Platinum chloride-based viability RT-qPCR for SARS-CoV-2 detection in complex samples

Isolation, contact tracing and restrictions on social movement are being globally implemented to prevent and control onward spread of SARS-CoV-2, even though the infection risk modelled on RNA detection by RT-qPCR remains biased as viral shedding and infectivity are not discerned. Thus, we aimed to...

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Autores: Cuevas Ferrando, Enric, Randazzo, Walter, Pérez-Cataluña, Alba, Falcó, Irene, Navarro, David, Martin-Latin, Sandra, Díaz-Reolid, Azahara, Girón-Guzmán, Inés, Allende, Ana, Sánchez Moragas, Gloria
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2021
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:dnet:digitalcsic_::7747df670cae170e7e67230f40d024a4
Acceso en línea:http://hdl.handle.net/10261/250739
Access Level:acceso abierto
Palabra clave:Biological techniques
Environmental microbiology
Environmental sciences
Microbiology
Molecular biology
Virology
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spelling Platinum chloride-based viability RT-qPCR for SARS-CoV-2 detection in complex samplesCuevas Ferrando, EnricRandazzo, WalterPérez-Cataluña, AlbaFalcó, IreneNavarro, DavidMartin-Latin, SandraDíaz-Reolid, AzaharaGirón-Guzmán, InésAllende, AnaSánchez Moragas, GloriaBiological techniquesEnvironmental microbiologyEnvironmental sciencesMicrobiologyMolecular biologyVirologyIsolation, contact tracing and restrictions on social movement are being globally implemented to prevent and control onward spread of SARS-CoV-2, even though the infection risk modelled on RNA detection by RT-qPCR remains biased as viral shedding and infectivity are not discerned. Thus, we aimed to develop a rapid viability RT-qPCR procedure to infer SARS-CoV-2 infectivity in clinical specimens and environmental samples. We screened monoazide dyes and platinum compounds as viability molecular markers on five SARS-CoV-2 RNA targets. A platinum chloride-based viability RT-qPCR was then optimized using genomic RNA, and inactivated SARS-CoV-2 particles inoculated in buffer, stool, and urine. Our results were finally validated in nasopharyngeal swabs from persons who tested positive for COVID-19 and in wastewater samples positive for SARS-CoV-2 RNA. We established a rapid viability RT-qPCR that selectively detects potentially infectious SARS-CoV-2 particles in complex matrices. In particular, the confirmed positivity of nasopharyngeal swabs following the viability procedure suggests their potential infectivity, while the complete prevention of amplification in wastewater indicated either non-infectious particles or free RNA. The viability RT-qPCR approach provides a more accurate ascertainment of the infectious viruses detection and it may complement analyses to foster risk-based investigations for the prevention and control of new or re-occurring outbreaks with a broad application spectrum.The study was supported by CSIC (202070E101), Generalitat Valenciana (Covid_19-SCI), MICINN co-founded by AEI/FEDER, UE (AGL2017-82909), and MICINN/AEI (PID2019-105509RJ-I00). EC-F is recipient of a predoctoral contract from the MICINN, Call 2018. We thank Agustin Garrido Fernández and Andrea Lopez de Mota at IATA-CSIC for providing support in sample processing. We acknowledge Global Omnium S.L., NILSA, Aguas de Malaga, ESAMUR and FACSA for coordinating and managing wastewater sampling.Peer reviewedNature Publishing GroupConsejo Superior de Investigaciones Científicas (España)Generalitat ValencianaMinisterio de Ciencia, Innovación y Universidades (España)Agencia Estatal de Investigación (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202120212021info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/250739reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/AGL2017-82909AGL2017-82909/AEI/10.13039/501100011033info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-105509RJ-I00PID2019-105509RJ-I00/AEI/10.13039/501100011033https://doi.org/10.1038/s41598-021-97700-xSíinfo:eu-repo/semantics/openAccessoai:dnet:digitalcsic_::7747df670cae170e7e67230f40d024a42026-05-22T06:33:51Z
dc.title.none.fl_str_mv Platinum chloride-based viability RT-qPCR for SARS-CoV-2 detection in complex samples
title Platinum chloride-based viability RT-qPCR for SARS-CoV-2 detection in complex samples
spellingShingle Platinum chloride-based viability RT-qPCR for SARS-CoV-2 detection in complex samples
Cuevas Ferrando, Enric
Biological techniques
Environmental microbiology
Environmental sciences
Microbiology
Molecular biology
Virology
title_short Platinum chloride-based viability RT-qPCR for SARS-CoV-2 detection in complex samples
title_full Platinum chloride-based viability RT-qPCR for SARS-CoV-2 detection in complex samples
title_fullStr Platinum chloride-based viability RT-qPCR for SARS-CoV-2 detection in complex samples
title_full_unstemmed Platinum chloride-based viability RT-qPCR for SARS-CoV-2 detection in complex samples
title_sort Platinum chloride-based viability RT-qPCR for SARS-CoV-2 detection in complex samples
dc.creator.none.fl_str_mv Cuevas Ferrando, Enric
Randazzo, Walter
Pérez-Cataluña, Alba
Falcó, Irene
Navarro, David
Martin-Latin, Sandra
Díaz-Reolid, Azahara
Girón-Guzmán, Inés
Allende, Ana
Sánchez Moragas, Gloria
author Cuevas Ferrando, Enric
author_facet Cuevas Ferrando, Enric
Randazzo, Walter
Pérez-Cataluña, Alba
Falcó, Irene
Navarro, David
Martin-Latin, Sandra
Díaz-Reolid, Azahara
Girón-Guzmán, Inés
Allende, Ana
Sánchez Moragas, Gloria
author_role author
author2 Randazzo, Walter
Pérez-Cataluña, Alba
Falcó, Irene
Navarro, David
Martin-Latin, Sandra
Díaz-Reolid, Azahara
Girón-Guzmán, Inés
Allende, Ana
Sánchez Moragas, Gloria
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Consejo Superior de Investigaciones Científicas (España)
Generalitat Valenciana
Ministerio de Ciencia, Innovación y Universidades (España)
Agencia Estatal de Investigación (España)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Biological techniques
Environmental microbiology
Environmental sciences
Microbiology
Molecular biology
Virology
topic Biological techniques
Environmental microbiology
Environmental sciences
Microbiology
Molecular biology
Virology
description Isolation, contact tracing and restrictions on social movement are being globally implemented to prevent and control onward spread of SARS-CoV-2, even though the infection risk modelled on RNA detection by RT-qPCR remains biased as viral shedding and infectivity are not discerned. Thus, we aimed to develop a rapid viability RT-qPCR procedure to infer SARS-CoV-2 infectivity in clinical specimens and environmental samples. We screened monoazide dyes and platinum compounds as viability molecular markers on five SARS-CoV-2 RNA targets. A platinum chloride-based viability RT-qPCR was then optimized using genomic RNA, and inactivated SARS-CoV-2 particles inoculated in buffer, stool, and urine. Our results were finally validated in nasopharyngeal swabs from persons who tested positive for COVID-19 and in wastewater samples positive for SARS-CoV-2 RNA. We established a rapid viability RT-qPCR that selectively detects potentially infectious SARS-CoV-2 particles in complex matrices. In particular, the confirmed positivity of nasopharyngeal swabs following the viability procedure suggests their potential infectivity, while the complete prevention of amplification in wastewater indicated either non-infectious particles or free RNA. The viability RT-qPCR approach provides a more accurate ascertainment of the infectious viruses detection and it may complement analyses to foster risk-based investigations for the prevention and control of new or re-occurring outbreaks with a broad application spectrum.
publishDate 2021
dc.date.none.fl_str_mv 2021
2021
2021
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/250739
url http://hdl.handle.net/10261/250739
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
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#PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/AGL2017-82909
AGL2017-82909/AEI/10.13039/501100011033
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-105509RJ-I00
PID2019-105509RJ-I00/AEI/10.13039/501100011033
https://doi.org/10.1038/s41598-021-97700-x
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Nature Publishing Group
publisher.none.fl_str_mv Nature Publishing Group
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
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