Comparison Between a Standard and SalivaDirect RNA Extraction Protocol for Molecular Diagnosis of SARS-CoV-2 Using Nasopharyngeal Swab and Saliva Clinical Samples

Sofía N. Rodríguez Flores, Mario A. Rodríguez-Pérez*, Luis Mario Rodríguez Martínez, Bernardita L. Reyes-Berrones, Nadia A. Fernández-Santos, Elthon J. Sierra-Moncada

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)

Abstract

During the COVID-19 pandemic, a certified laboratory of Tamaulipas, Mexico has processed over 100,000 samples of COVID-19 suspected patients, working a minimum of 100 tests daily. Thus, it would be beneficial for such certified laboratories nationwide to reduce the time and cost involved in performing the diagnosis of COVID-19, from sample collection, transportation to local lab, processing of samples, and data acquisition. Here, 30 nasopharyngeal swab and saliva samples from the same COVID-19 individuals were assessed by a standard nucleic acid extraction protocol, including protein lysis with proteinase K followed by binding to column, washing, and elution, and by the SalivaDirect protocol based on protein lysis, skipping the other steps to reduce processing time and costs. The genomic RNA was amplified using a SARS-CoV-2 Real-Time PCR kit. A variation (P > 0.05) in the 95% CIs = 72.6%–96.7% was noted by using the SalivaDirect protocol and saliva samples (sensitivity of 88.2%) in comparison to those of standard protocol with oropharyngeal swab samples (95% CIs = 97.5%–100%; sensitivity of 100%) as reported elsewhere. However, when using nasopharyngeal swab samples in the SalivaDirect protocol (sensitivity of 93.6%; 95% CIs = 79.2%–99.2%), it was in concordance (P < 0.05) with those of the standard one. The logical explanation to this was that two samples with Ct values of 38, and 40 cycles for gene E produced two false negatives in the SalivaDirect protocol in relation to the standard one; thus, there was a reduction of the sensitivity of 6.4% in the overall assay performance.

Original languageEnglish
Article number638902
Pages (from-to)638902
JournalFrontiers in Bioengineering and Biotechnology
Volume9
DOIs
Publication statusPublished - 29 Mar 2021
Externally publishedYes

Bibliographical note

Funding Information:
The present work was performed under the auspices of the Laboratorio Estatal de Salud Pública de Tamaulipas (Secretaría de Salud-México) in collaboration with the Consejo Nacional de Ciencia y Tecnología (CONACYT), México (Grant No. 314311) where Dr. Lihua Wei was PI. SRF holds a M.Sc. scholarship from CONACYT, México (1004818). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Funding Information:
We are grateful to the individuals of the municipalities of Ciudad Victoria, Tamaulipas who granted us permission to obtain their clinical samples for COVID-19 testing. Funding. The present work was performed under the auspices of the Laboratorio Estatal de Salud P?blica de Tamaulipas (Secretar?a de Salud-M?xico) in collaboration with the Consejo Nacional de Ciencia y Tecnolog?a (CONACYT), M?xico (Grant No. 314311) where Dr. Lihua Wei was PI. SRF holds a M.Sc. scholarship from CONACYT, M?xico (1004818). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Publisher Copyright:
© Copyright © 2021 Rodríguez Flores, Rodríguez-Martínez, Reyes-Berrones, Fernández-Santos, Sierra-Moncada and Rodríguez-Pérez.

Fingerprint

Dive into the research topics of 'Comparison Between a Standard and SalivaDirect RNA Extraction Protocol for Molecular Diagnosis of SARS-CoV-2 Using Nasopharyngeal Swab and Saliva Clinical Samples'. Together they form a unique fingerprint.

Cite this