Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

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 Contreras
,
Camilo Andres Velandia-Piedrahita
ORCID logo ,
Adriana Steevens
,
Luisa Caldas
,
Juan Pablo Ribón
,
Martha Sanchez
,
Carlos Martín Restrepo
,
Rodrigo Cabrera
*
Version 1 : Received: 27 July 2022 / Approved: 29 July 2022 / Online: 29 July 2022 (03:10:47 CEST)

A peer-reviewed article of this Preprint also exists.

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. 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 Protoc. 2022, 5, 73. 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. 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 Protoc. 2022, 5, 73.

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 most widely available equipment and reagents found in different regions, is 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 lowest cost nucleic acid extraction and amplification platforms, this modified test shows a 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.

Keywords

COVID-19; molecular diagnostic; SARS-CoV-2; Real-time PCR

Subject

Biology and Life Sciences, Biochemistry and Molecular Biology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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