Comparison of BinaxNOW and SARS-CoV-2 qRT-PCR Detection of the Omicron Variant from Matched Anterior Nares Swabs

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1. Version published to 10.1128/spectrum.01307-22

   Dec 21, 2022
2. 

   ScreenIT

   Feb 4, 2022

   SciScore for 10.1101/2022.01.31.22270206: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Abbott BinaxNOW™ COVID-19 Antigen Test: The additional matched AN swabs were tested according to the manufacturer instructions.	Abbott suggested: (Abbott, RRID:SCR_010477)
   Full length genomes for each amplified sample were then assembled through alignment to the Wuhan-Hu-1 reference sequence (NC_045512.2) (16) using Bowtie2(17).	Bowtie2 suggested: (Bowtie 2, RRID:SCR_016368)
   Nucleotide substitutions, insertions, and deletions were identified with LoFreq (18) Lineage assignment for each genome was carried out …

   SciScore for 10.1101/2022.01.31.22270206: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Abbott BinaxNOW™ COVID-19 Antigen Test: The additional matched AN swabs were tested according to the manufacturer instructions.	Abbott suggested: (Abbott, RRID:SCR_010477)
   Full length genomes for each amplified sample were then assembled through alignment to the Wuhan-Hu-1 reference sequence (NC_045512.2) (16) using Bowtie2(17).	Bowtie2 suggested: (Bowtie 2, RRID:SCR_016368)
   Nucleotide substitutions, insertions, and deletions were identified with LoFreq (18) Lineage assignment for each genome was carried out using Pangolin(19).	LoFreq suggested: (LoFreq, RRID:SCR_013054)
   Data Analysis: Data analysis was performed on MATLAB (MathWorks, Natick, Massachusetts)	MATLAB suggested: (MATLAB, RRID:SCR_001622)

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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:

   Limitations of this study include the relatively small sample size. The disease prevalence at our clinic as measured by qRT-PCR on the two days of testing was approaching 50%, thus we are confident that the conclusions drawn from our sample size of 110 swabs are sound. It is also important to note that we asked individuals to swab each nostril twice, and the swab for the BinaxNOWTM test was always taken second. It is possible that less material was present on the swabs taken for the RDT, which could account for some of the lower sensitivity. Finally, we would like to note that four individuals tested on both days, and thus, our dataset includes 110 matched samples from 106 individuals. We do know that the 4 individuals who tested twice tested negative both times on both tests. To be sure, tests like BinaxNOW™ are still valuable tools, as they provide immediate results, require no additional instrumentation, and are effective at rule-in diagnosis. However, there is still an unmet need for more sensitive rapid diagnostics for SARS-CoV-2 that could augment qRT-PCR testing at times of high-demand. Alternative approaches could include increased investment to increase the availability of qRT-PCR testing facilities.

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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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   Results from scite Reference Check: We found no unreliable references.

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3. 

   Version published to 10.1101/2022.01.31.22270206 on medRxiv

   Feb 1, 2022