Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies

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1. Version published to 10.1016/j.cell.2020.06.025

   Aug 1, 2020
2. 

   ScreenIT

   Jun 9, 2020

   SciScore for 10.1101/2020.05.28.121533: (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
   After 2 h incubation at RT, plates were washed 5 times with washing buffer and incubated with goat-anti-human IgG or goat-anti-human IgG(H+L) secondary antibody conjugated to horseradish peroxidase (HRP) (SouthernBiotech) in blocking buffer at a 1:4000 or 1:2000 dilution, respectively.	IgG suggested: None goat-anti-human IgG(H+L suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   For SARS-CoV-2, MERS-CoV, HCoV-NL63 and HCoV-OC43 mutations to remove the S1/S2 furin cleavage site were introduced.	HCoV-NL63 suggested: RRID:CVCL_RW88)
   After incubation with 293TACE2 cells for 48 hours at 37°C, cells …

   SciScore for 10.1101/2020.05.28.121533: (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
   After 2 h incubation at RT, plates were washed 5 times with washing buffer and incubated with goat-anti-human IgG or goat-anti-human IgG(H+L) secondary antibody conjugated to horseradish peroxidase (HRP) (SouthernBiotech) in blocking buffer at a 1:4000 or 1:2000 dilution, respectively.	IgG suggested: None goat-anti-human IgG(H+L suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   For SARS-CoV-2, MERS-CoV, HCoV-NL63 and HCoV-OC43 mutations to remove the S1/S2 furin cleavage site were introduced.	HCoV-NL63 suggested: RRID:CVCL_RW88)
   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)
   Software and Algorithms
   Sentences	Resources
   Phylogenetic trees: Sequence alignments of S proteins and RBD/S1B domains were made with Clustal Omega (Sievers et al., 2011).	Clustal Omega suggested: (Clustal Omega, RRID:SCR_001591)
   Phylogenetic trees were calculated from these amino acid alignments using PhyML 3.0 (Guindon et al., 2010) and visualized with PRESTO (http://www.atgc-montpellier.fr/presto).	PhyML suggested: (PhyML, RRID:SCR_014629)
   The developing reaction was quenched by addition of 100µl 1N HCl and absorbance was measured at 450nm using Gen5 software on a Synergy Neo2 Reader (BioTek)	Gen5 suggested: (Gen5, RRID:SCR_017317)
   Half-maximal inhibitory concentrations (IC50 values) for purified plasma IgGs and Fabs were determined as molar concentrations (to account for the IgG versus Fab difference in molecular weight) using 4-parameter nonlinear regression (Prism, GraphPad).	Prism suggested: (PRISM, RRID:SCR_005375) GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   Grids were imaged at 300 keV using a Titan Krios transmission electron microscope (Thermo Fisher) operating at RT, equipped with a K3 direct electron detector (Gatan) using SerialEM 3.7? (Mastronarde, 2005).	SerialEM suggested: (SerialEM, RRID:SCR_017293)
   Extracted particles were used to generate ab initio models in cryoSPARC that were further processed by 3D classification to separate out complexes and S trimer structures alone.	cryoSPARC suggested: (cryoSPARC, RRID:SCR_016501)
   The C105 Fab coordinates were refined using Phenix (Adams et al., 2010) and cycles of manual building in Coot (Emsley et al., 2010) (Table S1).	Phenix suggested: (Phenix, RRID:SCR_014224) Coot suggested: (Coot, RRID:SCR_014222)

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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 10.1101/2020.05.28.121533v1 on bioRxiv

   May 29, 2020