Whole genome sequencing of respiratory syncytial (RSV) virus from clinical samples with low viral load

Autores
Goya, Stephanie; Rojo, Gabriel Lihue; Nabaes Jodar, Mercedes Soledad; Valinotto, Laura Elena; Mistchenko, Alicia Susana; Viegas, Mariana
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Here is a description of a protocol for whole genome sequencing of RSV from clinical samples (nasopharyngeal aspirates -NPA-). The protocol was tested with samples with viral loads as low as 10+03 viral copies/ml NPA. The RNA is amplified by RT-PCR in five overlapped fragments of around 2300-4500 nt in length by using specific primers which anneal in conserved regions of the genome. Briefly the protocol includes: viral RNA extraction from NPA done with silica membrane columns and fragment amplification performed in five independent reaction tubes with OneStep RT-PCR Kit (Qiagen). Each fragment size check performed in an agarose gel electrophoresis, clean-up step done with silica membrane columns and the quantification step performed by Qubit. Finally, amplicons pooled equimolarly and library prep done with Nextera XT Kit.
Fil: Goya, Stephanie. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Rojo, Gabriel Lihue. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Nabaes Jodar, Mercedes Soledad. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Valinotto, Laura Elena. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Mistchenko, Alicia Susana. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina
Fil: Viegas, Mariana. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Materia
WHOLE GENOME SEQUENCING
METAGENOMICS
NGS
HUMAN RESPIRATORY SYNCYTIAL VIRUS
SISPA
HUMAN METAPNEUMOVIRUS
HUMAN PARAINFLUENZA VIRUS
HUMAN RHINOVIRUS
VIRAL GENOME SEQUENCING
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/176709
Acceder
id CONICETDig_3e2fbb5007815dafa877109b22110203
oai_identifier_str oai:ri.conicet.gov.ar:11336/176709
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Whole genome sequencing of respiratory syncytial (RSV) virus from clinical samples with low viral loadGoya, StephanieRojo, Gabriel LihueNabaes Jodar, Mercedes SoledadValinotto, Laura ElenaMistchenko, Alicia SusanaViegas, MarianaWHOLE GENOME SEQUENCINGMETAGENOMICSNGSHUMAN RESPIRATORY SYNCYTIAL VIRUSSISPAHUMAN METAPNEUMOVIRUSHUMAN PARAINFLUENZA VIRUSHUMAN RHINOVIRUSVIRAL GENOME SEQUENCINGhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1https://purl.org/becyt/ford/3.4https://purl.org/becyt/ford/3Here is a description of a protocol for whole genome sequencing of RSV from clinical samples (nasopharyngeal aspirates -NPA-). The protocol was tested with samples with viral loads as low as 10+03 viral copies/ml NPA. The RNA is amplified by RT-PCR in five overlapped fragments of around 2300-4500 nt in length by using specific primers which anneal in conserved regions of the genome. Briefly the protocol includes: viral RNA extraction from NPA done with silica membrane columns and fragment amplification performed in five independent reaction tubes with OneStep RT-PCR Kit (Qiagen). Each fragment size check performed in an agarose gel electrophoresis, clean-up step done with silica membrane columns and the quantification step performed by Qubit. Finally, amplicons pooled equimolarly and library prep done with Nextera XT Kit.Fil: Goya, Stephanie. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Rojo, Gabriel Lihue. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Nabaes Jodar, Mercedes Soledad. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Valinotto, Laura Elena. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Mistchenko, Alicia Susana. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; ArgentinaFil: Viegas, Mariana. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaLife Sciences Protocol Repository2018-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/176709Goya, Stephanie; Rojo, Gabriel Lihue; Nabaes Jodar, Mercedes Soledad; Valinotto, Laura Elena; Mistchenko, Alicia Susana; et al.; Whole genome sequencing of respiratory syncytial (RSV) virus from clinical samples with low viral load; Life Sciences Protocol Repository; protocols.io; 2018; 6-2018; 1-22473-1838CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.protocols.io/view/whole-genome-sequencing-of-respiratory-syncytial-r-qsedwbe?abstractinfo:eu-repo/semantics/altIdentifier/doi/10.17504/protocols.io.qsedwbeinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T14:48:17Zoai:ri.conicet.gov.ar:11336/176709instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-15 14:48:17.312CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Whole genome sequencing of respiratory syncytial (RSV) virus from clinical samples with low viral load
title Whole genome sequencing of respiratory syncytial (RSV) virus from clinical samples with low viral load
spellingShingle Whole genome sequencing of respiratory syncytial (RSV) virus from clinical samples with low viral load
Goya, Stephanie
WHOLE GENOME SEQUENCING
METAGENOMICS
NGS
HUMAN RESPIRATORY SYNCYTIAL VIRUS
SISPA
HUMAN METAPNEUMOVIRUS
HUMAN PARAINFLUENZA VIRUS
HUMAN RHINOVIRUS
VIRAL GENOME SEQUENCING
title_short Whole genome sequencing of respiratory syncytial (RSV) virus from clinical samples with low viral load
title_full Whole genome sequencing of respiratory syncytial (RSV) virus from clinical samples with low viral load
title_fullStr Whole genome sequencing of respiratory syncytial (RSV) virus from clinical samples with low viral load
title_full_unstemmed Whole genome sequencing of respiratory syncytial (RSV) virus from clinical samples with low viral load
title_sort Whole genome sequencing of respiratory syncytial (RSV) virus from clinical samples with low viral load
dc.creator.none.fl_str_mv Goya, Stephanie
Rojo, Gabriel Lihue
Nabaes Jodar, Mercedes Soledad
Valinotto, Laura Elena
Mistchenko, Alicia Susana
Viegas, Mariana
author Goya, Stephanie
author_facet Goya, Stephanie
Rojo, Gabriel Lihue
Nabaes Jodar, Mercedes Soledad
Valinotto, Laura Elena
Mistchenko, Alicia Susana
Viegas, Mariana
author_role author
author2 Rojo, Gabriel Lihue
Nabaes Jodar, Mercedes Soledad
Valinotto, Laura Elena
Mistchenko, Alicia Susana
Viegas, Mariana
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv WHOLE GENOME SEQUENCING
METAGENOMICS
NGS
HUMAN RESPIRATORY SYNCYTIAL VIRUS
SISPA
HUMAN METAPNEUMOVIRUS
HUMAN PARAINFLUENZA VIRUS
HUMAN RHINOVIRUS
VIRAL GENOME SEQUENCING
topic WHOLE GENOME SEQUENCING
METAGENOMICS
NGS
HUMAN RESPIRATORY SYNCYTIAL VIRUS
SISPA
HUMAN METAPNEUMOVIRUS
HUMAN PARAINFLUENZA VIRUS
HUMAN RHINOVIRUS
VIRAL GENOME SEQUENCING
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
https://purl.org/becyt/ford/3.4
https://purl.org/becyt/ford/3
dc.description.none.fl_txt_mv Here is a description of a protocol for whole genome sequencing of RSV from clinical samples (nasopharyngeal aspirates -NPA-). The protocol was tested with samples with viral loads as low as 10+03 viral copies/ml NPA. The RNA is amplified by RT-PCR in five overlapped fragments of around 2300-4500 nt in length by using specific primers which anneal in conserved regions of the genome. Briefly the protocol includes: viral RNA extraction from NPA done with silica membrane columns and fragment amplification performed in five independent reaction tubes with OneStep RT-PCR Kit (Qiagen). Each fragment size check performed in an agarose gel electrophoresis, clean-up step done with silica membrane columns and the quantification step performed by Qubit. Finally, amplicons pooled equimolarly and library prep done with Nextera XT Kit.
Fil: Goya, Stephanie. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Rojo, Gabriel Lihue. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Nabaes Jodar, Mercedes Soledad. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Valinotto, Laura Elena. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Mistchenko, Alicia Susana. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina
Fil: Viegas, Mariana. Gobierno de la Ciudad de Buenos Aires. Hospital General de Niños "Ricardo Gutiérrez". Laboratorio de Virología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description Here is a description of a protocol for whole genome sequencing of RSV from clinical samples (nasopharyngeal aspirates -NPA-). The protocol was tested with samples with viral loads as low as 10+03 viral copies/ml NPA. The RNA is amplified by RT-PCR in five overlapped fragments of around 2300-4500 nt in length by using specific primers which anneal in conserved regions of the genome. Briefly the protocol includes: viral RNA extraction from NPA done with silica membrane columns and fragment amplification performed in five independent reaction tubes with OneStep RT-PCR Kit (Qiagen). Each fragment size check performed in an agarose gel electrophoresis, clean-up step done with silica membrane columns and the quantification step performed by Qubit. Finally, amplicons pooled equimolarly and library prep done with Nextera XT Kit.
publishDate 2018
dc.date.none.fl_str_mv 2018-06
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/176709
Goya, Stephanie; Rojo, Gabriel Lihue; Nabaes Jodar, Mercedes Soledad; Valinotto, Laura Elena; Mistchenko, Alicia Susana; et al.; Whole genome sequencing of respiratory syncytial (RSV) virus from clinical samples with low viral load; Life Sciences Protocol Repository; protocols.io; 2018; 6-2018; 1-2
2473-1838
CONICET Digital
CONICET
url http://hdl.handle.net/11336/176709
identifier_str_mv Goya, Stephanie; Rojo, Gabriel Lihue; Nabaes Jodar, Mercedes Soledad; Valinotto, Laura Elena; Mistchenko, Alicia Susana; et al.; Whole genome sequencing of respiratory syncytial (RSV) virus from clinical samples with low viral load; Life Sciences Protocol Repository; protocols.io; 2018; 6-2018; 1-2
2473-1838
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.protocols.io/view/whole-genome-sequencing-of-respiratory-syncytial-r-qsedwbe?abstract
info:eu-repo/semantics/altIdentifier/doi/10.17504/protocols.io.qsedwbe
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Life Sciences Protocol Repository
publisher.none.fl_str_mv Life Sciences Protocol Repository
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1846083002279395328
score 13.22299

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