A role for Nucleocapsid-specific antibody function in Covid-19 Convalescent plasma therapy

Article activity feed

1. 

   ScreenIT

   Feb 25, 2022

   SciScore for 10.1101/2022.02.19.22271230: (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
   Antibody Titer and Fc-Receptor Binding Assays: Antigen-specific antibody subclass, isotype, and Fc-receptor (FcR) binding levels were assayed with a customized multiplexed Luminex bead array, as previously described.	Antigen-specific antibody subclass, isotype, suggested: None
   Antigen-specific antibody titers were detected with Phycoerythrin (PE)-coupled antibodies against IgG1, IgG2, IgG3, IgG4, IgA1, and IgM (SouthernBiotech, Birmingham, AL).	Phycoerythrin ( PE)-coupled antibodies against IgG1 suggested: None IgG1 suggested: None IgG2 suggested: None IgG3 suggested: None IgG4 suggested: None IgA1 suggested: None I…

   SciScore for 10.1101/2022.02.19.22271230: (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
   Antibody Titer and Fc-Receptor Binding Assays: Antigen-specific antibody subclass, isotype, and Fc-receptor (FcR) binding levels were assayed with a customized multiplexed Luminex bead array, as previously described.	Antigen-specific antibody subclass, isotype, suggested: None
   Antigen-specific antibody titers were detected with Phycoerythrin (PE)-coupled antibodies against IgG1, IgG2, IgG3, IgG4, IgA1, and IgM (SouthernBiotech, Birmingham, AL).	Phycoerythrin ( PE)-coupled antibodies against IgG1 suggested: None IgG1 suggested: None IgG2 suggested: None IgG3 suggested: None IgG4 suggested: None IgA1 suggested: None IgM ( SouthernBiotech , Birmingham , AL) suggested: None IgM suggested: None
   PE median fluorescence intensity (MFI) was measured as the readout of each antigen-specific antibody measurements.	antigen-specific suggested: None
   Ab-Directed Functional Assays: Bead-based assays were used to quantify antibody-dependent cellular phagocytosis (ADCP), antibody-dependent neutrophil phagocytosis (ADNP) and antibody-dependent complement deposition (ADCD), as previously described(Ackerman et al., 2018; Ackerman et al., 2011; Fischinger et al., 2019; Karsten et al., 2019; Lu et al., 2016).	antibody-dependent neutrophil phagocytosis ( ADNP suggested: None antibody-dependent complement deposition ( ADCD) suggested: None
   Neutrophils were stained with an anti-CD66b PacBlue detection antibody (Biolegend) and fixed with 4% paraformaldehyde (Alfa Aesar).	anti-CD66b suggested: None
   To measure antibody-dependent deposition of C3, lyophilized guinea pig complement (Cedarlane) was reconstituted according to manufacturer’s instructions and diluted in gelatin veronal buffer with calcium and magnesium (GBV++) (Boston BioProducts) and mixed with immune complexes.	C3 suggested: None
   After a 20-minute incubation at 37°C, C3 was detected with an anti-C3 fluorescein-conjugated goat IgG fraction detection antibody (Mpbio).	anti-C3 fluorescein-conjugated goat IgG suggested: None
   Antibody-dependent NK (ADNK) cell activity was measured via an ELISA-based assay, as described previously (Chung et al., 2015).	Antibody-dependent NK suggested: None
   NK cells were mixed with a staining cocktail containing anti-CD107a BV605 antibody (Biolegand), Golgi stop (BD Biosciences) and Brefeldin A (BFA, Sigma Aldrich).	anti-CD107a suggested: (BioLegend Cat# 328634, RRID:AB_2563851)
   Subsequently, cells were permeabilized using Perm B (Invitrogen) and intracellularly stained with an anti-MIP-1ß-BV421 (BD Biosciences) and IFNγ-PE (BioLegend) antibodies.	anti-MIP-1ß-BV421 suggested: None IFNγ-PE suggested: None
   For the purpose of visualization, the correlation networks were visualized using ‘ggraph’ (v.2.0.4) and ‘igraph’ (v.1.2.6) packages. 4. Mixed Linear Model: We used two nested mixed linear models (null and full model) without/with treatment group information to assess the significance of the association between measured antibody levels and treatment groups while controlling for potential confounding clinical characteristics.	v.2.0.4 suggested: None
   Software and Algorithms
   Sentences	Resources
   The UMAP visualization was performed on principal components whose cumulative explained variance is larger than 90% by umap function in R package ‘umap’ (version 0.2.7.0) with fine-tuning parameters (neighbor = 8, min.dist = 0.1), and visualized by ggplot function in R package ggplot2 (version 3.3.5) Polar Plots: Polar plots were used to visualize the mean percentile of groups in Figure 2C, 3C, 5A.	ggplot2 suggested: (ggplot2, RRID:SCR_014601)

   ---

   Results from OddPub: Thank you for sharing your data.

   ---

   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   Despite these limitations, we were able to use deep humoral immune profiling to understand how CCP modulates host immunodominance and provides clinical benefit. Expanding this approach in larger clinical trials will be essential to validate these findings. The emergence of the omicron variant has rendered most of our monoclonal antibody therapeutics no longer active.(Aggarwal et al., 2021; Cameroni et al., 2021; Cao et al., 2021; Planas et al., 2021) Now there is a renewed interest in use of polyclonal antibody therapies like CCP, which are less likely to loose efficacy to new variants because they target multiple sites in the virus and plasma from survivors of recently circulating variants can be procured relatively quickly. By using a systemic approach to study correlates of therapeutic benefit of CCP, we have found novel targets for future severe COVID-19 disease modifying treatments. Our findings contribute to a burgeoning literature showing the promise of anti-N monoclonal antibodies as disease modifying treatment for severe COVID-19 induced hyperinflammation. Further, our findings show that by choosing CCP based on high S titers alone and selecting patients based on low pre-existing S titers, we are likely incorrectly matching patients with therapies. Finally, our research confirms the importance of the functional S and N antibody response in treatment of COVID-19 disease and should guide development of COVID-19 monoclonal and polyclonal antibody therapeutics that focus...

   ---

   Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04397757	Completed	COVID-19 Convalescent Plasma for the Treatment of Hospitaliz…

   ---

   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

   ---

   Results from JetFighter: We did not find any issues relating to colormaps.

   ---

   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.

   ---

   Results from scite Reference Check: We found no unreliable references.

   ---

   Read the original source
2. 

   Version published to 10.1101/2022.02.19.22271230 on medRxiv

   Feb 22, 2022