Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display

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1. Version published to 10.1016/j.celrep.2022.110348

   Feb 1, 2022
2. 

   ScreenIT

   Sep 17, 2021

   SciScore for 10.1101/2021.09.14.460356: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   g, anti-Human antibody was added to the wells and incubated for 1 hour followed by six washes as before.	anti-Human suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   RBD-SD1, wild type RBD and mutant RBD domains were subcloned into pcDNA.	RBD-SD1 suggested: None
   One day before transfection, CHO-S cells were seeded at a density of 1 x 106 cells/mL in 45 mL culture flask.	CHO-S suggested: None
   Lipofectamine® transient transfection of RBD constructs: For transient expression of …

   SciScore for 10.1101/2021.09.14.460356: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   g, anti-Human antibody was added to the wells and incubated for 1 hour followed by six washes as before.	anti-Human suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   RBD-SD1, wild type RBD and mutant RBD domains were subcloned into pcDNA.	RBD-SD1 suggested: None
   One day before transfection, CHO-S cells were seeded at a density of 1 x 106 cells/mL in 45 mL culture flask.	CHO-S suggested: None
   Lipofectamine® transient transfection of RBD constructs: For transient expression of RBD-SD1, RBD wild-type and RBD mutants, 293T cells were cultured and and incubated at at 37℃ with 5% CO2.	293T suggested: None
   Vero E6 neutralization assay: All aspects of the assay utilizing virus were performed in a BSL3 containment facility according to the ISMMS Conventional Biocontainment Facility SOPs for SARS-CoV-2 cell culture studies.	Vero E6 suggested: RRID:CVCL_XD71)
   After incubation with 293TACE2 cells for 48 hours at 37°C, cells were washed twice with PBS, lysed with Luciferase Cell Culture Lysis 5x reagent (Promega), and NanoLuc Luciferase activity in lysates was measured using the Nano-Glo Luciferase Assay System (Promega)	293TACE2 suggested: RRID:CVCL_YZ65)
   Recombinant DNA
   Sentences	Resources
   SARS-CoV-2 Spike ECD 1-1208 (682-GSAS-685; 986-PP-987) fused to the T4 fibritin trimerization domain with C-terminal Avi- and His-tag were synthesized with gene block (IDT) and cloned into pcDNA.	pcDNA suggested: RRID:Addgene_66792)
   On the day of transfection, 75 µL of FectoPRO® transfection reagent (PolyPlus-transfection®) was mixed with 5 mL of 15 µg/mL pcDNA3 plasmid DNA harboring antibody encoding sequence in CD-CHO media and incubated for 10 min at room temperature.	pcDNA3 suggested: RRID:Addgene_15475)
   Software and Algorithms
   Sentences	Resources
   The atomic models and cryo-EM maps generated for the N-612-017, N-612-014, and N-612-004 Fabs complexed with SARS-CoV-2 S have been deposited at the PDB (http://www.rcsb.org/) and the Electron Microscopy Databank (EMDB) (http://www.emdataresource.org/) under accession codes 7S0C, 7S0D, 7S0E and EMD-24786, EMD-24787, EMD-24788, respectively.	http://www.emdataresource.org/ suggested: (EMDataResource.org, RRID:SCR_003207)
   Half-maximal inhibitory concentrations (IC50 values) for mAbs were determined using 4-parameter nonlinear regression (Prism, GraphPad).	Prism suggested: (PRISM, RRID:SCR_005375) GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   Movies were collected using a 3x3 beam image shift pattern with SerialEM automated data collection software (Mastronarde, 2005) at a nominal magnification of 45,000x (super-resolution 0.4345 Å/pixel) using a defocus range of −0.7 to −2.0 µm.	SerialEM suggested: (SerialEM, RRID:SCR_017293)
   For all datasets, movies were patch motion corrected for beam-induced motion including dose-weighting within cryoSPARC v3.1 (Punjani et al.,	cryoSPARC suggested: (cryoSPARC, RRID:SCR_016501)
   Coordinates were rigid body and B-factor refined in PHENIX v1.19 (Adams et al., 2010) followed by sequence matching and repeated cycles of phenix.	PHENIX suggested: (Phenix, RRID:SCR_014224)
   refine and manual building in Coot (v0.9.3) (Emsley et al., 2010) (Table S6)	Coot suggested: (Coot, RRID:SCR_014222)

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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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   Results from scite Reference Check: We found no unreliable references.

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3. 

   Version published to 10.1101/2021.09.14.460356 on bioRxiv

   Sep 15, 2021