Structural basis for potent neutralization of SARS-CoV-2 and role of antibody affinity maturation

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1. Version published to 10.1038/s41467-020-19231-9

   Oct 27, 2020
2. 

   ScreenIT

   Jun 14, 2020

   SciScore for 10.1101/2020.06.12.148692: (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

   Experimental Models: Cell Lines
   Sentences	Resources
   Briefly, plasmids expressing the HIV-1 Gag and pol (pHDM540 Hgpm2), HIV-1Rev (pRC-CMV-rev1b), HIV-1 Tat (pHDM-tat1b), the SARS-CoV-2 spike (pHDM-SARS-CoV-2 Spike) and a luciferase/GFP reporter (pHAGE-CMV-Luc2-IRES542 ZsGreen-W) were co-transfected into 293T cells at a 1:1:1:1.6:4.6 ratio using 293 Free transfection reagent according to the manufacturer’s instructions.	293T suggested: None
   72 hours later the culture supernatant was …

   SciScore for 10.1101/2020.06.12.148692: (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

   Experimental Models: Cell Lines
   Sentences	Resources
   Briefly, plasmids expressing the HIV-1 Gag and pol (pHDM540 Hgpm2), HIV-1Rev (pRC-CMV-rev1b), HIV-1 Tat (pHDM-tat1b), the SARS-CoV-2 spike (pHDM-SARS-CoV-2 Spike) and a luciferase/GFP reporter (pHAGE-CMV-Luc2-IRES542 ZsGreen-W) were co-transfected into 293T cells at a 1:1:1:1.6:4.6 ratio using 293 Free transfection reagent according to the manufacturer’s instructions.	293T suggested: None
   72 hours later the culture supernatant was harvested, clarified by centrifugation and frozen at -80°C. 293 cells stably expressing ACE2 (HEK-293T-hACE2) were seeded at a density of 4×103 cells/well in a 100 µL volume in 96 well flat bottom tissue culture plates.	293 suggested: NIH-ARP Cat# 103-306, RRID:CVCL_0045)
   The media was aspirated from 293T-ACE2 cells and 100 µL of the virus-antibody mixture was added.	293T-ACE2 suggested: RRID:CVCL_YZ65)
   Software and Algorithms
   Sentences	Resources
   Structural figures were made in Pymol.	Pymol suggested: (PyMOL, RRID:SCR_000305)
   The antibody concentration that neutralized 50% of infectivity (IC50) was interpolated from the neutralization curves determined using the log(inhibitor) vs. response -- Variable slope (four parameters) fit using automatic outlier detection in Graphpad Prism Software.	Graphpad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

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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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3. 

   Version published to 10.1101/2020.06.12.148692v1 on bioRxiv

   Jun 12, 2020