Evaluation of alternative RNA extraction methods for detection of SARS-CoV-2 in nasopharyngeal samples using the recommended CDC primer-probe set
Background: The efficiency of isolation and purification of the viral genome is a critical step to the accuracy and reliability of RT-qPCR to detect SARS-CoV-2. However, COVID-19 testing laboratories were overwhelmed by a surge in diagnostic demand that affected supply chains especially in low and m...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-09-01
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| Series: | Journal of Clinical Virology Plus |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667038021000247 |
| _version_ | 1818678186148364288 |
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| author | Vinícius Pietta Perez Wallace Felipe Blohem Pessoa Bruno Henrique Andrade Galvão Eduardo Sergio Soares Sousa Naiara Naiana Dejani Eloiza Helena Campana Marilia Gabriela dos Santos Cavalcanti Vlademir Vicente Cantarelli |
| author_facet | Vinícius Pietta Perez Wallace Felipe Blohem Pessoa Bruno Henrique Andrade Galvão Eduardo Sergio Soares Sousa Naiara Naiana Dejani Eloiza Helena Campana Marilia Gabriela dos Santos Cavalcanti Vlademir Vicente Cantarelli |
| author_sort | Vinícius Pietta Perez |
| collection | DOAJ |
| description | Background: The efficiency of isolation and purification of the viral genome is a critical step to the accuracy and reliability of RT-qPCR to detect SARS-CoV-2. However, COVID-19 testing laboratories were overwhelmed by a surge in diagnostic demand that affected supply chains especially in low and middle-income facilities. Objectives: Thus, this study compares the performance of alternative methods to extraction and purification of viral RNA in samples of patients diagnosed with COVID-19. Study design: Nasopharyngeal swabs were submitted to three in-house protocols and three commercial methods; viral genome was detected using the primer-probe (N1 and N2) described by CDC and viral load of samples were determined. Results: The in-house protocols resulted in detection of virus in 82.4 to 86.3% of samples and commercial methods in 94.1 to 98%. The disagreement results were observed in samples with low viral load or below the estimated limit of detection of RT-qPCR. Conclusion: The simplified methods proposed might be less reliable for patients with low viral load and alternative commercial methods showed comparable performance. |
| first_indexed | 2024-12-17T09:11:15Z |
| format | Article |
| id | doaj.art-e92d7209f16841b78dbfb063f80ab597 |
| institution | Directory Open Access Journal |
| issn | 2667-0380 |
| language | English |
| last_indexed | 2024-12-17T09:11:15Z |
| publishDate | 2021-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Clinical Virology Plus |
| spelling | doaj.art-e92d7209f16841b78dbfb063f80ab5972022-12-21T21:55:13ZengElsevierJournal of Clinical Virology Plus2667-03802021-09-0113100032Evaluation of alternative RNA extraction methods for detection of SARS-CoV-2 in nasopharyngeal samples using the recommended CDC primer-probe setVinícius Pietta Perez0Wallace Felipe Blohem Pessoa1Bruno Henrique Andrade Galvão2Eduardo Sergio Soares Sousa3Naiara Naiana Dejani4Eloiza Helena Campana5Marilia Gabriela dos Santos Cavalcanti6Vlademir Vicente Cantarelli7Departamento de Fisiologia e Patologia, Centro de Ciências da Saúde, Universidade Federal da Paraíba, Campus I - Cidade Universitária s/n, João Pessoa, PB 58051-900, Brazil; Corresponding author.Departamento de Fisiologia e Patologia, Centro de Ciências da Saúde, Universidade Federal da Paraíba, Campus I - Cidade Universitária s/n, João Pessoa, PB 58051-900, BrazilDepartamento de Fisiologia e Patologia, Centro de Ciências da Saúde, Universidade Federal da Paraíba, Campus I - Cidade Universitária s/n, João Pessoa, PB 58051-900, BrazilLaBiMol, Centro de Ciências Médicas, Universidade Federal da Paraíba, João Pessoa, BrazilDepartamento de Fisiologia e Patologia, Centro de Ciências da Saúde, Universidade Federal da Paraíba, Campus I - Cidade Universitária s/n, João Pessoa, PB 58051-900, Brazil; LaBiMol, Centro de Ciências Médicas, Universidade Federal da Paraíba, João Pessoa, BrazilLaBiMol, Centro de Ciências Médicas, Universidade Federal da Paraíba, João Pessoa, Brazil; Departamento de Ciências Farmacêuticas, Centro de Ciências da Saúde, Universidade Federal da Paraíba, João Pessoa, BrazilDepartamento de Fisiologia e Patologia, Centro de Ciências da Saúde, Universidade Federal da Paraíba, Campus I - Cidade Universitária s/n, João Pessoa, PB 58051-900, BrazilUniversidade Feevale, Rio Grande de Sul, Brazil; Universidade Federal de Ciências de Saúde de Porto Alegre (UFCSPA), Porto Alegre, BrazilBackground: The efficiency of isolation and purification of the viral genome is a critical step to the accuracy and reliability of RT-qPCR to detect SARS-CoV-2. However, COVID-19 testing laboratories were overwhelmed by a surge in diagnostic demand that affected supply chains especially in low and middle-income facilities. Objectives: Thus, this study compares the performance of alternative methods to extraction and purification of viral RNA in samples of patients diagnosed with COVID-19. Study design: Nasopharyngeal swabs were submitted to three in-house protocols and three commercial methods; viral genome was detected using the primer-probe (N1 and N2) described by CDC and viral load of samples were determined. Results: The in-house protocols resulted in detection of virus in 82.4 to 86.3% of samples and commercial methods in 94.1 to 98%. The disagreement results were observed in samples with low viral load or below the estimated limit of detection of RT-qPCR. Conclusion: The simplified methods proposed might be less reliable for patients with low viral load and alternative commercial methods showed comparable performance.http://www.sciencedirect.com/science/article/pii/S2667038021000247RNA extractionDirect RT-qPCRViral diagnosticCOVID-19 |
| spellingShingle | Vinícius Pietta Perez Wallace Felipe Blohem Pessoa Bruno Henrique Andrade Galvão Eduardo Sergio Soares Sousa Naiara Naiana Dejani Eloiza Helena Campana Marilia Gabriela dos Santos Cavalcanti Vlademir Vicente Cantarelli Evaluation of alternative RNA extraction methods for detection of SARS-CoV-2 in nasopharyngeal samples using the recommended CDC primer-probe set Journal of Clinical Virology Plus RNA extraction Direct RT-qPCR Viral diagnostic COVID-19 |
| title | Evaluation of alternative RNA extraction methods for detection of SARS-CoV-2 in nasopharyngeal samples using the recommended CDC primer-probe set |
| title_full | Evaluation of alternative RNA extraction methods for detection of SARS-CoV-2 in nasopharyngeal samples using the recommended CDC primer-probe set |
| title_fullStr | Evaluation of alternative RNA extraction methods for detection of SARS-CoV-2 in nasopharyngeal samples using the recommended CDC primer-probe set |
| title_full_unstemmed | Evaluation of alternative RNA extraction methods for detection of SARS-CoV-2 in nasopharyngeal samples using the recommended CDC primer-probe set |
| title_short | Evaluation of alternative RNA extraction methods for detection of SARS-CoV-2 in nasopharyngeal samples using the recommended CDC primer-probe set |
| title_sort | evaluation of alternative rna extraction methods for detection of sars cov 2 in nasopharyngeal samples using the recommended cdc primer probe set |
| topic | RNA extraction Direct RT-qPCR Viral diagnostic COVID-19 |
| url | http://www.sciencedirect.com/science/article/pii/S2667038021000247 |
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