A new method for next-generation sequencing of the full Hepatitis B virus genome from a clinical specimen: impact for vitus genotyping

Detalhes bibliográficos
Autor(a) principal: Barbosa, Flavia Hebeler
Data de Publicação: 2020
Outros Autores: Wolf, Ivan Rodrigo, Valente, Guilherme Targino, Mello, Francisco Campello do Amaral, Lampe, Elisabeth, Pardini, Maria Inês de Moura Campos, Grotto, Rejane Maria Tommasini
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.
id CRUZ_f3e1d769d0397f40d3164e751749bff6
oai_identifier_str oai:www.arca.fiocruz.br:icict/45445
network_acronym_str CRUZ
network_name_str Repositório Institucional da FIOCRUZ (ARCA)
repository_id_str 2135
spelling 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 12:33:38.103oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352020-12-29T15:33:38Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
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
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/45445/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/45445/2/ElisabethLampe_FranciscoMelo_etal_IOC_2020.pdf
https://www.arca.fiocruz.br/bitstream/icict/45445/3/ElisabethLampe_FranciscoMelo_etal_IOC_2020.pdf.txt
bitstream.checksum.fl_str_mv 5a560609d32a3863062d77ff32785d58
aa786d3537b511418d3d745ded0b8dc9
047c310a456753cc7ef6c55ce6d791e2
bitstream.checksumAlgorithm.fl_str_mv MD5
MD5
MD5
repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
repository.mail.fl_str_mv repositorio.arca@fiocruz.br
_version_ 1798325088728121344

Registros relacionados