Comparison of Four Real-Time Polymerase Chain Reaction Assays for the Detection of SARS-CoV-2 in Respiratory Samples from Tunja, Boyacá, Colombia
Coronavirus disease (COVID-19) is an infectious disease caused by SARS-CoV-2. In Colombia, many commercial methods are now available to perform the RT-qPCR assays, and laboratories must evaluate their diagnostic accuracy to ensure reliable results for patients suspected of being positive for COVID-1...
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| Format: | Article |
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MDPI AG
2022-09-01
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| Series: | Tropical Medicine and Infectious Disease |
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| Online Access: | https://www.mdpi.com/2414-6366/7/9/240 |
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| author | Lorenzo H. Salamanca-Neita Óscar Carvajal Juan Pablo Carvajal Maribel Forero-Castro Nidya Alexandra Segura |
| author_facet | Lorenzo H. Salamanca-Neita Óscar Carvajal Juan Pablo Carvajal Maribel Forero-Castro Nidya Alexandra Segura |
| author_sort | Lorenzo H. Salamanca-Neita |
| collection | DOAJ |
| description | Coronavirus disease (COVID-19) is an infectious disease caused by SARS-CoV-2. In Colombia, many commercial methods are now available to perform the RT-qPCR assays, and laboratories must evaluate their diagnostic accuracy to ensure reliable results for patients suspected of being positive for COVID-19. The purpose of this study was to compare four commercial RT-qPCR assays with respect to their ability to detect the SARS-CoV2 virus from nasopharyngeal swab samples referred to Laboratorio Carvajal IPS, SAS in Tunja, Boyacá, Colombia. We utilized 152 respiratory tract samples (Nasopharyngeal Swabs) from patients suspected of having SARS-CoV-2. The diagnostic accuracy of GeneFinder<sup>TM</sup> COVID-19 Plus RealAmp (In Vitro Diagnostics) (GF-TM), One-Step Real-Time RT-PCR (Vitro Master Diagnostica) (O-S RT-qPCR), and the Berlin modified protocol (BM) were assessed using the gold-standard Berlin protocol (Berlin Charité Probe One-Step RT-qPCR Kit, New England Biolabs) (BR) as a reference. Operational characteristics were estimated in terms of sensitivity, specificity, agreement, and predictive values. Using the gold-standard BR as a reference, the sensitivity/specificity of the diagnostic tests was found to be 100%/92.7% for GF-TM, 92.75%/67.47% for O-S RT-qPCR, and 100%/96.39% for the BM protocol. Using BR as a reference, the sensitivity/specificity for the diagnostic tests were found to be 100%/92.7% for the GF-TM assay, 92.72%/67.47% for the O-S RT-qPCR, and 100%/96.39% for BM. Relative to the BR reference protocol, the GF-TM and BM RT-PCR assays obtained similar results (k = 0.92 and k = 0.96, respectively), whereas the results obtained by O-S-RT-qPCR were only moderately similar. We conclude that the GF-TM and BM protocols offer the best sensitivity and specificity, with similar results in comparison to the gold-standard BR protocol. We recommend evaluating the diagnostic accuracy of the OS-RT-qPCR protocol in future studies with a larger number of samples. |
| first_indexed | 2024-03-09T22:18:59Z |
| format | Article |
| id | doaj.art-3219e8d7de834741a992254423c273c6 |
| institution | Directory Open Access Journal |
| issn | 2414-6366 |
| language | English |
| last_indexed | 2024-03-09T22:18:59Z |
| publishDate | 2022-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Tropical Medicine and Infectious Disease |
| spelling | doaj.art-3219e8d7de834741a992254423c273c62023-11-23T19:18:14ZengMDPI AGTropical Medicine and Infectious Disease2414-63662022-09-017924010.3390/tropicalmed7090240Comparison of Four Real-Time Polymerase Chain Reaction Assays for the Detection of SARS-CoV-2 in Respiratory Samples from Tunja, Boyacá, ColombiaLorenzo H. Salamanca-Neita0Óscar Carvajal1Juan Pablo Carvajal2Maribel Forero-Castro3Nidya Alexandra Segura4Laboratorio Carvajal IPS, SAS, Tunja 150003, ColombiaLaboratorio Carvajal IPS, SAS, Tunja 150003, ColombiaLaboratorio Carvajal IPS, SAS, Tunja 150003, ColombiaFacultad de Ciencias, Grupo de Investigación en Ciencias Biomédicas, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, ColombiaFacultad de Ciencias, Grupo de Investigación en Ciencias Biomédicas, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, ColombiaCoronavirus disease (COVID-19) is an infectious disease caused by SARS-CoV-2. In Colombia, many commercial methods are now available to perform the RT-qPCR assays, and laboratories must evaluate their diagnostic accuracy to ensure reliable results for patients suspected of being positive for COVID-19. The purpose of this study was to compare four commercial RT-qPCR assays with respect to their ability to detect the SARS-CoV2 virus from nasopharyngeal swab samples referred to Laboratorio Carvajal IPS, SAS in Tunja, Boyacá, Colombia. We utilized 152 respiratory tract samples (Nasopharyngeal Swabs) from patients suspected of having SARS-CoV-2. The diagnostic accuracy of GeneFinder<sup>TM</sup> COVID-19 Plus RealAmp (In Vitro Diagnostics) (GF-TM), One-Step Real-Time RT-PCR (Vitro Master Diagnostica) (O-S RT-qPCR), and the Berlin modified protocol (BM) were assessed using the gold-standard Berlin protocol (Berlin Charité Probe One-Step RT-qPCR Kit, New England Biolabs) (BR) as a reference. Operational characteristics were estimated in terms of sensitivity, specificity, agreement, and predictive values. Using the gold-standard BR as a reference, the sensitivity/specificity of the diagnostic tests was found to be 100%/92.7% for GF-TM, 92.75%/67.47% for O-S RT-qPCR, and 100%/96.39% for the BM protocol. Using BR as a reference, the sensitivity/specificity for the diagnostic tests were found to be 100%/92.7% for the GF-TM assay, 92.72%/67.47% for the O-S RT-qPCR, and 100%/96.39% for BM. Relative to the BR reference protocol, the GF-TM and BM RT-PCR assays obtained similar results (k = 0.92 and k = 0.96, respectively), whereas the results obtained by O-S-RT-qPCR were only moderately similar. We conclude that the GF-TM and BM protocols offer the best sensitivity and specificity, with similar results in comparison to the gold-standard BR protocol. We recommend evaluating the diagnostic accuracy of the OS-RT-qPCR protocol in future studies with a larger number of samples.https://www.mdpi.com/2414-6366/7/9/240severe acute respiratory syndrome coronavirus 2 (SARS-CoV2)COVID-19molecular diagnosticsreal-time polymerase chain reaction (RT-qPCR) |
| spellingShingle | Lorenzo H. Salamanca-Neita Óscar Carvajal Juan Pablo Carvajal Maribel Forero-Castro Nidya Alexandra Segura Comparison of Four Real-Time Polymerase Chain Reaction Assays for the Detection of SARS-CoV-2 in Respiratory Samples from Tunja, Boyacá, Colombia Tropical Medicine and Infectious Disease severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) COVID-19 molecular diagnostics real-time polymerase chain reaction (RT-qPCR) |
| title | Comparison of Four Real-Time Polymerase Chain Reaction Assays for the Detection of SARS-CoV-2 in Respiratory Samples from Tunja, Boyacá, Colombia |
| title_full | Comparison of Four Real-Time Polymerase Chain Reaction Assays for the Detection of SARS-CoV-2 in Respiratory Samples from Tunja, Boyacá, Colombia |
| title_fullStr | Comparison of Four Real-Time Polymerase Chain Reaction Assays for the Detection of SARS-CoV-2 in Respiratory Samples from Tunja, Boyacá, Colombia |
| title_full_unstemmed | Comparison of Four Real-Time Polymerase Chain Reaction Assays for the Detection of SARS-CoV-2 in Respiratory Samples from Tunja, Boyacá, Colombia |
| title_short | Comparison of Four Real-Time Polymerase Chain Reaction Assays for the Detection of SARS-CoV-2 in Respiratory Samples from Tunja, Boyacá, Colombia |
| title_sort | comparison of four real time polymerase chain reaction assays for the detection of sars cov 2 in respiratory samples from tunja boyaca colombia |
| topic | severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) COVID-19 molecular diagnostics real-time polymerase chain reaction (RT-qPCR) |
| url | https://www.mdpi.com/2414-6366/7/9/240 |
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