Anti-Severe Acute Respiratory Syndrome Coronavirus 2 Hyperimmune Immunoglobulin Demonstrates Potent Neutralization and Antibody-Dependent Cellular Cytotoxicity and Phagocytosis Through N and S Proteins

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1. Version published to 10.1093/infdis/jiab540

   Oct 25, 2021
2. 

   ScreenIT

   Jun 14, 2021

   SciScore for 10.1101/2021.06.11.447942: (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	For CCLA at IRTA-CReSA, SARS-CoV-2 isolated from nasopharyngeal swab from an 89-year-old male patient from Badalona (Spain) in March 2020 (accession ID EPI ISL 418268 at GISAID repository: http://gisaid.org) with the following mutations Spike D614G, NSP12 P323L.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Finally, the capacity of hIG to induce antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP) on the same samples and the viral protein responsible of eliciting these responses were evaluated.	anti…

   SciScore for 10.1101/2021.06.11.447942: (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	For CCLA at IRTA-CReSA, SARS-CoV-2 isolated from nasopharyngeal swab from an 89-year-old male patient from Badalona (Spain) in March 2020 (accession ID EPI ISL 418268 at GISAID repository: http://gisaid.org) with the following mutations Spike D614G, NSP12 P323L.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Finally, the capacity of hIG to induce antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP) on the same samples and the viral protein responsible of eliciting these responses were evaluated.	antibody-dependent cellular phagocytosis ( ADCP suggested: None
   COVID-19 specific antibody levels of the plasma units were classified as high (positive at least at 1/10000 dilution), medium (positive at 1/1000), and low (positive at 1/100) as determined by anti-SARS-CoV-2 S ELISA methods: human anti-SARS-CoV-2 virus spike 1 [S1] IgG ELISA Kit (Alpha Diagnostic Intl.	anti-SARS-CoV-2 suggested: None anti-SARS-CoV-2 virus spike 1 suggested: None
   Potentially accompanying impurity proteins (IgM, IgA, and anti-A, anti-B and anti-D antibodies) are reduced to minimal levels.	IgM suggested: None IgA suggested: None anti-A , anti-B and anti-D antibodies suggested: None anti-A suggested: None anti-B suggested: None anti-D suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   2.3 SARS-CoV-2 Strains: Stock viruses were prepared by collecting the supernatant from Vero cells, as previously described [16].	Vero suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)
   For this assay, a fixed concentration of the SARS-CoV-2 stock (101.8 TCID50/mL, a concentration that achieves 50% cytopathic effect) was mixed with decreasing concentrations of the hIG samples and added to Vero E6 cells.	Vero E6 suggested: RRID:CVCL_XD71)
   Then, 1×104 HEK293T/hACE2 cells treated with DEAE-Dextran (Sigma-Aldrich) were added.	HEK293T/hACE2 suggested: RRID:CVCL_A7UK)
   A SARS-CoV-2 spike glycoprotein cell line was stably developed transfecting the HEK293T cell line with a SARS-CoV-2 spike glycoprotein expression plasmid (Innoprot, Derio, Basque Country, Spain).	HEK293T suggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)
   Recombinant DNA
   Sentences	Resources
   Sequences were human-codon optimized and inserted into pcDNA3.1(+).	pcDNA3.1 suggested: RRID:Addgene_79663)
   HIV reporter pseudovirus expressing SARS-CoV-2 S protein and Luciferase were generated using a plasmid coding for a non-replicative HIV reporter pNL4-3.Luc.R-.	pNL4-3.Luc suggested: None
   Software and Algorithms
   Sentences	Resources
   2.2 Cell Lines and Culture: Each of the four testing laboratories used their own cell lines, as follows: At NIH, Vero cells were acquired from the American Type Culture Collection (ATCC #CCL-81; Manassas, VA, USA) and cultured in DMEM (Lonza, Walkersville, MD, USA) containing 2% FBS (SAFC Biosciences, Lenexa, KS, USA).	SAFC suggested: (SAFC, RRID:SCR_008554)
   Final mutated DNA was then fully sequenced for validation. 2.8 Pseudovirus Generation and Neutralization Assay: In these experiments performed at IrsiCaixa AIDS Research Institute,	IrsiCaixa AIDS Research Institute suggested: None
   The values were normalized, and the ID50 (the reciprocal dilution inhibiting 50% of the infection) was calculated by plotting and fitting the log of plasma dilution vs. response to a 4-parameters equation in Prism 8.4.3 (GraphPad Software, USA).	Prism suggested: (PRISM, RRID:SCR_005375) GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   2.10 Statistics: Neutralization titers were calculated using GraphPad Prism 8 version 8.4.3. nonlinear regression curve fit as half-maximal inhibitory dilution (ID50).	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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   Results from scite Reference Check: We found no unreliable references.

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3. 

   Version published to 10.1101/2021.06.11.447942v1 on bioRxiv

   Jun 11, 2021