Comparative clinical sample preparation of DNA and RNA viral nucleic acids for a commercial deep sequencing system (Illumina MiSeq (R))

Detalhes bibliográficos
Autor(a) principal: Ullmann, Leila Sabrina [UNESP]
Data de Publicação: 2015
Outros Autores: Tozato, Claudia de Camargo [UNESP], Malossi, Camila Dantas [UNESP], Cruz, Tais Fukuta da [UNESP], Cavalcante, Raissa Vasconcelos [UNESP], Kurissio, Jacqueline Kazue [UNESP], Cagnini, Didier Quevedo [UNESP], Rodrigues, Marianna Vaz [UNESP], Biondo, Alexander Welker, Araujo, Joao Pessoa [UNESP]
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://www.sciencedirect.com/science/article/pii/S0166093415001457
http://hdl.handle.net/11449/128604
Resumo: Sequence-independent methods for viral discovery have been widely used for whole genome sequencing of viruses. Different protocols for viral enrichment, library preparation and sequencing have increasingly been more available and at lower costs. However, no study to date has focused on optimization of viral sample preparation for commercial deep sequencing. Accordingly, the aim of the present study was to evaluate an In-House enzymatic protocol for double-stranded DNA (dsDNA) synthesis and also compare the use of a commercially available kit protocol (Nextera XT, Illumina Inc, San Diego, CA, USA) and its combination with a library quantitation kit (Kapa, Kapa Biosystems, Wilmington, MA, USA) for deep sequencing (Illumina Miseq). Two RNA viruses (canine distemper virus and dengue virus) and one ssDNA virus (porcine circovirus type 2) were tested with the optimized protocols. The tested method for dsDNA synthesis has shown satisfactory results and may be used in laboratory setting, particularly when enzymes are already available. Library preparation combining commercial kits (Nextera XT and Kapa) has yielded more reads and genome coverage, probably due to a lack of small fragment recovering at the normalization step of Nextera XT. In addition, libraries may be diluted or concentrated to provide increase on genome coverage with Kapa quantitation. (C) 2015 Elsevier B.V. All rights reserved.
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spelling Comparative clinical sample preparation of DNA and RNA viral nucleic acids for a commercial deep sequencing system (Illumina MiSeq (R))Double-stranded DNALibrary preparationDeep sequencingMiSeqSequence-independent methods for viral discovery have been widely used for whole genome sequencing of viruses. Different protocols for viral enrichment, library preparation and sequencing have increasingly been more available and at lower costs. However, no study to date has focused on optimization of viral sample preparation for commercial deep sequencing. Accordingly, the aim of the present study was to evaluate an In-House enzymatic protocol for double-stranded DNA (dsDNA) synthesis and also compare the use of a commercially available kit protocol (Nextera XT, Illumina Inc, San Diego, CA, USA) and its combination with a library quantitation kit (Kapa, Kapa Biosystems, Wilmington, MA, USA) for deep sequencing (Illumina Miseq). Two RNA viruses (canine distemper virus and dengue virus) and one ssDNA virus (porcine circovirus type 2) were tested with the optimized protocols. The tested method for dsDNA synthesis has shown satisfactory results and may be used in laboratory setting, particularly when enzymes are already available. Library preparation combining commercial kits (Nextera XT and Kapa) has yielded more reads and genome coverage, probably due to a lack of small fragment recovering at the normalization step of Nextera XT. In addition, libraries may be diluted or concentrated to provide increase on genome coverage with Kapa quantitation. (C) 2015 Elsevier B.V. All rights reserved.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)UNESP Univ Estadual Paulista, Lab Anim &Human Virol, Dept Microbiol &Immunol, Biosci Inst, BR-18618970 Sao Paulo, BrazilUniv Fed Parana, Dept Vet Med, BR-80035050 Curitiba, Parana, BrazilUniv Illinois, Dept Pathobiol, Urbana, IL 61802 USAUNESP Univ Estadual Paulista, Lab Anim &Human Virol, Dept Microbiol &Immunol, Biosci Inst, BR-18618970 Sao Paulo, BrazilFAPESP: 2011/09424-2FAPESP: 2014/13532-3Elsevier B.V.Universidade Estadual Paulista (Unesp)Universidade Federal do Paraná (UFPR)University of IllinoisUllmann, Leila Sabrina [UNESP]Tozato, Claudia de Camargo [UNESP]Malossi, Camila Dantas [UNESP]Cruz, Tais Fukuta da [UNESP]Cavalcante, Raissa Vasconcelos [UNESP]Kurissio, Jacqueline Kazue [UNESP]Cagnini, Didier Quevedo [UNESP]Rodrigues, Marianna Vaz [UNESP]Biondo, Alexander WelkerAraujo, Joao Pessoa [UNESP]2015-10-21T13:11:25Z2015-10-21T13:11:25Z2015-08-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article60-63http://www.sciencedirect.com/science/article/pii/S0166093415001457Journal Of Virological Methods, v. 220, p. 60-63, 2015.0166-0934http://hdl.handle.net/11449/12860410.1016/j.jviromet.2015.04.009WOS:000356112300012Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengJournal Of Virological Methods1.7560,858info:eu-repo/semantics/openAccess2021-10-23T22:03:55Zoai:repositorio.unesp.br:11449/128604Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T17:00:34.086494Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Comparative clinical sample preparation of DNA and RNA viral nucleic acids for a commercial deep sequencing system (Illumina MiSeq (R))
title Comparative clinical sample preparation of DNA and RNA viral nucleic acids for a commercial deep sequencing system (Illumina MiSeq (R))
spellingShingle Comparative clinical sample preparation of DNA and RNA viral nucleic acids for a commercial deep sequencing system (Illumina MiSeq (R))
Ullmann, Leila Sabrina [UNESP]
Double-stranded DNA
Library preparation
Deep sequencing
MiSeq
title_short Comparative clinical sample preparation of DNA and RNA viral nucleic acids for a commercial deep sequencing system (Illumina MiSeq (R))
title_full Comparative clinical sample preparation of DNA and RNA viral nucleic acids for a commercial deep sequencing system (Illumina MiSeq (R))
title_fullStr Comparative clinical sample preparation of DNA and RNA viral nucleic acids for a commercial deep sequencing system (Illumina MiSeq (R))
title_full_unstemmed Comparative clinical sample preparation of DNA and RNA viral nucleic acids for a commercial deep sequencing system (Illumina MiSeq (R))
title_sort Comparative clinical sample preparation of DNA and RNA viral nucleic acids for a commercial deep sequencing system (Illumina MiSeq (R))
author Ullmann, Leila Sabrina [UNESP]
author_facet Ullmann, Leila Sabrina [UNESP]
Tozato, Claudia de Camargo [UNESP]
Malossi, Camila Dantas [UNESP]
Cruz, Tais Fukuta da [UNESP]
Cavalcante, Raissa Vasconcelos [UNESP]
Kurissio, Jacqueline Kazue [UNESP]
Cagnini, Didier Quevedo [UNESP]
Rodrigues, Marianna Vaz [UNESP]
Biondo, Alexander Welker
Araujo, Joao Pessoa [UNESP]
author_role author
author2 Tozato, Claudia de Camargo [UNESP]
Malossi, Camila Dantas [UNESP]
Cruz, Tais Fukuta da [UNESP]
Cavalcante, Raissa Vasconcelos [UNESP]
Kurissio, Jacqueline Kazue [UNESP]
Cagnini, Didier Quevedo [UNESP]
Rodrigues, Marianna Vaz [UNESP]
Biondo, Alexander Welker
Araujo, Joao Pessoa [UNESP]
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade Estadual Paulista (Unesp)
Universidade Federal do Paraná (UFPR)
University of Illinois
dc.contributor.author.fl_str_mv Ullmann, Leila Sabrina [UNESP]
Tozato, Claudia de Camargo [UNESP]
Malossi, Camila Dantas [UNESP]
Cruz, Tais Fukuta da [UNESP]
Cavalcante, Raissa Vasconcelos [UNESP]
Kurissio, Jacqueline Kazue [UNESP]
Cagnini, Didier Quevedo [UNESP]
Rodrigues, Marianna Vaz [UNESP]
Biondo, Alexander Welker
Araujo, Joao Pessoa [UNESP]
dc.subject.por.fl_str_mv Double-stranded DNA
Library preparation
Deep sequencing
MiSeq
topic Double-stranded DNA
Library preparation
Deep sequencing
MiSeq
description Sequence-independent methods for viral discovery have been widely used for whole genome sequencing of viruses. Different protocols for viral enrichment, library preparation and sequencing have increasingly been more available and at lower costs. However, no study to date has focused on optimization of viral sample preparation for commercial deep sequencing. Accordingly, the aim of the present study was to evaluate an In-House enzymatic protocol for double-stranded DNA (dsDNA) synthesis and also compare the use of a commercially available kit protocol (Nextera XT, Illumina Inc, San Diego, CA, USA) and its combination with a library quantitation kit (Kapa, Kapa Biosystems, Wilmington, MA, USA) for deep sequencing (Illumina Miseq). Two RNA viruses (canine distemper virus and dengue virus) and one ssDNA virus (porcine circovirus type 2) were tested with the optimized protocols. The tested method for dsDNA synthesis has shown satisfactory results and may be used in laboratory setting, particularly when enzymes are already available. Library preparation combining commercial kits (Nextera XT and Kapa) has yielded more reads and genome coverage, probably due to a lack of small fragment recovering at the normalization step of Nextera XT. In addition, libraries may be diluted or concentrated to provide increase on genome coverage with Kapa quantitation. (C) 2015 Elsevier B.V. All rights reserved.
publishDate 2015
dc.date.none.fl_str_mv 2015-10-21T13:11:25Z
2015-10-21T13:11:25Z
2015-08-01
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.uri.fl_str_mv http://www.sciencedirect.com/science/article/pii/S0166093415001457
Journal Of Virological Methods, v. 220, p. 60-63, 2015.
0166-0934
http://hdl.handle.net/11449/128604
10.1016/j.jviromet.2015.04.009
WOS:000356112300012
url http://www.sciencedirect.com/science/article/pii/S0166093415001457
http://hdl.handle.net/11449/128604
identifier_str_mv Journal Of Virological Methods, v. 220, p. 60-63, 2015.
0166-0934
10.1016/j.jviromet.2015.04.009
WOS:000356112300012
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Journal Of Virological Methods
1.756
0,858
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 60-63
dc.publisher.none.fl_str_mv Elsevier B.V.
publisher.none.fl_str_mv Elsevier B.V.
dc.source.none.fl_str_mv Web of Science
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
repository.mail.fl_str_mv
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