Comparative evaluation of a novel saliva collection strip and nasopharyngeal swab for SARS-CoV-2 validated by in-house RT-qPCR

Abstract

Introduction: The most commonly used sample collection method for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is nasopharyngeal swab; however, sample collection, especially from pediatric patients, is difficult. Therefore, the aim of this study was to design a saliva collection strip and to compare the effectiveness of this strip with the nasopharyngeal swab. Additionally, the performance of different isolation procedures before real time quantitative polymerase chain reaction (RT-qPCR) were investigated and an in-house RT-qPCR assay was developed.

Methodology: A total of 200 samples was collected from patients and 92 samples were confirmed as SARS-CoV-2 positive. In the first technique, nucleic acid from the samples were isolated using different isolation methods, and then analyzed by RT-qPCR. In the second technique, the samples were analyzed directly by RT-qPCR without any isolation process. Additionally, in-house RT-qPCR assay was performed and the results were compared with conventional RT-qPCR.

Results: The cycle threshold (Ct) values were compared between the techniques, and very similar results were obtained with all of the methods. This reveals that both sample collection methods, both isolation methods, and both RT-qPCR assays had comparable accuracy.

Conclusions: In this study, in-house optimization, validation, and integration of the SARS-CoV-2 assay with both isolation-based and extraction (direct lysis) workflows were compared. In addition, its compatibility with the newly designed saliva strip collection system was analyzed. Very similar results were obtained from all of the methods. Therefore, the sample collection strip and in-house assay can be useful tools for detecting SARS-CoV-2.