Performance Comparison of a Duplex Implementation of the CDC EUA 2019-nCoV Assay with the Seegene Allplex-SARS-CoV-2 Assay for the Detection of SARS-CoV-2 in Nasopharyngeal Swab Samples

Karen Marcela Jiménez; Dora Janeth Fonseca-Mendoza; Adrien Morel; Oscar Ortega-Recalde; Nora Constanza Contreras Bravo; Camilo Andres Velandia-Piedrahita; Adriana Steevens; Luisa Daniela Caldas; Juan Pablo Ribón; Martha Sánchez; Carlos Martin Restrepo; Rodrigo Cabrera

doi:10.3390/mps5050073

Performance Comparison of a Duplex Implementation of the CDC EUA 2019-nCoV Assay with the Seegene Allplex-SARS-CoV-2 Assay for the Detection of SARS-CoV-2 in Nasopharyngeal Swab Samples

Título traducido de la contribución: Comparación del rendimiento de una implementación dúplex del ensayo CDC EUA 2019-nCoV con el ensayo Seegene Allplex-SARS-CoV-2 para la detección del SARS-CoV-2 en muestras de hisopos nasofaríngeos

Karen Marcela Jiménez, Dora Janeth Fonseca-Mendoza, Adrien Morel, Oscar Ortega-Recalde, Nora Constanza Contreras Bravo, Camilo Andres Velandia-Piedrahita, Adriana Steevens, Luisa Daniela Caldas, Juan Pablo Ribón, Martha Sánchez, Carlos Martin Restrepo, Rodrigo Cabrera

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Resumen

Las pruebas RT-PCR se han convertido en el estándar de oro para detectar el virus SARS-CoV-2 en el contexto de la pandemia de COVID-19. Debido al número extremo de casos en oleadas periódicas de infección, existe una grave tensión financiera y logística en los laboratorios de diagnóstico. Por esta razón, son esenciales implementaciones alternativas y validaciones de protocolos académicos que empleen el menor costo y los equipos y reactivos más ampliamente disponibles que se encuentran en diferentes regiones. En este estudio, informamos una implementación alternativa del ensayo CDC EUA 2019-nCoV que utiliza una reacción de PCR dúplex previamente caracterizada para las regiones objetivo N1 y RNAsa P y una reacción uniplex adicional para la región objetivo N2. Aprovechando el sistema de preparación de muestras Abbott m2000 y el kit NEB Luna Universal Probe One-Step RT-qPCR, algunas de las plataformas de amplificación y extracción de ácidos nucleicos más económicas y disponibles, esta prueba modificada muestra análisis y análisis de última generación. sensibilidades y especificidades clínicas en comparación con el ensayo Seegene Allplex-SARS-CoV-2. Esta implementación tiene el potencial de ser verificada e implementada por laboratorios de diagnóstico de todo el mundo para garantizar pruebas de RT-PCR de bajo costo que puedan aprovechar equipos y reactivos ampliamente disponibles.

Título traducido de la contribución	Comparación del rendimiento de una implementación dúplex del ensayo CDC EUA 2019-nCoV con el ensayo Seegene Allplex-SARS-CoV-2 para la detección del SARS-CoV-2 en muestras de hisopos nasofaríngeos
Idioma original	Inglés estadounidense
Número de artículo	73
Páginas (desde-hasta)	1-10
Número de páginas	10
Publicación	Methods and Protocols
Volumen	5
N.º	5
DOI	https://doi.org/10.3390/mps5050073
Estado	Publicada - sep. 21 2022

Áreas temáticas de ASJC Scopus

Biotecnología
Biología estructural
Bioquímica, genética y biología molecular (miscelánea)

ODS de las Naciones Unidas

Este resultado contribuye a los siguientes Objetivos de Desarrollo Sostenible

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Jiménez, K. M., Fonseca-Mendoza, D. J., Morel, A., Ortega-Recalde, O., Contreras Bravo, N. C., Velandia-Piedrahita, C. A., Steevens, A., Caldas, L. D., Ribón, J. P., Sánchez, M., Restrepo, C. M., & Cabrera, R. (2022). Performance Comparison of a Duplex Implementation of the CDC EUA 2019-nCoV Assay with the Seegene Allplex-SARS-CoV-2 Assay for the Detection of SARS-CoV-2 in Nasopharyngeal Swab Samples. Methods and Protocols, 5(5), 1-10. Artículo 73. https://doi.org/10.3390/mps5050073

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abstract = "RT-PCR tests have become the gold standard for detecting the SARS-CoV-2 virus in the context of the COVID-19 pandemic. Because of the extreme number of cases in periodic waves of infection, there is a severe financial and logistical strain on diagnostic laboratories. For this reason, alternative implementations and validations of academic protocols that employ the lowest cost and the most widely available equipment and reagents found in different regions are essential. In this study, we report an alternative implementation of the EUA 2019-nCoV CDC assay which uses a previously characterized duplex PCR reaction for the N1 and RNAse P target regions and an additional uniplex reaction for the N2 target region. Taking advantage of the Abbott m2000 Sample Preparation System and NEB Luna Universal Probe One-Step RT-qPCR kit, some of the most widely available and inexpensive nucleic acid extraction and amplification platforms, this modified test shows state-of-the-art analytical and clinical sensitivities and specificities when compared with the Seegene Allplex-SARS-CoV-2 assay. This implementation has the potential to be verified and implemented by diagnostic laboratories around the world to guarantee low-cost RT-PCR tests that can take advantage of widely available equipment and reagents.",

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Jiménez, KM, Fonseca-Mendoza, DJ , Morel, A, Ortega-Recalde, O, Contreras Bravo, NC, Velandia-Piedrahita, CA, Steevens, A, Caldas, LD, Ribón, JP, Sánchez, M, Restrepo, CM & Cabrera, R 2022, 'Performance Comparison of a Duplex Implementation of the CDC EUA 2019-nCoV Assay with the Seegene Allplex-SARS-CoV-2 Assay for the Detection of SARS-CoV-2 in Nasopharyngeal Swab Samples', Methods and Protocols, vol. 5, n.º 5, 73, pp. 1-10. https://doi.org/10.3390/mps5050073

Performance Comparison of a Duplex Implementation of the CDC EUA 2019-nCoV Assay with the Seegene Allplex-SARS-CoV-2 Assay for the Detection of SARS-CoV-2 in Nasopharyngeal Swab Samples. / Jiménez, Karen Marcela; Fonseca-Mendoza, Dora Janeth ; Morel, Adrien et al.
En: Methods and Protocols, Vol. 5, N.º 5, 73, 21.09.2022, p. 1-10.

Producción científica: Contribución a una revista › Artículo de Investigación › revisión exhaustiva

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AU - Fonseca-Mendoza, Dora Janeth

AU - Morel, Adrien

AU - Ortega-Recalde, Oscar

AU - Contreras Bravo, Nora Constanza

AU - Velandia-Piedrahita, Camilo Andres

AU - Steevens, Adriana

AU - Caldas, Luisa Daniela

AU - Ribón, Juan Pablo

AU - Sánchez, Martha

AU - Restrepo, Carlos Martin

AU - Cabrera, Rodrigo

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N2 - RT-PCR tests have become the gold standard for detecting the SARS-CoV-2 virus in the context of the COVID-19 pandemic. Because of the extreme number of cases in periodic waves of infection, there is a severe financial and logistical strain on diagnostic laboratories. For this reason, alternative implementations and validations of academic protocols that employ the lowest cost and the most widely available equipment and reagents found in different regions are essential. In this study, we report an alternative implementation of the EUA 2019-nCoV CDC assay which uses a previously characterized duplex PCR reaction for the N1 and RNAse P target regions and an additional uniplex reaction for the N2 target region. Taking advantage of the Abbott m2000 Sample Preparation System and NEB Luna Universal Probe One-Step RT-qPCR kit, some of the most widely available and inexpensive nucleic acid extraction and amplification platforms, this modified test shows state-of-the-art analytical and clinical sensitivities and specificities when compared with the Seegene Allplex-SARS-CoV-2 assay. This implementation has the potential to be verified and implemented by diagnostic laboratories around the world to guarantee low-cost RT-PCR tests that can take advantage of widely available equipment and reagents.

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Jiménez KM, Fonseca-Mendoza DJ , Morel A, Ortega-Recalde O, Contreras Bravo NC, Velandia-Piedrahita CA et al. Performance Comparison of a Duplex Implementation of the CDC EUA 2019-nCoV Assay with the Seegene Allplex-SARS-CoV-2 Assay for the Detection of SARS-CoV-2 in Nasopharyngeal Swab Samples. Methods and Protocols. 2022 sept. 21;5(5):1-10. 73. doi: 10.3390/mps5050073