Longitudinal characterization of humoral and cellular immunity in hospitalized COVID-19 patients reveal immune persistence up to 9 months after infection

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1. 

   ScreenIT

   Mar 24, 2021

   SciScore for 10.1101/2021.03.17.435581: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: All patients or next of kin and control donors provided informed consent in line with the ethical approval.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Patients were primarily male, with median age of 57 (range 18-76) for moderate and median age of 58 (range 40-74) for severe patients (Figure 1A-C).
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Antibodies against Ki67, IgG, IgA and IgM in permeabilization buffer were added to the cells and incubated in the dark for 30 minutes at 4°C.	Ki67, IgG suggested: None
   SARS-CoV-2-specific antibody ELISAs: RBD-specific …

   SciScore for 10.1101/2021.03.17.435581: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: All patients or next of kin and control donors provided informed consent in line with the ethical approval.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Patients were primarily male, with median age of 57 (range 18-76) for moderate and median age of 58 (range 40-74) for severe patients (Figure 1A-C).
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Antibodies against Ki67, IgG, IgA and IgM in permeabilization buffer were added to the cells and incubated in the dark for 30 minutes at 4°C.	Ki67, IgG suggested: None
   SARS-CoV-2-specific antibody ELISAs: RBD-specific IgG/IgM antibodies was assessed using WANTAI SARS-CoV-2 Ab ELISA (Beijing Wantai Biological Pharmacy Ent.), while S1- and N-specific IgG antibody levels were assessed using semi-quantitative IgG ELISAs (Euroimmun) according to the manufacturer’s instructions.	RBD-specific IgG/IgM suggested: None N-specific IgG suggested: None
   Ethanol-activated low autofluorescent polyvinylidene difluoride membrane plates were coated overnight with either 1) anti-IgA and anti-IgG capture antibodies (15 mg/mL) or 2) SARS-CoV-2 S1 (20 μg/ mL) or N protein (10 mg/mL).	anti-IgA suggested: None anti-IgG suggested: None
   Cells were then discarded from plates and the captured antibodies were developed with anti-human IgG-550 and anti-human IgA-490 detection antibodies (1:500 dilution).	anti-human IgG-550 suggested: None anti-human IgA-490 suggested: None
   All wells with SARS-CoV-2 peptide pool stimulations contained the final concentration of 2 μg/mL of peptides and anti-CD28 antibody diluted at 1:100.	anti-CD28 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Final serum dilutions were incubated for 1 hour at 37°C and 5% CO2 in duplicate and then moved to 96-well plates seeded with confluent Vero E6 cells, followed by a 4-day incubation at 37°C 5% CO2.	Vero E6 suggested: None
   Software and Algorithms
   Sentences	Resources
   Samples were acquired with a BD LSRFortessa (BD Biosciences) followed by analysis with FlowJo software version 10 (FlowJo Inc).	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Statistics: Statistical analyses were performed using GraphPad Prism (GraphPad Software).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   Correlation and hierarchical clustering analysis were performed with GraphPad Prism (v9.0.1) or R (v4.0.2) and RStudio (v1.3.1056) using packages corrplot (v0.84) and heatmaply (v1.1.1).	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798) RStudio suggested: (RStudio, RRID:SCR_000432)

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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:

   Limitations of Study: The current study, although extensive in regard to immunological analyses performed, is limited by a relatively small COVID-19 patient cohort size (acute phase n = 26, 5-months n = 17, and 9-months n = 13). Here, we assessed SARS-CoV-2-specific immune responses in moderately and severely sick COVID-19 patients who required hospitalization, however, we were not able to include asymptomatic or mild cases. Therefore, the longitudinal characteristics and magnitude of the immune responses observed in the current COVID-19 patient cohort may only be applicable to hospitalized patients.

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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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2. 

   Version published to 10.1101/2021.03.17.435581v1 on bioRxiv

   Mar 17, 2021