Potent SARS-CoV-2 binding and neutralization through maturation of iconic SARS-CoV-1 antibodies

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1. Version published to 10.1080/19420862.2021.1922134

   Jan 1, 2021
2. 

   ScreenIT

   Dec 16, 2020

   SciScore for 10.1101/2020.12.14.422791: (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
   Generation of site-directed mutagenesis antibody libraries: m396, CR3022, CR3014, and 80R scFv were gene synthesized (Genscript) and cloned into the pHEN1 phagemid vector.	CR3022 suggested: (Imported from the IEDB Cat# CR3022, RRID:AB_2848080) CR3014 suggested: None
   Plates were washed with PBST, incubated with HRP-conjugated anti-M13 antibody (GE Healthcare) for 1h and washed again.	anti-M13 suggested: None
   The plates were subsequently incubated with …

   SciScore for 10.1101/2020.12.14.422791: (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
   Generation of site-directed mutagenesis antibody libraries: m396, CR3022, CR3014, and 80R scFv were gene synthesized (Genscript) and cloned into the pHEN1 phagemid vector.	CR3022 suggested: (Imported from the IEDB Cat# CR3022, RRID:AB_2848080) CR3014 suggested: None
   Plates were washed with PBST, incubated with HRP-conjugated anti-M13 antibody (GE Healthcare) for 1h and washed again.	anti-M13 suggested: None
   The plates were subsequently incubated with HRP-conjugated chicken anti c-myc antibody (ICL Lab) for 1h and washed again.	anti c-myc suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   The plasmid was transfected into Expi293 cells (Thermo Scientific) according to the manufacturer’s protocol and the protein expressed for 7 days at 37°C, 5% CO2.	Expi293 suggested: RRID:CVCL_D615)
   Retroviral SARS-CoV-1 and 2 pseudo-particles (SARS-2pp) were generated by co-transfecting expression plasmids containing SARS-CoV-1 or SARS-CoV-1 spike which were kindly provided by Prof Gary Whitaker and Dr Markus Hoffmannr, respectively, and the MLV gag/pol and luciferase vectors which were kindly provided by Prof. Francois-Loic Cosset, in CD81KO 293T cells, which were kindly provided by Dr Joe Grove30, using mammalian Calphos transfection kit (Takara Bio)	293T suggested: None
   293T-ACE2 cells were seeded 24 hours earlier at 1.5 × 104 cells per well in 96-well white flat bottom plates (Sigma-Aldrich).	293T-ACE2 suggested: RRID:CVCL_YZ65)
   Experimental Models: Organisms/Strains
   Sentences	Resources
   For the double-Fab 1:1:1 complex (RBD + CR3014-C8 + CR3022-B6), cell content analysis suggested that, should all components be present in the expected stoichiometric ratio, the solvent content would be 50%.	RBD + CR3014-C8 + CR3022-B6 suggested: None
   Software and Algorithms
   Sentences	Resources
   After 3 days, the plates were observed for cytopathic effect (CPE) and IC50 values were calculated from four parameter dose-response curves (GraphPad Prism).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   Extracted particles were subjected to multiple rounds of 2D classification and ab initio reconstruction in cryoSPARC before their locations were exported to Relion 3.0 36.	cryoSPARC suggested: (cryoSPARC, RRID:SCR_016501)
   Motion correction and CTF estimation was then implemented in Relion 3.0 and particles were reextracted and again subjected to 2D classification before 3D auto-refinement and Bayesian polishing.	Relion suggested: (RELION, RRID:SCR_016274)

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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 10.1101/2020.12.14.422791v1 on bioRxiv

   Dec 15, 2020