Molecular detection of SARS-CoV-2 in Córdoba, Argentina: evaluation of alternative diagnostic tools
Since its initial detection in Argentina in March 2020, the spread of SARS-CoV-2 has been exponential, producing a large number of clinical cases. The explosion of COVID-19 cases highlighted the critical role that diagnostic tests play in medical and public health decision-making to contain and...
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| Formato: | Artículo revista |
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Universidad Nacional Córdoba. Facultad de Ciencias Médicas. Secretaria de Ciencia y Tecnología
2022
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| Acceso en línea: | https://revistas.unc.edu.ar/index.php/med/article/view/39128 |
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I10-R327-article-39128 |
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ojs |
| institution |
Universidad Nacional de Córdoba |
| institution_str |
I-10 |
| repository_str |
R-327 |
| container_title_str |
Revista de la Facultad de Ciencias Médicas de Córdoba |
| format |
Artículo revista |
| topic |
SARS-CoV-2 infection covid-19 molecular diagnostic techniques viral RNA SARS-CoV-2 covid-19 técnicas de diagnóstico molecular RNA viral |
| spellingShingle |
SARS-CoV-2 infection covid-19 molecular diagnostic techniques viral RNA SARS-CoV-2 covid-19 técnicas de diagnóstico molecular RNA viral Castro, GM Sicilia, PE Sosa, MJ Castellaro, A Barbas, MG Pisano, MB Re, VE Molecular detection of SARS-CoV-2 in Córdoba, Argentina: evaluation of alternative diagnostic tools |
| topic_facet |
SARS-CoV-2 infection covid-19 molecular diagnostic techniques viral RNA SARS-CoV-2 covid-19 técnicas de diagnóstico molecular RNA viral |
| author |
Castro, GM Sicilia, PE Sosa, MJ Castellaro, A Barbas, MG Pisano, MB Re, VE |
| author_facet |
Castro, GM Sicilia, PE Sosa, MJ Castellaro, A Barbas, MG Pisano, MB Re, VE |
| author_sort |
Castro, GM |
| title |
Molecular detection of SARS-CoV-2 in Córdoba, Argentina: evaluation of alternative diagnostic tools |
| title_short |
Molecular detection of SARS-CoV-2 in Córdoba, Argentina: evaluation of alternative diagnostic tools |
| title_full |
Molecular detection of SARS-CoV-2 in Córdoba, Argentina: evaluation of alternative diagnostic tools |
| title_fullStr |
Molecular detection of SARS-CoV-2 in Córdoba, Argentina: evaluation of alternative diagnostic tools |
| title_full_unstemmed |
Molecular detection of SARS-CoV-2 in Córdoba, Argentina: evaluation of alternative diagnostic tools |
| title_sort |
molecular detection of sars-cov-2 in córdoba, argentina: evaluation of alternative diagnostic tools |
| description |
Since its initial detection in Argentina in March 2020, the spread of SARS-CoV-2 has been exponential, producing a large number of clinical cases. The explosion of COVID-19 cases highlighted the critical role that diagnostic tests play in medical and public health decision-making to contain and mitigate the SARS-CoV-2 pandemic. The aim of this study was to evaluate and implement different assays for the molecular detection of SARS-CoV-2.
We evaluated 10 real time RT-PCR assays (Coronavirus “in house” CDC, LightMix® Modular SARS-CoV-2, GENESIG®, TaqMan™ 2019-nCoV Applied Biosystems, GeneFinderTM, VIASURE, Novel Coronavirus Anatolia, BGI, DisCoVery and WGene) analysing and comparing the following qualitative and quantitative parameters: target genes, internal control, single reaction/multiplex, sample volume, reagent yield, required equipment and reaction time. Besides, using internal panels of negative and positive samples with different concentrations of viral RNA, we evaluated 2 nucleic acid extraction methods [MagaBio plus Virus DNA/RNA Purification Kit II (BioFlux), 35-minute vs. 9-minute], a pre-analytical reagent (FlashPrep®) and 2 isothermal amplification tests (Neokit Plus and ELA CHEMSTRIP®).
Three real time RT-PCR assays were selected as optimal according to its characteristics and performance (use of IC, shorter reaction time, detection of at least 2 target genes, lower initial sample volume): DisCoVery > GeneFinderTM > WGene. The 2 RNA extraction methods showed similar good results: MagaBio plus Virus RNA Purification Kit II (BioFlux) 9-min was selected due to its faster performance. FlashPrep® reagent showed excellent results to perform direct RNA detection. Isothermal amplification assays showed acceptable sensibility and specificity values (>80%), except in samples with Ct>30.
The results show some of the best real-time RT-PCR kit options available in our country for SARS-CoV-2 diagnosis. These alternative assays evaluated, proved to be acceptable for its use in adverse contexts, in the decentralization of diagnosis and in different epidemiological scenarios, for the rapid and accurate detection of SARS-CoV-2.
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| publisher |
Universidad Nacional Córdoba. Facultad de Ciencias Médicas. Secretaria de Ciencia y Tecnología |
| publishDate |
2022 |
| url |
https://revistas.unc.edu.ar/index.php/med/article/view/39128 |
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I10-R327-article-391282024-04-15T16:14:45Z Molecular detection of SARS-CoV-2 in Córdoba, Argentina: evaluation of alternative diagnostic tools Detección molecular de SARS-CoV-2 en Córdoba, Argentina: evaluación de herramientas diagnósticas alternativas Castro, GM Sicilia, PE Sosa, MJ Castellaro, A Barbas, MG Pisano, MB Re, VE SARS-CoV-2 infection covid-19 molecular diagnostic techniques viral RNA SARS-CoV-2 covid-19 técnicas de diagnóstico molecular RNA viral Since its initial detection in Argentina in March 2020, the spread of SARS-CoV-2 has been exponential, producing a large number of clinical cases. The explosion of COVID-19 cases highlighted the critical role that diagnostic tests play in medical and public health decision-making to contain and mitigate the SARS-CoV-2 pandemic. The aim of this study was to evaluate and implement different assays for the molecular detection of SARS-CoV-2. We evaluated 10 real time RT-PCR assays (Coronavirus “in house” CDC, LightMix® Modular SARS-CoV-2, GENESIG®, TaqMan™ 2019-nCoV Applied Biosystems, GeneFinderTM, VIASURE, Novel Coronavirus Anatolia, BGI, DisCoVery and WGene) analysing and comparing the following qualitative and quantitative parameters: target genes, internal control, single reaction/multiplex, sample volume, reagent yield, required equipment and reaction time. Besides, using internal panels of negative and positive samples with different concentrations of viral RNA, we evaluated 2 nucleic acid extraction methods [MagaBio plus Virus DNA/RNA Purification Kit II (BioFlux), 35-minute vs. 9-minute], a pre-analytical reagent (FlashPrep®) and 2 isothermal amplification tests (Neokit Plus and ELA CHEMSTRIP®). Three real time RT-PCR assays were selected as optimal according to its characteristics and performance (use of IC, shorter reaction time, detection of at least 2 target genes, lower initial sample volume): DisCoVery > GeneFinderTM > WGene. The 2 RNA extraction methods showed similar good results: MagaBio plus Virus RNA Purification Kit II (BioFlux) 9-min was selected due to its faster performance. FlashPrep® reagent showed excellent results to perform direct RNA detection. Isothermal amplification assays showed acceptable sensibility and specificity values (>80%), except in samples with Ct>30. The results show some of the best real-time RT-PCR kit options available in our country for SARS-CoV-2 diagnosis. These alternative assays evaluated, proved to be acceptable for its use in adverse contexts, in the decentralization of diagnosis and in different epidemiological scenarios, for the rapid and accurate detection of SARS-CoV-2. Desde su detección inicial en Argentina en marzo de 2020, la diseminación del SARS-CoV-2 fue exponencial, produciendo una gran cantidad de casos clínicos. Esta explosión de casos de COVID-19 resaltó el rol fundamental que desempeñan las pruebas de diagnóstico en la toma de decisiones médicas y de salud pública, para contener y mitigar la pandemia de SARS-CoV-2. El objetivo de este trabajo fue evaluar e implementar diferentes ensayos para la detección molecular de SARS-CoV-2. Se evaluaron 10 ensayos de RT-PCR en tiempo real (Coronavirus “in-house” CDC, LightMix® Modular SARS-CoV-2, GENESIG®, TaqMan™ 2019-nCoV Applied Biosystems, GeneFinder™, VIASURE, Novel Coronavirus Anatolia, BGI, DisCoVery y WGene), analizando y comparando parámetros cualitativos y cuantitativos: genes blanco, uso de control interno, tipo de reacción (individual o múltiple), volumen inicial de muestra, rendimiento de los reactivos, equipamiento requerido y tiempo de reacción. Además, usando paneles internos de muestras negativas y positivas con diferentes concentraciones de ARN viral, se evaluaron 2 métodos de extracción de ácidos nucleicos [MagaBio plus Virus DNA/RNA Purification Kit II (BioFlux), 35-minutos vs. 9-minutos], un reactivo pre-analítico (FlashPrep®) y 2 tests de amplificación isotérmica (Neokit Plus y ELA CHEMSTRIP®). Se seleccionaron 3 ensayos de PCR en tiempo real de acuerdo a sus características y rendimiento (uso de CI, menor tiempo de reacción, detección de al menos 2 genes blanco, menor volumen inicial de muestra): DisCoVery > GeneFinder™ > WGene. Los 2 métodos de extracción de RNA arrojaron buenos resultados y fueron similares en su rendimiento; se seleccionó el MagaBio plus Virus RNA Purification Kit II (BioFlux) 9-minutos debido a su rapidez. El reactivo FlashPrep® mostró excelentes resultados para realizar detección directa del RNA de SARS-CoV-2. Los ensayos de amplificación isotérmica arrojaron valores de sensibilidad y especificidad aceptables (>80%), excepto en muestras con Ct>30. Los resultados muestran algunas de las mejores opciones de kits de RT-PCR en tiempo real disponibles en nuestro medio para el diagnóstico de SARS-CoV-2. Los ensayos alternativos evaluados mostraron ser aceptables para su uso en contextos adversos, en la descentralización del diagnóstico y en diversos escenarios epidemiológicos, para la detección rápida y precisa del SARS-CoV-2. Universidad Nacional Córdoba. Facultad de Ciencias Médicas. Secretaria de Ciencia y Tecnología 2022-10-26 info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion texto https://revistas.unc.edu.ar/index.php/med/article/view/39128 Revista de la Facultad de Ciencias Médicas de Córdoba.; Vol. 79 No. Suplemento JIC XXIII (2022): Suplemento JIC XXIII Revista de la Facultad de Ciencias Médicas de Córdoba; Vol. 79 Núm. Suplemento JIC XXIII (2022): Suplemento JIC XXIII Revista da Faculdade de Ciências Médicas de Córdoba; v. 79 n. Suplemento JIC XXIII (2022): Suplemento JIC XXIII 1853-0605 0014-6722 http://creativecommons.org/licenses/by-nc/4.0 |