Validation of the RT-LAMP assay in a large cohort of nasopharyngeal swab samples shows that it is a useful screening method for detecting SARS-CoV-2 and its VOC variants
Cisneros-Villanueva, M.; Blancas, S. S.; Cedro-Tanda, A.; Rios-Romero, M.; Hurtado-Cordova, E.; Almaraz-Rojas, O.; Ortiz-Soriano, D. R.; Alvarez-Hernandez, V.; Arriaga-Guzman, I. E.; Tolentino-Garcia, L.; Sanchez-Vizcarra, A.; Lozada-Rodriguez, L. F.; Peralta-Arrieta, I.; Perez-Aquino, J. E.; Andonegui-Elguera, M. A.; Cendejas-Orozco, M.; Mendoza-Vargas, A.; Reyes-Grajeda, J. P.; Campos-Romero, A.; Alcantar-Fernandez, J.; Moreno-Camacho, J. L.; Gallegos-Rodriguez, J.; Esparza-Luna-Ruiz, M.; Ortiz-Ramirez, J.; Benitez-Gonzalez, M.; Uribe-Figueroa, L.; Angulo, O.; Ruiz, R.; Herrera, L. A.; Hidal
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The COVID-19 pandemic is challenging the global supply chain and equipment needed for mass testing with RT-qPCR, the gold standard for SARS-CoV-2 diagnosis. Here, we propose the RT-LAMP assay as an additional strategy for rapid virus diagnosis. However, its validation as a diagnostic method remains uncertain. In this work, we validated the RT-LAMP assay in 1,266 nasopharyngeal swab samples with confirmed diagnosis by CDC 2019-nCoV RT-qPCR. Our cohort was divided, the first (n=984) was used to evaluate two sets of oligonucleotides (S1 and S3) and the second (n=281) to determine whether RT-LAMP could detect samples with several types of variants. This assay can identify positive samples by color change or fluorescence within 40 minutes and shows high concordance with RT-qPCR in samples with CT [≤]35. Also, S1 and S3 are able to detect SARS-CoV-2 with a sensitivity of 68.4% and 65.8%, and a specificity of 98.9% and 97.1%, respectively. Furthermore, RT-LAMP assay identified 279 sequenced samples as positive (99.3% sensitivity) corresponding to the Alpha, Beta, Gamma, Delta, Epsilon, Iota, Kappa, Lambda, Mu and Omicron variants. In conclusion, RT-LAMP is able to identify SARS-CoV-2 with good sensitivity and excellent specificity, including all VOC, VOI, VUM and FMV variants.
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