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Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants and Lineages of Concern Direct from Nasopharyngeal Swab Samples without RNA Isolation

Since, during the Coronavirus disease 19 (COVID-19) pandemic, a large part of the human population has become infected, a rapid and simple diagnostic method has been necessary to detect its causative agent, the Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2), and control its spr...

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Autores principales: Werbajh, Santiago, Larocca, Luciana, Carrillo, Carolina, Stolowicz, Fabiana, Ogas, Lorena, Pallotto, Sergio, Cassará, Solange, Mammana, Liliana, Zapiola, Inés, Bouzas, María Belén, Vojnov, Adrian A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10537693/
https://www.ncbi.nlm.nih.gov/pubmed/37766315
http://dx.doi.org/10.3390/v15091910
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author Werbajh, Santiago
Larocca, Luciana
Carrillo, Carolina
Stolowicz, Fabiana
Ogas, Lorena
Pallotto, Sergio
Cassará, Solange
Mammana, Liliana
Zapiola, Inés
Bouzas, María Belén
Vojnov, Adrian A.
author_facet Werbajh, Santiago
Larocca, Luciana
Carrillo, Carolina
Stolowicz, Fabiana
Ogas, Lorena
Pallotto, Sergio
Cassará, Solange
Mammana, Liliana
Zapiola, Inés
Bouzas, María Belén
Vojnov, Adrian A.
author_sort Werbajh, Santiago
collection PubMed
description Since, during the Coronavirus disease 19 (COVID-19) pandemic, a large part of the human population has become infected, a rapid and simple diagnostic method has been necessary to detect its causative agent, the Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2), and control its spread. Thus, in the present study, we developed a colorimetric reverse transcription-loop-mediated isothermal amplification (RT-LAMP) kit that allows the detection of SARS-CoV-2 from nasopharyngeal swab samples without the need for RNA extraction. The kit utilizes three sets of LAMP primers targeting two regions of ORF1ab and one region in the E gene. The results are based on the colorimetric change of hydroxynaphthol blue, which allows visual interpretation without needing an expensive instrument. The kit demonstrated sensitivity to detect between 50 and 100 copies of the viral genome per reaction. The kit was authorized by the National Administration of Drugs, Food and Technology (ANMAT) of Argentina after validation using samples previously analyzed by the gold standard RT-qPCR. The results showed a sensitivity of 90.6% and specificity of 100%, consistent with conventional RT-qPCR. In silico analysis confirmed the recognition of SARS-CoV-2 variants of concern (B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.427, and B.1.429), and lineages of the Omicron variant (B.1.1.529) with 100% homology. This rapid, simple, and sensitive RT-LAMP method paves the way for a large screening strategy to be carried out at locations lacking sophisticated instrumental and trained staff, as it particularly happens in regional hospitals and medical centers from rural areas.
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spelling pubmed-105376932023-09-29 Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants and Lineages of Concern Direct from Nasopharyngeal Swab Samples without RNA Isolation Werbajh, Santiago Larocca, Luciana Carrillo, Carolina Stolowicz, Fabiana Ogas, Lorena Pallotto, Sergio Cassará, Solange Mammana, Liliana Zapiola, Inés Bouzas, María Belén Vojnov, Adrian A. Viruses Article Since, during the Coronavirus disease 19 (COVID-19) pandemic, a large part of the human population has become infected, a rapid and simple diagnostic method has been necessary to detect its causative agent, the Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2), and control its spread. Thus, in the present study, we developed a colorimetric reverse transcription-loop-mediated isothermal amplification (RT-LAMP) kit that allows the detection of SARS-CoV-2 from nasopharyngeal swab samples without the need for RNA extraction. The kit utilizes three sets of LAMP primers targeting two regions of ORF1ab and one region in the E gene. The results are based on the colorimetric change of hydroxynaphthol blue, which allows visual interpretation without needing an expensive instrument. The kit demonstrated sensitivity to detect between 50 and 100 copies of the viral genome per reaction. The kit was authorized by the National Administration of Drugs, Food and Technology (ANMAT) of Argentina after validation using samples previously analyzed by the gold standard RT-qPCR. The results showed a sensitivity of 90.6% and specificity of 100%, consistent with conventional RT-qPCR. In silico analysis confirmed the recognition of SARS-CoV-2 variants of concern (B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.427, and B.1.429), and lineages of the Omicron variant (B.1.1.529) with 100% homology. This rapid, simple, and sensitive RT-LAMP method paves the way for a large screening strategy to be carried out at locations lacking sophisticated instrumental and trained staff, as it particularly happens in regional hospitals and medical centers from rural areas. MDPI 2023-09-12 /pmc/articles/PMC10537693/ /pubmed/37766315 http://dx.doi.org/10.3390/v15091910 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Werbajh, Santiago
Larocca, Luciana
Carrillo, Carolina
Stolowicz, Fabiana
Ogas, Lorena
Pallotto, Sergio
Cassará, Solange
Mammana, Liliana
Zapiola, Inés
Bouzas, María Belén
Vojnov, Adrian A.
Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants and Lineages of Concern Direct from Nasopharyngeal Swab Samples without RNA Isolation
title Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants and Lineages of Concern Direct from Nasopharyngeal Swab Samples without RNA Isolation
title_full Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants and Lineages of Concern Direct from Nasopharyngeal Swab Samples without RNA Isolation
title_fullStr Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants and Lineages of Concern Direct from Nasopharyngeal Swab Samples without RNA Isolation
title_full_unstemmed Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants and Lineages of Concern Direct from Nasopharyngeal Swab Samples without RNA Isolation
title_short Colorimetric RT-LAMP Detection of Multiple SARS-CoV-2 Variants and Lineages of Concern Direct from Nasopharyngeal Swab Samples without RNA Isolation
title_sort colorimetric rt-lamp detection of multiple sars-cov-2 variants and lineages of concern direct from nasopharyngeal swab samples without rna isolation
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10537693/
https://www.ncbi.nlm.nih.gov/pubmed/37766315
http://dx.doi.org/10.3390/v15091910
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