Patient-collected tongue, nasal, and mid-turbinate swabs for SARS-CoV-2 yield equivalent sensitivity to health care worker collected nasopharyngeal swabs
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Abstract
Background
Current testing for SARS-CoV-2 requires health care workers to collect a nasopharyngeal (NP) sample from a patient. NP sampling requires the use of personal protective equipment that are in limited supply, is uncomfortable for the patient, and reduces clinical efficiency. This study explored the equivalency of patient-collected tongue, anterior nares (nasal), and mid-turbinate (MT) samples to health care worker-collected NP samples for detecting SARS-CoV-2.
Methods
Patients presenting to five urgent care facilities with symptoms indicative of an upper respiratory infection provided self-collected samples from three anatomic sites along with a health care worker-collected NP sample. Using NP as the comparator, sensitivities and one-sided 95% confidence intervals for the tongue, nasal, and MT samples for detection of SARS-CoV-2 were calculated.
Results
The sensitivity for detecting SARS-CoV-2 in patient-collected tongue, nasal, and mid-turbinate samples was 89.8% (95% CI: 80.2 -100.0), 94.0 (95% CI: 84.6-100.0) and 96.2 (95% CI: 87.7-100.0), respectively. Among samples yielding positive results, cycle threshold (Ct) values (a measure of viral load) had correlation coefficients of 0.48, 0.78, and 0.86 between the NP samples and the tongue, nasal, and MT samples, respectively.
Conclusions
Patient-collected nasal and MT samples demonstrated high sensitivity for SARS-CoV-2 detection using health care worker-collected NP samples as the comparator. Among patients testing positive with NP samples, nasal and MT Ct values demonstrated high correlations with those Ct values of the NP samples. Patient-collected nasal or MT sampling may improve efficiency for COVID-19 testing while reducing the risk of exposure of the health workforce.
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SciScore for 10.1101/2020.04.01.20050005: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Inclusion criteria included evidence of symptoms suggestive of an upper respiratory illness (subjective and objective fevers, cough, sore throat, fevers, myalgia, or rhinorrhea, indicating higher risk of COVID-19 in this community) and the ability to consent and agree to participate in the study. Randomization not detected. Blinding not detected. Power Analysis Forty-eight positive NP test results are needed for 80% power at 0.05 significance. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources All samples were stored in viral transport media and refrigerated at 4°C before shipping on ice packs to a reference … SciScore for 10.1101/2020.04.01.20050005: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Inclusion criteria included evidence of symptoms suggestive of an upper respiratory illness (subjective and objective fevers, cough, sore throat, fevers, myalgia, or rhinorrhea, indicating higher risk of COVID-19 in this community) and the ability to consent and agree to participate in the study. Randomization not detected. Blinding not detected. Power Analysis Forty-eight positive NP test results are needed for 80% power at 0.05 significance. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources All samples were stored in viral transport media and refrigerated at 4°C before shipping on ice packs to a reference laboratory for rRT-PCR testing (Quest Diagnostics, San Juan Capistrano, CA). Questsuggested: (QUEST, RRID:SCR_005210)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:This study has a number of limitations. Samples were collected in five urgent care clinics located in a single region of the US. Our analysis was cross-sectional and limited to single comparisons to NP. With additional analysis and longitudinal data collection, we hope to understand how self-collection of samples from multiple upper respiratory anatomical sites contribute to test performance. Despite these limitations, we believe that self-collected samples for SARS-CoV-2 testing from sites other than NP is a useful approach during the COVID-19 pandemic.
Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT04321369 Completed Impact of Swab Site and Sample Collector on Testing Sensitiv… Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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