Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes

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   ScreenIT

   Mar 15, 2021

   SciScore for 10.1101/2021.03.09.434592: (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
   Anti-T7 tag HRP-conjugated secondary antibodies were diluted at 1:5000 and incubated at room temperature for 1 hour.	Anti-T7 tag suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   To express the S protein, HEK293-ES cells were transiently transfected with the plasmid using polyethyleneimine and 3.5 mM valproic acid sodium salt to enhance protein production.	HEK293-ES suggested: None
   Pseudovirus neutralization assay: The 293T-hsACE2 stable cell line and the pseudotyped SARS-CoV-2 particles (wild-type and mutants) with luciferase reporters were purchased from the Integral Molecular.	293T-hsACE2 sug…

   SciScore for 10.1101/2021.03.09.434592: (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
   Anti-T7 tag HRP-conjugated secondary antibodies were diluted at 1:5000 and incubated at room temperature for 1 hour.	Anti-T7 tag suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   To express the S protein, HEK293-ES cells were transiently transfected with the plasmid using polyethyleneimine and 3.5 mM valproic acid sodium salt to enhance protein production.	HEK293-ES suggested: None
   Pseudovirus neutralization assay: The 293T-hsACE2 stable cell line and the pseudotyped SARS-CoV-2 particles (wild-type and mutants) with luciferase reporters were purchased from the Integral Molecular.	293T-hsACE2 suggested: None
   Software and Algorithms
   Sentences	Resources
   Movies of the specimen were recorded with a nominal defocus setting in the range of −0.5 to −2.5 μm using SerialEM with beam-tilt image-shift data collection strategy with a 3 x 3 pattern and 3 shot per hole.	SerialEM suggested: (SerialEM, RRID:SCR_017293)
   Beam-induced motion correction was performed using the motion correction program implemented in Relion to generate average micrographs and dose-weighted micrographs from all frames.	Relion suggested: (RELION, RRID:SCR_016274)
   For other structures, each movie stack was processed on-the-fly using CryoSPARC live (version 3.0.0) 44,45.	CryoSPARC suggested: (cryoSPARC, RRID:SCR_016501)
   After refinement, each residue of the sequence-updated models was manually checked and refined iteratively in Coot and Phenix.	Coot suggested: (Coot, RRID:SCR_014222) Phenix suggested: (Phenix, RRID:SCR_014224)
   Structural models were validated by MolProbity.	MolProbity suggested: (MolProbity, RRID:SCR_014226)
   The Nb-RBD complex structure was superimposed on its best matched Fab-RBD structure and protein volume was calculated using ProteinVolume51.	ProteinVolume51 suggested: None
   The data was then processed by Prism GraphPad 9.0 to fit into a 4PL curve and to calculate the logIC50 (half-maximal inhibitory concentration).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   Analysis of the data was performed using Excel.	Excel suggested: None

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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: 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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2. 

   Version published to 10.1101/2021.03.09.434592 on bioRxiv

   Mar 10, 2021