Dataset Information

Ultimate COVID-19 Detection Protocol Based on Saliva Sampling and qRT-PCR with Risk Probability Assessment.

ABSTRACT: In the era of COVID-19 outbreak, various efforts are undertaken to develop a quick, easy, inexpensive, and accurate way for diagnosis. Although many commercial diagnostic kits are available, detailed scientific evaluation is lacking, making the public vulnerable to fear of false-positive results. Moreover, current tissue sampling method from respiratory tract requires personal contact of medical staff with a potential asymptomatic SARSCOV-2 carrier and calls for safe and less invasive sampling method. Here, we have developed a convenient detection protocol for SARS-COV-2 based on a non-invasive saliva self-sampling method by extending our previous studies on development of a laboratory-safe and low-cost detection protocol based on qRT-PCR. We tested and compared various self-sampling methods of self-pharyngeal swab and self-saliva sampling from non-carrier volunteers. We found that the self-saliva sampling procedure gave expected negative results from all of the non-carrier volunteers within 2 hours, indicating cost-effectiveness, speed and reliability of the saliva-based method. For an automated assessment of the sampling quality and degree of positivity for COVID-19, we developed scalable formulae based on a logistic classification model using both cycle threshold and melting temperature from the qRT-PCR results. Our newly developed protocol will allow easy sampling and spatial-separation between patient and experimenter for guaranteed safety. Furthermore, our newly established risk assessment formula can be applied to a large-scale diagnosis in health institutions and agencies around the world.

SUBMITTER: Won J

PROVIDER: S-EPMC7926046 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Publications

Ultimate COVID-19 Detection Protocol Based on Saliva Sampling and qRT-PCR with Risk Probability Assessment.

Won Joungha J Kazan Hasan Hüseyin HH Kwon Jea J Park Myungsun M Ergun Mehmet Ali MA Ozcan Sureyya S Choi Byung Yoon BY Heo Won Do WD Lee C Justin CJ

Experimental neurobiology 20210201 1

In the era of COVID-19 outbreak, various efforts are undertaken to develop a quick, easy, inexpensive, and accurate way for diagnosis. Although many commercial diagnostic kits are available, detailed scientific evaluation is lacking, making the public vulnerable to fear of false-positive results. Moreover, current tissue sampling method from respiratory tract requires personal contact of medical staff with a potential asymptomatic SARSCOV-2 carrier and calls for safe and less invasive sampling m ...[more]

PMID: 33556920

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Project description:We examined the detection rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using reverse transcription-PCR (RT-PCR) of side-by-side saliva and oropharyngeal swab (OPS) samples from 639 symptomatic and asymptomatic subjects, of which 47 subjects were found to be positive for SARS-CoV-2 in the OPS or saliva sample or both. It was found that the detection rate (93.6% for both OPS and saliva) as well as the sensitivity and specificity were comparable between the two sampling methods in this cohort. The sensitivity was 0.932 (95% confidence interval [CI], 0.818 to 0.977) and the specificity was 0.995 (95% CI, 0.985 to 0.998), both for saliva when OPS sampling was used as the reference and for OPS when saliva was used as the reference. Furthermore, the Cohen's kappa value was 0.926 (95% CI, 0.868 to 0.985), indicating strong agreement between the two sampling methods. In addition, the viral RNA stability in pure saliva and saliva mixed with preservation buffers was examined following storage at room temperature and at 4°C. It was found that pure saliva kept the viral RNA stable for 9 days at both temperatures and that the type of preservation buffer can either enhance or reduce the stability of the RNA. We conclude that self-administered saliva sampling is an attractive alternative to oropharyngeal swabbing for SARS-CoV-2 detection, and it might be useful in large-scale testing. IMPORTANCE It is not inconceivable that we will witness recurring surges of COVID-19 before the pandemic finally recedes. It is therefore still relevant to look for feasible, simple, and flexible screening methods so that schools, workplaces, and communities in general can avoid lockdowns. In this work, we analyzed two different sampling methods: oropharyngeal swabs and saliva collection. Oropharyngeal swabs must be collected by trained health personnel at clinics, whereas self-assisted saliva collection can be performed at any given location. It was found that the two sampling methods were comparable. Saliva sampling is a simple method that allows easy mass testing using minimal resources from the existing health care system, and this method may therefore prove to be an effective tool for containing the COVID-19 pandemic.

Dataset Information

Ultimate COVID-19 Detection Protocol Based on Saliva Sampling and qRT-PCR with Risk Probability Assessment.

Publications

Ultimate COVID-19 Detection Protocol Based on Saliva Sampling and qRT-PCR with Risk Probability Assessment.

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