, SP, Brasil / Universidade do Estado de São Paulo. Escola de Agricultura. Botucatu, SP, Brasil.Hepatitis B virus (HBV) is an enveloped virus that induces chronic liver disease. HBV has been classified into eight genotypes (A–H) according to its genome sequence by using Sanger sequencing or reverse hybridization. Sanger sequencing is often restricted to analyzing the S gene and is inaccurate for detecting minority genetic variants, whereas reverse hybridization detects only known mutations. Next-generation sequencing (NGS) is a robust tool for clinical virology with different protocols available. The objective of this study was to develop a new method for the study of viral genetic polymorphisms or more accurate genotyping using genome amplification followed by NGS. Plasma obtained from five chronically infected HBV individuals was used for viral DNA isolation. HBV full-genome PCR amplification was the enrichment method for NGS. Primers were used to amplify all HBV genotypes in three overlapping amplicons, following a tagmentation step and Illumina NGS. For phylogenetic analysis, sequences were extracted from the HBVdb database. We were able to amplify a full HBV genome; further, NGS was shown to be a robust method and allowed better genotyping, mainly in patients carrying mixed genotypes, classified according to other techniques. This new method may be significant for whole genome analyses, including other viruses.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/45445/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALElisabethLampe_FranciscoMelo_etal_IOC_2020.pdfElisabethLampe_FranciscoMelo_etal_IOC_2020.pdfapplication/pdf1645111https://www.arca.fiocruz.br/bitstream/icict/45445/2/ElisabethLampe_FranciscoMelo_etal_IOC_2020.pdfaa786d3537b511418d3d745ded0b8dc9MD52TEXTElisabethLampe_FranciscoMelo_etal_IOC_2020.pdf.txtElisabethLampe_FranciscoMelo_etal_IOC_2020.pdf.txtExtracted texttext/plain42873https://www.arca.fiocruz.br/bitstream/icict/45445/3/ElisabethLampe_FranciscoMelo_etal_IOC_2020.pdf.txt047c310a456753cc7ef6c55ce6d791e2MD53icict/454452020-12-29 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dc.title.pt_BR.fl_str_mv |
A new method for next-generation sequencing of the full Hepatitis B virus genome from a clinical specimen: impact for vitus genotyping |
title |
A new method for next-generation sequencing of the full Hepatitis B virus genome from a clinical specimen: impact for vitus genotyping |
spellingShingle |
A new method for next-generation sequencing of the full Hepatitis B virus genome from a clinical specimen: impact for vitus genotyping Barbosa, Flavia Hebeler Vírus da Hepatite B Genotipagem NGS Análise filogenia Hepatitis B virus NGS Genotyping Phylogeny analysis |
title_short |
A new method for next-generation sequencing of the full Hepatitis B virus genome from a clinical specimen: impact for vitus genotyping |
title_full |
A new method for next-generation sequencing of the full Hepatitis B virus genome from a clinical specimen: impact for vitus genotyping |
title_fullStr |
A new method for next-generation sequencing of the full Hepatitis B virus genome from a clinical specimen: impact for vitus genotyping |
title_full_unstemmed |
A new method for next-generation sequencing of the full Hepatitis B virus genome from a clinical specimen: impact for vitus genotyping |
title_sort |
A new method for next-generation sequencing of the full Hepatitis B virus genome from a clinical specimen: impact for vitus genotyping |
author |
Barbosa, Flavia Hebeler |
author_facet |
Barbosa, Flavia Hebeler Wolf, Ivan Rodrigo Valente, Guilherme Targino Mello, Francisco Campello do Amaral Lampe, Elisabeth Pardini, Maria Inês de Moura Campos Grotto, Rejane Maria Tommasini |
author_role |
author |
author2 |
Wolf, Ivan Rodrigo Valente, Guilherme Targino Mello, Francisco Campello do Amaral Lampe, Elisabeth Pardini, Maria Inês de Moura Campos Grotto, Rejane Maria Tommasini |
author2_role |
author author author author author author |
dc.contributor.author.fl_str_mv |
Barbosa, Flavia Hebeler Wolf, Ivan Rodrigo Valente, Guilherme Targino Mello, Francisco Campello do Amaral Lampe, Elisabeth Pardini, Maria Inês de Moura Campos Grotto, Rejane Maria Tommasini |
dc.subject.other.pt_BR.fl_str_mv |
Vírus da Hepatite B Genotipagem NGS Análise filogenia |
topic |
Vírus da Hepatite B Genotipagem NGS Análise filogenia Hepatitis B virus NGS Genotyping Phylogeny analysis |
dc.subject.en.pt_BR.fl_str_mv |
Hepatitis B virus NGS Genotyping Phylogeny analysis |
description |
Universidade do Estado de São Paulo. Escola de Medicina. Botucatu, SP, Brasil / Hospital de Clínicas de Botucatu. Laboratório de Biologia Molecular. Botucatu, SP, Brasil. |
publishDate |
2020 |
dc.date.accessioned.fl_str_mv |
2020-12-28T14:54:22Z |
dc.date.available.fl_str_mv |
2020-12-28T14:54:22Z |
dc.date.issued.fl_str_mv |
2020 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.citation.fl_str_mv |
BARBOSA, Flavia Hebeler et al. A new method for next-generation sequencing of the full Hepatiti B virus genome from a clinical specimen: impact for virus genotyping. Microorganims, v. 8, n.1291, p. 1-12, Sept. 2020. |
dc.identifier.uri.fl_str_mv |
https://www.arca.fiocruz.br/handle/icict/45445 |
dc.identifier.issn.pt_BR.fl_str_mv |
2076-2607 |
dc.identifier.doi.none.fl_str_mv |
10.3390/microorganisms8091391 |
identifier_str_mv |
BARBOSA, Flavia Hebeler et al. A new method for next-generation sequencing of the full Hepatiti B virus genome from a clinical specimen: impact for virus genotyping. Microorganims, v. 8, n.1291, p. 1-12, Sept. 2020. 2076-2607 10.3390/microorganisms8091391 |
url |
https://www.arca.fiocruz.br/handle/icict/45445 |
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eng |
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eng |
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info:eu-repo/semantics/openAccess |
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openAccess |
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MDPI |
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MDPI |
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