SARS-CoV-2 detection by rRT-PCR on self-collected anterior nares swabs or saliva compared with clinician-collected nasopharyngeal swabs — Denver and Atlanta, August – November, 2020

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   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2021.02.16.21251521: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	Consent: After consent, participants were coached to self-collect an ANS and provide a saliva specimen; NPS was then collected by a trained public health professional*. IRB: The Institutional Review Boards in Denver (Colorado Department of Public Health and Environment; University of Colorado) and Emory University in Atlanta also determined this activity was an exempt public health activity, consistent with applicable federal law and CDC policy.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Trained interviewers administered structured …

   SciScore for 10.1101/2021.02.16.21251521: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	Consent: After consent, participants were coached to self-collect an ANS and provide a saliva specimen; NPS was then collected by a trained public health professional*. IRB: The Institutional Review Boards in Denver (Colorado Department of Public Health and Environment; University of Colorado) and Emory University in Atlanta also determined this activity was an exempt public health activity, consistent with applicable federal law and CDC policy.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Trained interviewers administered structured surveys in English or Spanish to collect demographic characteristics, COVID-19 symptoms†, onset of symptoms (Atlanta only), and whether they had close contact§ with COVID-19 in the past two weeks; data were entered into Research Electronic Data Capture (REDCap) software (Vanderbilt University).	REDCap suggested: (REDCap, RRID:SCR_003445)

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   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).

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   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   When patients are unable or unwilling to undergo NPS collection, or when PPE or trained healthcare personnel are limited, self-collected saliva or ANS could be offered, with the caveat that some infections might be missed that would have been detected by NPS (13% to 29% of participants in this investigation). Whether cases detected by NPS but negative by saliva/ANS are infectious should be investigated further. Most participants with discordant results between the three specimens had NPS Ct values >30, consistent with decreased genetic material in the sample and potentially non-viable virus (9,10). Self-collected saliva or ANS specimens could be most useful when people report current COVID-19 symptoms†, particularly with recent onset. Testing both saliva and ANS in parallel for individual participants appeared to increase sensitivity, but this strategy is an unlikely option; given the increased burden on laboratory resources. Pooled saliva/ANS specimens could be a subject of future research. When developing testing strategies with specific SARS-CoV-2 assays, including non-PCR assays such as antigen-based tests, differences in testing accuracy by specimen type should be considered, along with patient population characteristics. Sensitivity for both saliva and ANS specimens for the detection of SARS-CoV-2 was higher among participants in Denver than in Atlanta, but the patterns in test performance were the same across sites. The higher test performance among the Denver particip...

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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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   Version published to 10.1101/2021.02.16.21251521 on medRxiv

   Feb 19, 2021