A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection

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1. Version published to 10.1016/j.chom.2021.04.005

   May 1, 2021
2. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2021.02.11.430866: (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
   Expression and purification of antibodies: Expression plasmids encoding the heavy (HC) and light chains (LC) of the CV38-142 and CV07-250 (Kreye et al., 2020), COVA1-16 and COVA2-39 (Brouwer et al., 2020), CC12.1 (Rogers et al., 2020), and S309 (Pinto et al., 2020) IgG or Fab were transiently co-transfected into ExpiCHO cells at a ratio of 2:1 (HC:LC) using ExpiFectamine™ CHO Reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions.	COVA2-39 suggested: None S309 suggested: None
   The IgG antibodies and Fabs were purified with a CaptureSelect™ CH1-XL Matrix column (Thermo Fisher …

   SciScore for 10.1101/2021.02.11.430866: (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
   Expression and purification of antibodies: Expression plasmids encoding the heavy (HC) and light chains (LC) of the CV38-142 and CV07-250 (Kreye et al., 2020), COVA1-16 and COVA2-39 (Brouwer et al., 2020), CC12.1 (Rogers et al., 2020), and S309 (Pinto et al., 2020) IgG or Fab were transiently co-transfected into ExpiCHO cells at a ratio of 2:1 (HC:LC) using ExpiFectamine™ CHO Reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions.	COVA2-39 suggested: None S309 suggested: None
   The IgG antibodies and Fabs were purified with a CaptureSelect™ CH1-XL Matrix column (Thermo Fisher Scientific) for affinity purification and a HiLoad Superdex 200 pg column (Cytiva) for size exclusion chromatography.	IgG suggested: None
   The biosensors were transferred to wells containing either SARS-CoV-2 RBD or S-HexaPro proteins in kinetics buffer to allow for antigen association for 200 s followed by testing association of a second antibody Fab or ACE2 for 120 s.	ACE2 suggested: None
   Enzyme-linked immunosorbent assay (ELISA) measuring antibody binding to RBD: Rabbit IgG1 Fc-tagged RBD-SD1 regions of MERS-CoV, SARS-CoV and SARS-CoV-2 as well as point mutants thereof (SARS-CoV: N330Q and T332A, SARS-CoV-2: N343Q and T345A) were expressed in HEK293T cells and immobilized onto 96-well plates as previously described (Kreye et al., 2020).	SARS-CoV-2 suggested: None N343Q suggested: None
   Human anti-spike RBD monoclonal antibodies were applied at 1 μg/ml and detected using horseradish peroxidase (HRP)-conjugated anti-human IgG (Dianova) and the HRP substrate 1-step Ultra TMB (Thermo Fisher Scientific).	anti-human IgG suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   CV38-142 IgG used in the SPR assay was produced in CHO cells and was kindly provided by Miltenyi Biotec, Bergisch Gladbach, Germany.	CHO suggested: CLS Cat# 603479/p746_CHO, RRID:CVCL_0213)
   Pseudovirions were generated by co-transfection of HEK293T cells with plasmids encoding MLV-gag/pol, MLV-CMV-Luciferase, and SARS-CoV-2Δ18 spike (GenBank: MN908947) or SARS-CoV spike (GenBank: AFR58672.1).	HEK293T suggested: None
   After the incubation, 10,000 Hela-hACE2 cells were added to the mixture and supplemented 20 μg/ml Dextran (Sigma, 93556-1G) for enhanced infectivity.	Hela-hACE2 suggested: None
   Software and Algorithms
   Sentences	Resources
   Iterative model building and refinement were carried out in COOT (Emsley and Cowtan, 2004) and PHENIX (Adams et al., 2010), respectively.	COOT suggested: (Coot, RRID:SCR_014222) PHENIX suggested: (Phenix, RRID:SCR_014224)
   Epitope and paratope residues, as well as their interactions, were identified by using PISA program (Krissinel and Henrick, 2007) with buried surface area (BSA >0 Å2) as the criterion.	PISA suggested: (PISA, RRID:SCR_015749)
   Selected 3D classes were auto-refined on Relion and used to illustrate with UCSF Chimera (Pettersen et al., 2004).	Relion suggested: (RELION, RRID:SCR_016274)
   The IgG half-maximal inhibitory concentration (IC50) values were calculated using “One Site - Fit LogIC50” regression in GraphPad Prism 9.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

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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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

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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 10.1101/2021.02.11.430866v1 on bioRxiv

   Feb 12, 2021