Title
Standardization and validation of an in house RT-lamp molecular test for the diagnosis of SARS-CoV-2
Other title
Estandarización y validación de una prueba molecular RT-lamp in house para el diagnóstico de SARS-CoV-2
Date Issued
01 January 2021
Access level
open access
Resource Type
journal article
Author(s)
Escalante-Maldonado O.
Vidal-Anzardo M.
Gallesi I.
Pampa-Espinoza L.
Durães-Carvalho R.
Mendez-Rico J.
Marques-Simas P.V.
Publisher(s)
Instituto Nacional de Salud
Abstract
Objectives: To standardize and validate an in-house RT-LAMP test for the detection of SARS-CoV-2, based on laboratory and field assays using samples from COVID-19 suspected patients. Materials and methods: An in-house SARS-CoV-2 RT-LAMP molecular test was standardized, establishing the detection limit with Vero cells of isolated Peruvian strains of SARS-CoV-2, and the robustness to various concentrations of primers. The laboratory validation was performed with 384 nasal and pharyngeal swab samples (UFH) obtained between March and July 2020. The field validation was performed with 383 UFH obtained from COVID-19 suspected symptomatic cases. All samples were tested by RT-LAMP and RT-qPCR. The RT-qPCR was considered as the reference standard test. The concordance measures and diagnostic performance were calculated. Results: The detection limit was consistent in cases with Ct <30 in both tests, showing efficiency to detect up to 1000 copies/μL of the target gene. Robustness was evidenced with half of the primer concentrations and 20 μL of final volume. Absence of amplification was identified for other HCoVs. Concordance showed a kappa index of 0.88 (95% CI: 0.83-0.93) and 0.89 (95% CI: 0.84-0.94) in laboratory and field settings, respectively. The sensitivity value in the laboratory was 87.4% (95% CI: 80.8-92.4) and 88.1% in the field (95% CI: 81.6-92.9). The specificity value in both settings was 98.8% (95% CI: 96.4-99.7). Conclusions: The in-house SARS-CoV-2 RT-LAMP test was successfully validated based on its adequate robustness, no cross-reactions, good concordance, and diagnostic performance compared to RT-qPCR.
Start page
7
End page
16
Volume
38
Issue
1
Language
Spanish
OCDE Knowledge area
Medicina clÃnica
Subjects
Scopus EID
2-s2.0-85110199199
PubMed ID
Source
Revista Peruana de Medicina Experimental y Salud Publica
ISSN of the container
17264634
Sources of information:
Directorio de Producción CientÃfica
Scopus