Detection of SARS-CoV-2 in Different Human Biofluids Using the Loop-Mediated Isothermal Amplification Assay: A Prospective Diagnostic Study in Fortaleza, Brazil

ABSTRACT

We adopted the reverse transcriptase - loop mediated isothermal amplification (RT-LAMP) to detect SARS-Cov-2 in patient samples. Two primer sets for genes N and Orf1ab were designed to detect SARS-CoV-2, and one primer set was designed to detect the human gene Actin. We collected prospective 138 nasopharyngeal swabs, 70 oropharyngeal swabs, 69 saliva, and 68 mouth saline wash samples from patients suspected to have severe acute respiratory syndrome (SARS) caused by SARS-CoV-2 to test the RT-LAMP in comparison with the golden standard technique RT-qPCR. Accuracy of diagnosis using both primers, N5 and Orf9, was evaluated. Sensitivity and specificity for diagnosis was 96% (95% CI 87-99) and 85% (95% CI 76-91) in 138 samples, respectively. Accurate diagnosis results were obtained only in nasopharyngeal swab processed via extraction kit. Accurate and rapid diagnosis could aid COVID-19 pandemic management by identifying, isolating, and treating patients rapidly. HighlightsO_LINew nucleic acid amplification test for the diagnosis of SARS-CoV-2 using the RT-LAMP C_LIO_LIN5 primer set showed mutations in strains of interest, such as the gamma strain (P.1) of SARS-CoV-2 C_LIO_LIWhen evaluated in combination N5 and Orf9 primer sets maintained high sensitivity and specificity C_LI