A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance
This article has been Reviewed by the following groups
Discuss this preprint
Start a discussion What are Sciety discussions?Listed in
- Evaluated articles (ScreenIT)
Abstract
No abstract available
Article activity feed
-
-
SciScore for 10.1101/2021.05.05.21256527: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: This study was approved by the University of Washington Institutional Review Board. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources Blotting was performed with 1:500 anti-SARS-CoV-2 Nucleocapsid Protein (E8R1L) mouse IgG2a monoclonal antibody (Cell Signaling Technology, Danvers, MA, USA) followed by staining with 1:2,000 IRDye 800CW anti-mouse IgG secondary antibody (Li-Cor Biosciences, Lincoln, NE, USA). anti-mouse IgGsuggested: NoneExperimental Models: Cell Lines Sentences Resources Cell culture, transfection, and cell lysis: 293T cells … SciScore for 10.1101/2021.05.05.21256527: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: This study was approved by the University of Washington Institutional Review Board. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources Blotting was performed with 1:500 anti-SARS-CoV-2 Nucleocapsid Protein (E8R1L) mouse IgG2a monoclonal antibody (Cell Signaling Technology, Danvers, MA, USA) followed by staining with 1:2,000 IRDye 800CW anti-mouse IgG secondary antibody (Li-Cor Biosciences, Lincoln, NE, USA). anti-mouse IgGsuggested: NoneExperimental Models: Cell Lines Sentences Resources Cell culture, transfection, and cell lysis: 293T cells were maintained in Dulbecco’s modified Eagle medium (DMEM) high glucose with 10% fetal bovine serum (FBS), 10 mM HEPES, penicillin and streptomycin. 293Tsuggested: NoneRecombinant DNA Sentences Resources Abbott BinaxNOW, Quidel Sofia 2, and Quidel QuickVue testing of cell lysates: Lysates from 293T cells transfected with N wildtype, N T205I, N D399N, N T205I/D399N, or pcDNA4/TO vector were kept frozen at -80°C prior to use in antigen testing. pcDNA4/TOsuggested: RRID:Addgene_45482)Software and Algorithms Sentences Resources Clinical specimen testing on Abbott BinaxNOW: Testing of clinical specimens with the Abbott BinaxNOW COVID-19 Ag Card was performed as described previously (15). Abbottsuggested: (Abbott, RRID:SCR_010477)Whole genome sequencing and genome mining: SARS-CoV-2 whole genome sequencing was performed using the Swift Biosciences v2 or Illumina COVID-Seq amplicon tiling platforms as described previously (17). Swift Biosciencessuggested: NoneResults 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:The main limitations of the study include the small number of specimens tested, use of specimens that do not follow the manufacturer’s recommended testing protocol, use of unpurified recombinant protein lysates to confirm mutation effects, and limited testing to initial determination of analytical sensitivity using recombinant protein. Nonetheless, we found consistent results between use of clinical specimens and recombinant proteins that bulwarks our results. The Quidel Sofia SARS Antigen FIA is a sandwich ELISA which involves both a capture and detection antibody. At this time, it is not clear whether the D399N mutation alters binding by the capture or the detection antibody. Without the antibodies used in these assays, it is difficult to determine equilibrium dissociation constants, perform epitope mapping, or measure other biochemical properties associated with the test reagents. Our data further highlight the increasing returns of widespread genome sequencing in the clinical microbiology community (26, 27). With routine SARS-CoV-2 whole genome sequencing available in our lab, we were rapidly able to determine the coding mutations present in a diagnostic edge case. This mutation could further be probed by examining more specimens for which routine genome sequencing had been performed. All told, the work in the clinical virology described here was completed in under four weeks and the antigen test manufacturer was made aware within four days of our testing of the genotyped...
Results from TrialIdentifier: No clinical trial numbers were referenced.
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.
Results from scite Reference Check: We found no unreliable references.
-
