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

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 performi...

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Published in:	Frontiers in bioengineering and biotechnology Vol. 9; p. 638902
Main Authors:	Rodríguez Flores, Sofía N, Rodríguez-Martínez, Luis Mario, Reyes-Berrones, Bernardita L, Fernández-Santos, Nadia A, Sierra-Moncada, Elthon J, Rodríguez-Pérez, Mario A
Format:	Journal Article
Language:	English
Published:	Switzerland Frontiers Media S.A 29-03-2021
Subjects:	Bioengineering and Biotechnology clinical samples COVID-19 molecular diagnosis RNA extraction protocol SARS-CoV-2 COVID-19 RNA extraction protocol SARS-CoV-2 clinical samples molecular diagnosis
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Summary:	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 ( > 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 ( < 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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Edited by: Segaran P. Pillai, United States Department of Homeland Security, United States This article was submitted to Biosafety and Biosecurity, a section of the journal Frontiers in Bioengineering and Biotechnology These authors have contributed equally to this work Reviewed by: Malaya Sahoo, Stanford University, United States; Bruno Jorge Antunes Colaço, University of Trás-os-Montes and Alto Douro, Portugal
ISSN:	2296-4185 2296-4185
DOI:	10.3389/fbioe.2021.638902