Clinical validation of the isothermal rt-lamp test for the rapid diagnosis of SARS-CoV-2

Introduction: Since the first report in Wuhan (China) in 2019, the SARS-CoV 2 virus has spread throughout the world, with a significant impact in public health. To contain the spread of SARS-CoV-2, the WHO has encouraged the development of rapid, simple, sensitive and specific tests that complement the gold standard RT-qPCR. Loop-mediated isothermal amplification (LAMP) has shown a good yield to detect SARS-CoV2 in different fluids. Objective: To validate the colorimetric RT-LAMP technique using two sets of oligonucleotides aimed at identifying the N gene of SARS-CoV-2 in 117 nasopharyngeal swab samples, previously confirmed by RT-qPCR using the Charite/Berlin protocol. Material and methods: 153 nasopharyngeal swab samples from individuals with suspected Covid-19 were subjected to qRT-PCR and RT-LAMP using a commercial colorimetric kit (NEB, Germany). RT-LAMP was run using both extracted RNA samples and raw samples without prior RNA extraction, and the result was assessed by a simple color change in the reaction. Results: RT-LAMP sensibility and specificity for gen N SARS-CoV-2 detection using one primers set previosly reported got values 0.97 (0.85, 1.00) and 0.81 (0.65, 0.92) respectively, for CI 95%. The other set primer used in this paper also reported previosly had 0.96 (0.78,1.00) sensibility and 0.77 (0.55,0.92) specificity to RT-LAMP. Without RNA extraction we found sensibility value of 0.95 (0.74, 1.00) and specificity 0.88 (0.64, 0.99). Conclusion: Taking together, the obtained results show RT-LAMP technique could be considered a rapid diagnostic test, easy to perform, free of sophisticated equipment, sensitive and specific to diagnose SARS-CoV-2 in nasopharyngeal swabs with and without prior RNA extraction, which that allows scaling its portability to places with scarce sources of resources.