Multi-clonal SARS-CoV-2 neutralization by antibodies isolated from severe COVID-19 convalescent donors

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1. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2020.10.06.323634: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Ethics statement: All COVID-19 convalescent donors, between the ages 25 and 65 recruited for this study provided a written informed consent prior to participating in this study. IRB: Tel Aviv University Institutional Review Board (IRB) approved all studies involving patient enrollment, sample collection, and clinical follow-up (protocol number 0001255-1).
   Randomization	not detected.
   Blinding	Plaque assays were performed and counted by a blinded experimenter.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Plates were then washed 3 times with washing buffer …

   SciScore for 10.1101/2020.10.06.323634: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Ethics statement: All COVID-19 convalescent donors, between the ages 25 and 65 recruited for this study provided a written informed consent prior to participating in this study. IRB: Tel Aviv University Institutional Review Board (IRB) approved all studies involving patient enrollment, sample collection, and clinical follow-up (protocol number 0001255-1).
   Randomization	not detected.
   Blinding	Plaque assays were performed and counted by a blinded experimenter.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Plates were then washed 3 times with washing buffer before adding secondary anti-IgG, or -IgM (Jackson ImmmunoResearch 109-035-088 & 109-035-129) or anti-IgA (abcam ab97215) antibodies conjugated to horseradish peroxidase (HRP) diluted 1:5000 in blocking buffer, and incubated for 45 min at RT.	anti-IgG suggested: (Vector Laboratories Cat# BA-5000, RRID:AB_2336126) anti-IgA suggested: None
   After 3 washes, the plates were incubated at RT with a secondary anti-rabbit HRP-conjugated antibody (Jackson, West Grove, PA) at a dilution of 1:2500 in blocking solution for 45 min.	anti-rabbit suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   HEK-293 cells stably expressing hACE2 were seeded into 0.1 % Gelatin-coated 96-well plates (Greiner) at an initial density of 0.75 x 105 cells per well.	HEK-293 suggested: None
   The following day, titrations of mAbs were incubated with 104 PFU for 1 h in DMEM 10% FBS at room temperature, then added to Vero E6 cells for up to 48 h.	Vero E6 suggested: None
   Cell-to-cell fusion assay: HEK-293T cells were plated in a 6-well plate (Greiner) at an initial density of 0.5 x 106 cells per well.	HEK-293T suggested: None
   Software and Algorithms
   Sentences	Resources
   Libraries were sequenced by Genewiz on a NovaSeq 6000 System using the S4 2x 150 kit (Illumina).	Genewiz suggested: (GENEWIZ, RRID:SCR_003177)
   IC50 and IC80 were calculated by GraphPad Prism software fitting to a non-linear regression model.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   Fixed cells were washed with PBS x1 and permeabilized for immunofluorescence using BD Cytofix/Cytoperm according to the manufacturer’s protocol for fixed cells and stained for SARS-CoV-2 with a primary Nucleocapsid antibody (GeneTex GTX135357) conjugated to AF594 (ThermoFisher A20185) and nuclei counterstained with Hoechst. Eight images per well were obtained using a Nikon Ti2-E microscope equipped with a Spectra III light engine (Lumencor), appropriate filter cubes (Semrock), and a Qi-2 camera.	BD Cytofix/Cytoperm suggested: None
   For images acquired with the Nikon Ti2-E, analysis was performed using custom-scripted code for the Fiji distribution of ImageJ (PMID 22743772) and the DeepLearning plugin StarDist (Schmidt et al, 2012 – see below) as follows.	Fiji suggested: (Fiji, RRID:SCR_002285) ImageJ suggested: (ImageJ, RRID:SCR_003070)
   Data from all fields of view was logged and graphed with Graphpad Prism39	Graphpad suggested: (GraphPad, RRID:SCR_000306)

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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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   Read the original source
2. Version published to 10.1371/journal.ppat.1009165

   Feb 11, 2021
3. 

   Version published to 10.1101/2020.10.06.323634v1 on bioRxiv

   Oct 6, 2020