Rapid and accurate detection of the SARS-CoV-2 omicron variant with a CRISPR-Cas12a reaction in the RT-qPCR Pot

Gene sequencing in back of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the current approach for discriminating infections produced by different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in the clinic. However, sequencing is often a time-consu...

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Autores: Rodrigo, Guilermo, Ruiz González, Raúl, Montagud Martínez, Roser, Dorta Gorrín, Alexis, Pablo Marcos, Daniel, Gozalo Margüello, Mónica, Calvo Montes, Jorge, Navas Méndez, Jesús|||0000-0002-8199-9228
Tipo de recurso: artículo
Fecha de publicación:2024
País:España
Institución:Universidad de Cantabria (UC)
Repositorio:UCrea Repositorio Abierto de la Universidad de Cantabria
Idioma:inglés
OAI Identifier:oai:repositorio.unican.es:10902/32719
Acceso en línea:https://hdl.handle.net/10902/32719
Access Level:acceso abierto
Palabra clave:CRISPR diagnostics
Infectious disease
Virus evolution
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spelling Rapid and accurate detection of the SARS-CoV-2 omicron variant with a CRISPR-Cas12a reaction in the RT-qPCR PotRodrigo, GuilermoRuiz González, RaúlMontagud Martínez, RoserDorta Gorrín, AlexisPablo Marcos, DanielGozalo Margüello, MónicaCalvo Montes, JorgeNavas Méndez, Jesús|||0000-0002-8199-9228CRISPR diagnosticsInfectious diseaseVirus evolutionGene sequencing in back of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the current approach for discriminating infections produced by different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in the clinic. However, sequencing is often a time-consuming step, which hinders the deployment of a very fast response during a pandemic. Here, we propose to run a CRISPR-Cas12a reaction after completing the RT-qPCR and in the very same pot to detect with high specificity genetic marks characterizing variants of concern. A crRNA was appropriately designed to detect the S gene of the SARS-CoV-2 Omicron BA.1 variant. A significant response with >20-fold dynamic range was obtained for the Omicron BA.1 S gene, while the Delta S gene did not produce any detectable signal. The sensitivity of the method was analyzed with a series of diluted samples and different Cas12a nucleases. A correlation between the RT-qPCR CT values and the CRISPR-Cas12a reaction signals was observed. Variant discrimination with the CRISPR-Cas12a reaction was possible in some minutes with high accuracy from patient samples. In conclusion, CRISPR-Cas systems seem ready to be exploited in the clinic to boost personalized diagnoses and accelerate epidemiological surveillance in a cost-effective way.Work supported by Generalitat Valenciana (GVA-COVID19/2021/036), Ministerio de Ciencia e Innovación (PDC2022−133941-I00; cofunded by NextGenerationEU), CRUE and Banco Santander (Fondo Supera Covid-19), CSIC PTI Salud Global (NextGenerationEU Fund, regulation 2020/2094), and IDIVAL (INNVAL21/13).American Chemical SocietyUniversidad de Cantabria20242024-04-11journal articlehttp://purl.org/coar/resource_type/c_6501NAhttp://purl.org/coar/version/c_be7fb7dd8ff6fe43info:eu-repo/semantics/articlehttps://hdl.handle.net/10902/32719ACS Omega 2024, 9, 18046-18050reponame:UCrea Repositorio Abierto de la Universidad de Cantabriainstname:Universidad de Cantabria (UC)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2Attribution-NonCommercial-NoDerivatives 4.0 Internationalhttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessoai:repositorio.unican.es:10902/327192026-06-02T12:39:31Z
dc.title.none.fl_str_mv Rapid and accurate detection of the SARS-CoV-2 omicron variant with a CRISPR-Cas12a reaction in the RT-qPCR Pot
title Rapid and accurate detection of the SARS-CoV-2 omicron variant with a CRISPR-Cas12a reaction in the RT-qPCR Pot
spellingShingle Rapid and accurate detection of the SARS-CoV-2 omicron variant with a CRISPR-Cas12a reaction in the RT-qPCR Pot
Rodrigo, Guilermo
CRISPR diagnostics
Infectious disease
Virus evolution
title_short Rapid and accurate detection of the SARS-CoV-2 omicron variant with a CRISPR-Cas12a reaction in the RT-qPCR Pot
title_full Rapid and accurate detection of the SARS-CoV-2 omicron variant with a CRISPR-Cas12a reaction in the RT-qPCR Pot
title_fullStr Rapid and accurate detection of the SARS-CoV-2 omicron variant with a CRISPR-Cas12a reaction in the RT-qPCR Pot
title_full_unstemmed Rapid and accurate detection of the SARS-CoV-2 omicron variant with a CRISPR-Cas12a reaction in the RT-qPCR Pot
title_sort Rapid and accurate detection of the SARS-CoV-2 omicron variant with a CRISPR-Cas12a reaction in the RT-qPCR Pot
dc.creator.none.fl_str_mv Rodrigo, Guilermo
Ruiz González, Raúl
Montagud Martínez, Roser
Dorta Gorrín, Alexis
Pablo Marcos, Daniel
Gozalo Margüello, Mónica
Calvo Montes, Jorge
Navas Méndez, Jesús|||0000-0002-8199-9228
author Rodrigo, Guilermo
author_facet Rodrigo, Guilermo
Ruiz González, Raúl
Montagud Martínez, Roser
Dorta Gorrín, Alexis
Pablo Marcos, Daniel
Gozalo Margüello, Mónica
Calvo Montes, Jorge
Navas Méndez, Jesús|||0000-0002-8199-9228
author_role author
author2 Ruiz González, Raúl
Montagud Martínez, Roser
Dorta Gorrín, Alexis
Pablo Marcos, Daniel
Gozalo Margüello, Mónica
Calvo Montes, Jorge
Navas Méndez, Jesús|||0000-0002-8199-9228
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidad de Cantabria
dc.subject.none.fl_str_mv CRISPR diagnostics
Infectious disease
Virus evolution
topic CRISPR diagnostics
Infectious disease
Virus evolution
description Gene sequencing in back of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the current approach for discriminating infections produced by different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in the clinic. However, sequencing is often a time-consuming step, which hinders the deployment of a very fast response during a pandemic. Here, we propose to run a CRISPR-Cas12a reaction after completing the RT-qPCR and in the very same pot to detect with high specificity genetic marks characterizing variants of concern. A crRNA was appropriately designed to detect the S gene of the SARS-CoV-2 Omicron BA.1 variant. A significant response with >20-fold dynamic range was obtained for the Omicron BA.1 S gene, while the Delta S gene did not produce any detectable signal. The sensitivity of the method was analyzed with a series of diluted samples and different Cas12a nucleases. A correlation between the RT-qPCR CT values and the CRISPR-Cas12a reaction signals was observed. Variant discrimination with the CRISPR-Cas12a reaction was possible in some minutes with high accuracy from patient samples. In conclusion, CRISPR-Cas systems seem ready to be exploited in the clinic to boost personalized diagnoses and accelerate epidemiological surveillance in a cost-effective way.
publishDate 2024
dc.date.none.fl_str_mv 2024
2024-04-11
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
NA
http://purl.org/coar/version/c_be7fb7dd8ff6fe43
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/10902/32719
url https://hdl.handle.net/10902/32719
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivatives 4.0 International
http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivatives 4.0 International
http://creativecommons.org/licenses/by-nc-nd/4.0/
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv American Chemical Society
publisher.none.fl_str_mv American Chemical Society
dc.source.none.fl_str_mv ACS Omega 2024, 9, 18046-18050
reponame:UCrea Repositorio Abierto de la Universidad de Cantabria
instname:Universidad de Cantabria (UC)
instname_str Universidad de Cantabria (UC)
reponame_str UCrea Repositorio Abierto de la Universidad de Cantabria
collection UCrea Repositorio Abierto de la Universidad de Cantabria
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.301603

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