SARS-CoV-2-induced humoral immunity through B cell epitope analysis in COVID-19 infected individuals

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1. Version published to 10.1038/s41598-021-85202-9

   Mar 15, 2021
2. 

   ScreenIT

   Jul 25, 2020

   SciScore for 10.1101/2020.07.22.212761: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: The protocol was approved by the ethical committee of Osaka University Hospital (No. 19546)
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Control serum was obtained from pooled human serum (#BJ11787, Tennessee Blood Services, TN, USA) mixed from five males and five females, which were collected in February 2019 and confirmed to be noninfected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Antibody test kits: SARS-CoV-2-specific IgG and IgM antibodies of serum samples collected from COVID-19 patients were detected using a rapid immunochromatographic test for …

   SciScore for 10.1101/2020.07.22.212761: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: The protocol was approved by the ethical committee of Osaka University Hospital (No. 19546)
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Control serum was obtained from pooled human serum (#BJ11787, Tennessee Blood Services, TN, USA) mixed from five males and five females, which were collected in February 2019 and confirmed to be noninfected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Antibody test kits: SARS-CoV-2-specific IgG and IgM antibodies of serum samples collected from COVID-19 patients were detected using a rapid immunochromatographic test for detecting antibodies against SARS-CoV-2 (IgM; RF-NC001, IgG; RF-NC002, KURABO, Japan), a 2019-nCoV IgG/IgM detection kit (C6603C, Vazyme, China), a COVID-19 Human IgM/IgG Rapid Test (DC0301	IgM suggested: (Abgent Cat# AM2019a, RRID:AB_11138086) SARS-CoV-2 suggested: None
   After washing each well with 0.05% PBS Tween-20 (PBS-T), the cells were incubated with horseradish peroxidase (HRP)-conjugated antibodies specific for human IgG (1:10,000; AP004	human IgG suggested: None
   For the IgG subclass determination assay, anti-human IgG subclass-specific HRP-conjugated antibodies (1:10,000; IgG1 (AP006), IgG2 (AP007), IgG3 (AP008), and IgG4 (AP009), Binding Site) were used.	anti-human IgG subclass-specific HRP-conjugated antibodies ( 1:10,000; IgG1 suggested: None AP006 suggested: None IgG2 suggested: None AP007 suggested: None IgG3 suggested: None AP008 suggested: None IgG4 suggested: None AP009 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Either 293T or BHK cells were grown to 90% confluence on 35-mm tissue culture plates.	BHK suggested: None
   Software and Algorithms
   Sentences	Resources
   After washing the wells with PBS-T, color was developed with the peroxidase chromogenic substrate 3,3’,5,5’-tetramethylbenzidine (TMB; Sigma Aldrich, MO, USA), and the reactions were terminated with 0.9 N sulfuric acid.	TMB; Sigma Aldrich suggested: None
   Peptide array: CelluSpots peptide array was performed using CelluSpots™ covid19_hullB (98.301, Intavis) or CelluSpots™ covid19_hullS (98.302, Intavis) according to the manufacturers’ instructions: blocked by immersing the slides in PBS containing 5% skim milk overnight at 4°C on an orbital shaker, incubated with diluted serum samples (1:10) overnight at 4°C on an orbital shaker, washed with PBS-T buffer with 0.05% Tween-20, and incubated with diluted HRP-conjugated antibodies specific for human IgG (1:10,000; AP004	CelluSpots™ suggested: None
   A chemiluminescent signal visualized by Chemi-Lumi One L (07880-70, Nacalai Tesque) was detected with a ChemiDoc Touch imaging system (Bio-Rad) and analyzed with Image Lab software version 6.0.1 (Bio-Rad).	Image Lab suggested: (Image Lab Software, RRID:SCR_014210)
   Statistical analysis was performed using Prism GraphPad version 6.07 (GraphPad Software).	Prism suggested: (PRISM, RRID:SCR_005375) GraphPad 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: We detected the following sentences addressing limitations in the study:

   As a study limitation, this study protocol has been approved to analyze only human serum samples without any clinical information. Because the onset of infection or severity of patients cannot be known, we cannot discuss the time course of antibodies with the clinical status of the patients. Although the magnitude of IgG production might be dependent on the duration of COVID-19, we can evaluate the dominant B cell epitope of each patient. There have been concerns regarding vaccine enhancement of disease by certain candidate COVID-19 vaccine approaches via antibody-dependent enhancement (ADE). This phenomenon is observed when non-neutralizing virus-specific IgG facilitates entry of virus particles into Fc-receptor-expressing cells, leading to inflammatory activation of macrophages and monocytes (Taylor et al, 2015). A study in SARS-CoV-1-infected rhesus macaques found that anti-S IgG contributes to severe acute lung injury (ALI) and massive accumulation of monocytes/macrophages in the lung (Liu et al, 2019). To avoid this phenomenon, a specific neutralizing antibody is required, which can also be achieved by a B cell epitope vaccine. Therefore, we speculate that the next generation of vaccines for COVID-19 should consider the B cell epitope in terms of safety and efficiency. In summary, we conducted full B cell epitope mapping and validated the predicted B cell epitope of S protein, utilizing human sera from patients with COVID-19. Based on the analysis of neutralizing activit...

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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 10.1101/2020.07.22.212761v1 on bioRxiv

   Jul 23, 2020