Accuracy of a raw saliva-based COVID-19 RT-LAMP diagnostic assay
The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic demanded rapid diagnosis to isolate new COVID-19 cases and prevent disease transmission. Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) rapidly became the gold standard for diagnosis. However, due to the high cost...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-07-01
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| Series: | Brazilian Journal of Infectious Diseases |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1413867023000508 |
| _version_ | 1797741007678210048 |
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| author | Kátia Maria dos Santos Cabral Ramon Cid Gismonti Baptista Terezinha Marta Pereira Pinto Castineiras Amilcar Tanuri Fabiana Avila Carneiro Marcius da Silva Almeida Monica Montero-Lomeli |
| author_facet | Kátia Maria dos Santos Cabral Ramon Cid Gismonti Baptista Terezinha Marta Pereira Pinto Castineiras Amilcar Tanuri Fabiana Avila Carneiro Marcius da Silva Almeida Monica Montero-Lomeli |
| author_sort | Kátia Maria dos Santos Cabral |
| collection | DOAJ |
| description | The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic demanded rapid diagnosis to isolate new COVID-19 cases and prevent disease transmission. Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) rapidly became the gold standard for diagnosis. However, due to the high cost and delay of the results, other types of diagnosis were implemented, such as COVID-19 Ag Rapid Tests and Reverse Transcription Technique followed by Loop-Mediated isothermal Amplification (RT-LAMP). In this work, we validated the use of RT-LAMP in saliva samples rather than nasopharyngeal swabs, as the collection is more comfortable. First, we selected 5 primer sets based on the limit of detection for SARS-CoV-2 RNA, then validated their sensitivity and specificity in patient samples. A total of 117 samples were analyzed by fluorometric RT-LAMP and compared with qRT-PCR results. Our results show that the use of a high-sensitive primer ORF1-a, together with a low-sensitive primer set Gene E (time to threshold of 22.9 and 36.4 minutes, respectively, using 200 copies of viral RNA), achieved sensitivity in purified RNA from saliva samples of 95.2% (95% CI 76.1‒99.8) with 90.5% specificity (95% CI 69.6‒98.8) (n = 42).As RNA purification increases the turnaround time, we tested the outcome of RT-LAMP utilizing raw saliva samples without purification. The test achieved a sensitivity of 81.8% (95% CI 59.7‒94.8) and a specificity of 90.9% (95% CI 70.8‒98.8). As a result, the accuracy of 92.9% (95% CI 80.5‒98.5) in purified RNA-saliva samples was lowered to an acceptable level of 86.4% (95% CI 72.6‒94.8) in raw saliva. Although mass vaccination has been implemented, new strains and low vaccination progress helped to spread COVID-19. This study shows that it is feasible to track new COVID-19 cases in a large population with the use of raw saliva as sample in RT-LAMP assay which yields accurate results and offers a less invasive test. |
| first_indexed | 2024-03-12T14:20:40Z |
| format | Article |
| id | doaj.art-a6396ac6380e4085a71ebfc28e862bec |
| institution | Directory Open Access Journal |
| issn | 1413-8670 |
| language | English |
| last_indexed | 2024-03-12T14:20:40Z |
| publishDate | 2023-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Brazilian Journal of Infectious Diseases |
| spelling | doaj.art-a6396ac6380e4085a71ebfc28e862bec2023-08-19T04:31:52ZengElsevierBrazilian Journal of Infectious Diseases1413-86702023-07-01274102790Accuracy of a raw saliva-based COVID-19 RT-LAMP diagnostic assayKátia Maria dos Santos Cabral0Ramon Cid Gismonti Baptista1Terezinha Marta Pereira Pinto Castineiras2Amilcar Tanuri3Fabiana Avila Carneiro4Marcius da Silva Almeida5Monica Montero-Lomeli6Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Bioquímica Médica-Leopoldo de Meis, Rio de Janeiro, RJ, Brazil; Centro Nacional de Biologia Estrutural e Bioimagem, Plataforma Avançada de Biomoléculas, Rio de Janeiro, RJ, BrazilUniversidade Federal do Rio de Janeiro (UFRJ), Instituto de Bioquímica Médica-Leopoldo de Meis, Rio de Janeiro, RJ, BrazilUniversidade Federal do Rio de Janeiro (UFRJ), Faculdade de Medicina, Departamento de Doenças Infecciosas e Parasitárias, Rio de Janeiro, RJ, BrazilUniversidade Federal do Rio de Janeiro (UFRJ), Instituto de Biologia, Departamento de Genética, Rio de Janeiro, RJ, BrazilCentro de Pesquisa de Medicina de Precisão, Instituto de Biofísica Carlos Chagas Filho, Rio de Janeiro, RJ, Brazil; Núcleo de Pesquisa (Numpex-Bio), Campus Duque de Caxias Professor Geraldo Cidade, Duque de Caxias, RJ, BrazilUniversidade Federal do Rio de Janeiro (UFRJ), Instituto de Bioquímica Médica-Leopoldo de Meis, Rio de Janeiro, RJ, Brazil; Centro Nacional de Biologia Estrutural e Bioimagem, Plataforma Avançada de Biomoléculas, Rio de Janeiro, RJ, BrazilUniversidade Federal do Rio de Janeiro (UFRJ), Instituto de Bioquímica Médica-Leopoldo de Meis, Rio de Janeiro, RJ, Brazil; Corresponding author.The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic demanded rapid diagnosis to isolate new COVID-19 cases and prevent disease transmission. Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) rapidly became the gold standard for diagnosis. However, due to the high cost and delay of the results, other types of diagnosis were implemented, such as COVID-19 Ag Rapid Tests and Reverse Transcription Technique followed by Loop-Mediated isothermal Amplification (RT-LAMP). In this work, we validated the use of RT-LAMP in saliva samples rather than nasopharyngeal swabs, as the collection is more comfortable. First, we selected 5 primer sets based on the limit of detection for SARS-CoV-2 RNA, then validated their sensitivity and specificity in patient samples. A total of 117 samples were analyzed by fluorometric RT-LAMP and compared with qRT-PCR results. Our results show that the use of a high-sensitive primer ORF1-a, together with a low-sensitive primer set Gene E (time to threshold of 22.9 and 36.4 minutes, respectively, using 200 copies of viral RNA), achieved sensitivity in purified RNA from saliva samples of 95.2% (95% CI 76.1‒99.8) with 90.5% specificity (95% CI 69.6‒98.8) (n = 42).As RNA purification increases the turnaround time, we tested the outcome of RT-LAMP utilizing raw saliva samples without purification. The test achieved a sensitivity of 81.8% (95% CI 59.7‒94.8) and a specificity of 90.9% (95% CI 70.8‒98.8). As a result, the accuracy of 92.9% (95% CI 80.5‒98.5) in purified RNA-saliva samples was lowered to an acceptable level of 86.4% (95% CI 72.6‒94.8) in raw saliva. Although mass vaccination has been implemented, new strains and low vaccination progress helped to spread COVID-19. This study shows that it is feasible to track new COVID-19 cases in a large population with the use of raw saliva as sample in RT-LAMP assay which yields accurate results and offers a less invasive test.http://www.sciencedirect.com/science/article/pii/S1413867023000508COVID-19RT-LAMPRT-PCRSaliva samples |
| spellingShingle | Kátia Maria dos Santos Cabral Ramon Cid Gismonti Baptista Terezinha Marta Pereira Pinto Castineiras Amilcar Tanuri Fabiana Avila Carneiro Marcius da Silva Almeida Monica Montero-Lomeli Accuracy of a raw saliva-based COVID-19 RT-LAMP diagnostic assay Brazilian Journal of Infectious Diseases COVID-19 RT-LAMP RT-PCR Saliva samples |
| title | Accuracy of a raw saliva-based COVID-19 RT-LAMP diagnostic assay |
| title_full | Accuracy of a raw saliva-based COVID-19 RT-LAMP diagnostic assay |
| title_fullStr | Accuracy of a raw saliva-based COVID-19 RT-LAMP diagnostic assay |
| title_full_unstemmed | Accuracy of a raw saliva-based COVID-19 RT-LAMP diagnostic assay |
| title_short | Accuracy of a raw saliva-based COVID-19 RT-LAMP diagnostic assay |
| title_sort | accuracy of a raw saliva based covid 19 rt lamp diagnostic assay |
| topic | COVID-19 RT-LAMP RT-PCR Saliva samples |
| url | http://www.sciencedirect.com/science/article/pii/S1413867023000508 |
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