SARS-CoV-2 vaccination induces neutralizing antibodies against pandemic and pre-emergent SARS-related coronaviruses in monkeys

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   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2021.02.17.431492: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: The study protocol and all veterinarian procedures were approved by the Bioqual IACUC per a memorandum of understanding with the Duke IACUC, and were performed based on standard operating procedures.
   Randomization	For clusters of size >5, 5 spike sequences were randomly downsampled from each cluster.
   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
   To measure dissociation of the antibody-RBD-scNP complex, the tip was incubated in PBS for 600 s.	antibody-RBD-scNP suggested: None
   Plasma IgG blocking of RBD monoclonal antibody binding: …

   SciScore for 10.1101/2021.02.17.431492: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: The study protocol and all veterinarian procedures were approved by the Bioqual IACUC per a memorandum of understanding with the Duke IACUC, and were performed based on standard operating procedures.
   Randomization	For clusters of size >5, 5 spike sequences were randomly downsampled from each cluster.
   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
   To measure dissociation of the antibody-RBD-scNP complex, the tip was incubated in PBS for 600 s.	antibody-RBD-scNP suggested: None
   Plasma IgG blocking of RBD monoclonal antibody binding: Blocking assays for DH1041 and DH1047 were performed as stated above for ACE2, except plates were coated with either DH1041 or DH1047 instead of ACE2.	ACE2 suggested: None
   Antibody-virus and virus only mixtures were then incubated at 37°C with 5% CO2 for one hour.	Antibody-virus suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   The SARS-CoV-2 RBD was expressed in Freestyle293 cells and purified by StrepTactin affinity chromatography (IBA) and superdex200 size exclusion chromatography as stated above.	Freestyle293 suggested: ATCC Cat# PTA-5080, RRID:CVCL_D603)
   Pseudovirions were produced in HEK 293T/17 cells (ATCC cat. no. CRL-11268) by transfection using Fugene 6 (Promega, Catalog #E2692).	HEK 293T/17 suggested: ATCC Cat# CRL-11268, RRID:CVCL_1926)
   For the 96-well neutralization assay, Vero E6 USAMRID cells were plated at 20,000 cells per well the day prior in clear bottom black walled plates.	Vero E6 suggested: None
   Software and Algorithms
   Sentences	Resources
   The binding response at the end of the 400 s association phase was plotted in GraphPad Prism v9.0.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   Processing of negative stain images: The RELION 3.0 program was used for all negative stain image processing.	RELION suggested: (RELION, RRID:SCR_016274)
   Betacoronavirus sequence analysis: Heatmaps of amino acid sequence similarity were computed for a representative set of betacoronaviruses using the ComplexHeatmap package in R.	ComplexHeatmap suggested: (ComplexHeatmap, RRID:SCR_017270)
   To map group 2b betaCoV sequence conservation onto the RBD structure, group 2b spike sequences were retrieved from Genbank and clustered using USEARCH 67 with a sequence identity threshold of 0.99 resulting in 39 clusters.	USEARCH suggested: (mubiomics, RRID:SCR_006785)
   The resulting set of 73 sequences was aligned using MAFFT 68.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   The conservation scores were then mapped to the RBD domain coordinates (PDB: 7LD1) and images rendered with PyMol version 2.3.5.	PyMol suggested: (PyMOL, RRID:SCR_000305)
   Statistics Analysis: Data were plotted using Prism GraphPad 8.0.	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   Wilcoxon rank sum exact test was performed to compare differences between groups with p-value < 0.05 considered significant using SAS 9.4 (SAS Institute, Cary, NC).	SAS Institute suggested: (Statistical Analysis System, RRID:SCR_008567)

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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: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04177355	Recruiting	Evaluating the Safety and Immunogenicity of HIV-1 BG505 SOSI…

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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: Please consider improving the rainbow (“jet”) colormap(s) used on page 34. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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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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   Read the original source
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   Version published to 10.1101/2021.02.17.431492v1 on bioRxiv

   Feb 17, 2021