Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016

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1. Version published to 10.1016/j.xcrm.2021.100255

   Apr 1, 2021
2. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2021.02.17.431683: (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
   Data and Code Availability: Antibodies: The LY-CoV555 antibody variable domain sequences were acquired from the LY-CoV555 crystal structure file (PDB 7KMG, [4]), which was generously shared by Bryan Jones and Eli Lilly and Co. prior to its publication.	LY-CoV555 suggested: None
   Cells were then incubated with 1:200 PE-conjugated goat anti-human-IgG (Jackson ImmunoResearch 109-115-098) to label for bound antibody and 1:100 FITC-conjugated anti-Myc (Immunology Consultants Lab, CYMC-45F) to label for RBD surface expression.	anti-human-IgG suggested: None anti-Myc suggested: None
   Plasmid was purified from pre-sort …

   SciScore for 10.1101/2021.02.17.431683: (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
   Data and Code Availability: Antibodies: The LY-CoV555 antibody variable domain sequences were acquired from the LY-CoV555 crystal structure file (PDB 7KMG, [4]), which was generously shared by Bryan Jones and Eli Lilly and Co. prior to its publication.	LY-CoV555 suggested: None
   Cells were then incubated with 1:200 PE-conjugated goat anti-human-IgG (Jackson ImmunoResearch 109-115-098) to label for bound antibody and 1:100 FITC-conjugated anti-Myc (Immunology Consultants Lab, CYMC-45F) to label for RBD surface expression.	anti-human-IgG suggested: None anti-Myc suggested: None
   Plasmid was purified from pre-sort and antibody-escape populations, and mutant frequencies pre- and post-sort were determined by Illumina sequencing of variant-identifier barcodes, exactly as described in Starr et al. [20].	antibody-escape populations , suggested: None
   The escape fraction of each library variant was determined as the fraction of cells carrying a particular barcode that were sorted into the antibody-escape bin, using the equation given in Greaney et al. [18].	antibody-escape bin suggested: None
   Software and Algorithms
   Sentences	Resources
   3, escape scores were mapped to PDB b-factors and visualized in PyMol using antibody-bound RBD structures PDB 7KMG [4] and PDB 7C01 [22].	PyMol suggested: (PyMOL, RRID:SCR_000305)

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   Results from OddPub: Thank you for sharing your code and 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 10.1101/2021.02.17.431683v1 on bioRxiv

   Feb 22, 2021