Antibody responses to endemic coronaviruses modulate COVID-19 convalescent plasma functionality

Article activity feed

1. Version published to 10.1172/jci146927

   Apr 1, 2021
2. 

   ScreenIT

   Dec 19, 2020

   SciScore for 10.1101/2020.12.16.20248294: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: All donors provided informed consent and ∼25 mL of blood was collected in acid citrate dextrose (ACD) tubes. IRB: The Johns Hopkins University School of Medicine Institutional Review Board reviewed and approved the sample collection and this study.
   Randomization	not detected.
   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
   (11) Antigen specific antibodies were detected with secondary anti-IgG-PE and median flourescent intensity was measured on a FlexMap 3D array reader.	Antigen suggested: None anti-IgG-PE suggested: (Miltenyi Biotec Cat# …

   SciScore for 10.1101/2020.12.16.20248294: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: All donors provided informed consent and ∼25 mL of blood was collected in acid citrate dextrose (ACD) tubes. IRB: The Johns Hopkins University School of Medicine Institutional Review Board reviewed and approved the sample collection and this study.
   Randomization	not detected.
   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
   (11) Antigen specific antibodies were detected with secondary anti-IgG-PE and median flourescent intensity was measured on a FlexMap 3D array reader.	Antigen suggested: None anti-IgG-PE suggested: (Miltenyi Biotec Cat# 130-093-193, RRID:AB_1036187)
   Experimental Models: Cell Lines
   Sentences	Resources
   The virus was grown and infectious virus titrated on VeroE6TMPRSS2 cells at 33°C in infection media which is identical to the media used to grow the cells except the FBS was reduced to 2.5% as described previously for SARS-CoV-2. (25	VeroE6TMPRSS2 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
   (11) Briefly, uptake of fluorescent RBD-conjugated microspheres by monocytic human THP-1 cells in the presence of convalescent plasma was defined by flow cytometry.	THP-1 suggested: CLS Cat# 300356/p804_THP-1, RRID:CVCL_0006)
   The ability of convalescent plasma to induce luciferase expression in a Jurkat reporter cell line via ligation of FcgRIIIa was defined by culturing on RBD-coated high binding microtiter plates in the presence of convalescent plasma.	Jurkat suggested: TKG Cat# TKG 0209, RRID:CVCL_0065)
   Software and Algorithms
   Sentences	Resources
   First, all of the 56 amino acid peptides from SARS-CoV-2 or the endemic CoVs in the VirScan library were aligned with blastp.	blastp suggested: (BLASTP, RRID:SCR_001010)

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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: We detected the following sentences addressing limitations in the study:

   (23) An important limitation of VirScan is that the phage do not display highly conformational, discontinuous, or glycosylated epitopes. Some, if not most, of the antibody reactivities identified in this study do not confer functional activity to the plasma. However, these reactivities may track closely with functional antibody reactivities that are not detectable by VirScan. Regardless of whether HCoV peptide reactivities are pre-existing or arise in the context of CoV2 infection, we found clear differences in HCoV reactivity between poorly and highly functional plasma. For example, highly functional plasma contained a stronger polyclonal antibody response to NL63. Additionally, HKU1 S CS reactivity confounds prediction of NT AUC, while antibody preference for CoV2 RBD over HKU1 RBD identifies highly active plasma. An understanding of the fine specificities of anti-coronavirus antibody repertoires may be applied to therapeutic plasma prioritization and may serve to generate novel hypotheses regarding the molecular mechanisms underlying the complex immune responses elicited by COVID-19 infection.

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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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3. 

   Version published to 10.1101/2020.12.16.20248294 on medRxiv

   Dec 18, 2020