Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient

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1. Version published to 10.1038/s41594-020-0480-y

   Jul 31, 2020
2. 

   ScreenIT

   Jun 14, 2020

   SciScore for 10.1101/2020.06.12.148387: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: The study protocol and informed consent were approved by the ethics committee at the Chang Gung Medical Foundation and the Taoyuan General Hospital, Ministry of Health and Welfare, Taiwan.
   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
   PBMCs were stained with a mix of fluorescent-labelled antibodies to cellular surface markers, including anti-CD3 (BD Biosciences,	anti-CD3 suggested: None
   Sorted single cells were used to produce human IgG monoclonal antibodies as previously described26.	human IgG suggested: None
   T…

   SciScore for 10.1101/2020.06.12.148387: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: The study protocol and informed consent were approved by the ethics committee at the Chang Gung Medical Foundation and the Taoyuan General Hospital, Ministry of Health and Welfare, Taiwan.
   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
   PBMCs were stained with a mix of fluorescent-labelled antibodies to cellular surface markers, including anti-CD3 (BD Biosciences,	anti-CD3 suggested: None
   Sorted single cells were used to produce human IgG monoclonal antibodies as previously described26.	human IgG suggested: None
   The anti-influenza human monoclonal antibody BS 1A (in house), anti-SARS Spike monoclonal antibody CR3022 and convalescent serum were used as controls.	anti-influenza suggested: None anti-SARS suggested: None
   ACE2 expressing cells were then FACS sorted post staining with RBD-6H followed by a secondary anti-His AlexaFluor 647 labelled antibody.	anti-His suggested: None
   30 μL of biotinylated RBD (using EZ-link Sulfo-NHS-Biotin (A39256; Life Technologies)) at 25 nM was added to the titrated antibodies.	Sulfo-NHS-Biotin suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Expression vectors that carry variable domains of heavy and light chains were transfected into the 293T cell line for expression of recombinant full-length human IgG monoclonal antibodies in serum-free transfection medium.	293T suggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)
   Immunofluorescence assay: SARS-CoV-2 (strain CDC-4) infected Vero E6 cells were prepared and fixed with acetone in the biosafety level 3 (BSL-3) laboratory following biosafety rules and guidelines27.	Vero E6 suggested: None
   Cell-based ACE2 blocking assays: MDCK-SIAT1 cells were stably transfected with human ACE2 cDNA using a second-generation lentiviral vector.	MDCK-SIAT1 suggested: ECACC Cat# 05071502, RRID:CVCL_Z936)
   Software and Algorithms
   Sentences	Resources
   Inhibitory concentration at 50 % (IC50) of the antibodies against RBD was determined using non-linear regression [inhibitor] versus normalised response curve fit using GraphPad Prism 8.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   Structural comparisons used SHP39, residues forming the RBD/Fab interface were identified with PISA40, figures were prepared with PyMOL (The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrodinger, LLC).	PyMOL suggested: (PyMOL, RRID:SCR_000305)
   Contrast-transfer-function (CTF) of full-dose and non-weighted micrographs was estimated within a CryoSPARC wrapper for Gctf-v1.0642.	CryoSPARC suggested: (cryoSPARC, RRID:SCR_016501)

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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 10.1101/2020.06.12.148387v1 on bioRxiv

   Jun 13, 2020