Optimization and Clinical Evaluation of a Multi-Target Loop-Mediated Isothermal Amplification Assay for the Detection of SARS-CoV-2 in Nasopharyngeal Samples
| Autor: | Tatiana Varandas, Mafalda Timóteo, Sarah Azinheiro, Inês Baldaque, Joana Carvalho, Ana E. Sousa, Marta Prado, Daniela Fonseca-Silva, Hugo Sousa, Foteini Roumani, Alejandro Garrido-Maestu |
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| Rok vydání: | 2021 |
| Předmět: |
0301 basic medicine
Coronavirus disease 2019 (COVID-19) clinical evaluation ORF3a Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Concordance 030106 microbiology Loop-mediated isothermal amplification Real-Time Polymerase Chain Reaction medicine.disease_cause Microbiology Sensitivity and Specificity Article Viral Proteins 03 medical and health sciences COVID-19 Testing Nasopharynx Virology Humans Medicine RT-LAMP Coronavirus SARS-CoV-2 business.industry COVID-19 ORF8 Gold standard (test) Viral Load QR1-502 030104 developmental biology Infectious Diseases Molecular Diagnostic Techniques N RNA Viral business Nucleic Acid Amplification Techniques Clinical evaluation Viral load |
| Zdroj: | Viruses Volume 13 Issue 5 Viruses, Vol 13, Iss 940, p 940 (2021) |
| ISSN: | 1999-4915 |
| DOI: | 10.3390/v13050940 |
| Popis: | SARS-CoV-2 is the coronavirus responsible for COVID-19, which has spread worldwide, affecting more than 200 countries, infecting over 140 million people in one year. The gold standard to identify infected people is RT-qPCR, which is highly sensitive, but needs specialized equipment and trained personnel. The demand for these reagents has caused shortages in certain countries. Isothermal nucleic acid techniques, such as loop-mediated isothermal amplification (LAMP) have emerged as an alternative or as a complement to RT-qPCR. In this study, we developed and evaluated a multi-target RT-LAMP for the detection of SARS-CoV-2. The method was evaluated against an RT-qPCR in 152 clinical nasopharyngeal swab samples. The results obtained indicated that both assays presented a “good concordance” (Cohen’s k of 0.69), the RT-LAMP was highly specific (99%) but had lower sensitivity compared to the gold standard (63.3%). The calculated low sensitivity was associated with samples with very low viral load (RT-qPCR Cq values higher than 35) which may be associated with non-infectious individuals. If an internal Cq threshold below 35 was set, the sensitivity and Cohen’s k increased to 90.9% and 0.92, respectively. The interpretation of the Cohen’s k for this was “very good concordance”. The RT-LAMP is an attractive approach for frequent individual testing in decentralized setups. |
| Databáze: | OpenAIRE |
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