A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses

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1. Version published to 10.1080/22221751.2021.2011623

   Dec 28, 2021
2. 

   ScreenIT

   Oct 22, 2021

   SciScore for 10.1101/2021.10.13.464307: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The anti-His tag antibodies, diluted at 50 μg/mL in 10 mM sodium acetate, pH 4.5, were immobilized on both the active and reference flow cells surface of the activated CM5 sensor chip using amine coupling method.	anti-His tag suggested: None
   Approximately 200 RU of His-tagged SARS-CoV-2 and SARS-CoV spike trimers and RBDs were captured onto the chip for the active surface, and anti-His antibody alone served as the reference surface.	anti-His suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cell lines: HEK293T/17 (cat# CRL-11268) and Vero E6 cells (cat# CRL-1586) were from ATCC, 293T-ACE2 …

   SciScore for 10.1101/2021.10.13.464307: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The anti-His tag antibodies, diluted at 50 μg/mL in 10 mM sodium acetate, pH 4.5, were immobilized on both the active and reference flow cells surface of the activated CM5 sensor chip using amine coupling method.	anti-His tag suggested: None
   Approximately 200 RU of His-tagged SARS-CoV-2 and SARS-CoV spike trimers and RBDs were captured onto the chip for the active surface, and anti-His antibody alone served as the reference surface.	anti-His suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cell lines: HEK293T/17 (cat# CRL-11268) and Vero E6 cells (cat# CRL-1586) were from ATCC, 293T-ACE2 cells were kindly provided by J. Sodroski of Harvard Medical School, and they were cultured in 10% fetal bovine serum (FBS, GIBCO cat# 16140071) supplemented Dulbecco’s Modified Eagle Medium (DMEM, ATCC cat# 30-2002) at 37°C, 5% CO2.	Vero E6 suggested: None 293T-ACE2 suggested: None
   Briefly, HEK293T cells were grown to 80% confluency before transfection with the spike gene using Lipofectamine 3000 (Invitrogen).	HEK293T suggested: None
   The proteins were expressed in HEK293 Freestyle cells (Invitrogen) in suspension culture using serum-free media (Invitrogen) and transfected into HEK293 cells using polyethyleneimine (Polysciences).	HEK293 suggested: None
   Software and Algorithms
   Sentences	Resources
   The results were then converted into percentage neutralization at a given sample dilution or mAb concentration, and the averages ± SEM were plotted using a five-parameter dose-response curve in GraphPad Prism v.8.4.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   Data processing was performed using cryoSPARC v2.15 [14].	cryoSPARC suggested: (cryoSPARC, RRID:SCR_016501)
   Model building and refinement: The 2-36-RBD complex model was built starting from template PDB structures 6BE2 (Fab) and 7BZ5 (RBD) using Phenix Sculptor.	Phenix Sculptor suggested: None
   Automated and manual model building were iteratively performed using real space refinement in Phenix [16] and Coot [17].	Phenix suggested: (Phenix, RRID:SCR_014224) Coot suggested: (Coot, RRID:SCR_014222)
   Geometry validation and structure quality assessment were performed using Molprobity [18].	Molprobity suggested: (MolProbity, RRID:SCR_014226)
   The visualization of sequence entropy was displayed by PyMol version 2.3.2.	PyMol suggested: (PyMOL, RRID:SCR_000305)

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   Results from OddPub: Thank you for sharing your data.

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   Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

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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 10.1101/2021.10.13.464307v1 on bioRxiv

   Oct 14, 2021