Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2

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1. Version published to 10.1038/s41586-021-04388-0

   Dec 23, 2021
2. 

   ScreenIT

   Dec 21, 2021

   SciScore for 10.1101/2021.12.14.472719: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: All collections were conducted under protocols reviewed and approved by the Institutional Review Board of Columbia University.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	Cytopathic effects were then visually assessed in all wells and scored as either negative or positive for infection by comparison to control uninfected or infected wells in a blinded manner.
   Power Analysis	not detected.
   Cell Line Authentication	Authentication: Viruses were propagated in Vero-E6-TMPRSS2 cells and sequence confirmed by next-generation sequencing prior to use.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The structures of antibody-spike complexes were also obtained from PDB (7L5B …

   SciScore for 10.1101/2021.12.14.472719: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: All collections were conducted under protocols reviewed and approved by the Institutional Review Board of Columbia University.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	Cytopathic effects were then visually assessed in all wells and scored as either negative or positive for infection by comparison to control uninfected or infected wells in a blinded manner.
   Power Analysis	not detected.
   Cell Line Authentication	Authentication: Viruses were propagated in Vero-E6-TMPRSS2 cells and sequence confirmed by next-generation sequencing prior to use.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The structures of antibody-spike complexes were also obtained from PDB (7L5B for 2-15, 6XDG for REGN10933 and REGN10987, 7L2E for 4-18, 7RW2 for 5-7, 7C01 for CB6, 7KMG for LY-COV555, 7CDI for Brii-196, 7KS9 for 910-30, 7LD1 for DH1047, 7RAL for S2X259, 7LSS for 2-7, and 6WPT for S309).	REGN10987 suggested: None CB6 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Monoclonal antibodies: Antibodies were expressed as previously described22, by synthesis of VH and VL genes (GenScript), transfection of Expi293 cells (Thermo Fisher), and affinity purification from the supernatant by rProtein A Sepharose (GE).	Expi293 suggested: RRID:CVCL_D615)
   Briefly, HEK293T cells were transfected with a spike expression construct with PEI (1 mg/mL) and cultured overnight at 37 °C under 5% CO2, and then infected with VSV-G pseudotyped ΔG-luciferase (G*ΔG-luciferase, Kerafast) one day post-transfection.	HEK293T suggested: None
   Vero-E6 cells (ATCC) were then added at a density of 3 × 104 cells per well and plates were incubated at 37 °C for approximately 10 h.	Vero-E6 suggested: None
   Viruses were propagated in Vero-E6-TMPRSS2 cells and sequence confirmed by next-generation sequencing prior to use.	Vero-E6-TMPRSS2 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
   Software and Algorithms
   Sentences	Resources
   Raw reads were processed by Cutadapt v2.138 with default setting to remove adapters and then aligned to reference variants sequences using Bowtie2 v2.3.439 with default setting.	Cutadapt suggested: (cutadapt, RRID:SCR_011841) Bowtie2 suggested: (Bowtie 2, RRID:SCR_016368)
   Neutralization curves and IC50 values were derived by fitting a non-linear five-parameter dose-response curve to the data in GraphPad Prism version 9.2.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   The border for each footprint was then optimized by ImageMagick 7.0.10-31 (	ImageMagick suggested: (ImageMagick, RRID:SCR_014491)
   PyMOL 2.3.2 was used to perform mutagenesis and to make structural plots (Schrödinger).	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: Please consider improving the rainbow (“jet”) colormap(s) used on page 11. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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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 10.1101/2021.12.14.472719 on bioRxiv

   Dec 15, 2021