Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy

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1. Version published to 10.1016/j.cell.2020.09.035

   Nov 1, 2020
2. 

   ScreenIT

   Jul 11, 2020

   SciScore for 10.1101/2020.07.09.195263: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Anti-His-tag antibodies were loaded to a SA sensor chip by NHS to capture the His-tag labeled S trimer.	Anti-His-tag suggested: None His-tag labeled S trimer. suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   The antibodies were in vitro expressed using HEK293 cells, and the binding specificities were quantity by ELISA against the Spike protein and the RBD protein, as described previously.	HEK293 suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_00…

   SciScore for 10.1101/2020.07.09.195263: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Anti-His-tag antibodies were loaded to a SA sensor chip by NHS to capture the His-tag labeled S trimer.	Anti-His-tag suggested: None His-tag labeled S trimer. suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   The antibodies were in vitro expressed using HEK293 cells, and the binding specificities were quantity by ELISA against the Spike protein and the RBD protein, as described previously.	HEK293 suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)
   Pre-mixed Huh-7 cells were added to all wells and incubated for 24 h at 37 °C and supplied with 5% CO2.	Huh-7 suggested: None
   The Fabs of BD-236, BD-604, and BD-629 were obtained by transient transfection in HEK293F cells using polyethylenimine (Polysciences) when the cell density reached 1 million cells/mL.	HEK293F suggested: RRID:CVCL_6642)
   Software and Algorithms
   Sentences	Resources
   IC50 and IC80 were determined by a four-parameter logistic regression using GraphPad Prism 8.0 (GraphPad Software Inc.)	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   All structures were solved by the molecular replacement method using the Phaser program (McCoy et al., 2007) in Phenix (Liebschner et al., 2019).	Phaser suggested: (Phaser, RRID:SCR_014219) Phenix suggested: (Phenix, RRID:SCR_014224)
   The structural models were then manually adjusted in Coot (Emsley et al., 2010) and refined using Phenix.	Coot suggested: (Coot, RRID:SCR_014222)
   Movies were recorded on a K2 Summit direct electron detector (Gatan) using the SerialEM software (Mastronarde, 2005), in the super-resolution mode at a nominal magnification of 130,000, with an exposure rate of 7.1875 e-/Å2 per second.	SerialEM suggested: (SerialEM, RRID:SCR_017293)
   Raw movie frames were aligned and averaged into motion-corrected summed images with a pixel size of 1.055 Å by MotionCor2 (Zheng et al., 2017).	MotionCor2 suggested: (MotionCor2, RRID:SCR_016499)
   Figures were prepared using Pymol (Schrödinger) and UCSF Chimera.	Pymol suggested: (PyMOL, RRID:SCR_000305)

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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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3. 

   Version published to 10.1101/2020.07.09.195263v1 on bioRxiv

   Jul 9, 2020