Clinical course impacts early kinetics,magnitude, and amplitude of SARS-CoV-2 neutralizing antibodies beyond 1 year after infection

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1. Version published to 10.1016/j.xcrm.2022.100523

   Feb 1, 2022
2. 

   ScreenIT

   Aug 19, 2021

   SciScore for 10.1101/2021.08.12.21261921: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: SUBJECT DETAILS: Study overview and subjects: The study KING was approved by the Hospital Ethics Committee Board from Hospital Universitari Germans Trias i Pujol (HUGTiP, PI-20-122 and PI-20-217) and was further amended to include vaccinated individuals. Consent: All participants provided written informed consent before inclusion.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   …

   Experimental Models: Cell Lines
   Sentences	Resources
   Cell lines: HEK293T cells overexpressing WT human ACE-2 (Integral Molecular, USA) were used as target in pseudovirus-based neutralization assay.

   SciScore for 10.1101/2021.08.12.21261921: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: SUBJECT DETAILS: Study overview and subjects: The study KING was approved by the Hospital Ethics Committee Board from Hospital Universitari Germans Trias i Pujol (HUGTiP, PI-20-122 and PI-20-217) and was further amended to include vaccinated individuals. Consent: All participants provided written informed consent before inclusion.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   Cell lines: HEK293T cells overexpressing WT human ACE-2 (Integral Molecular, USA) were used as target in pseudovirus-based neutralization assay.	HEK293T suggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)
   Expi293F cells (Thermo Fisher Scientific) are a HEK293 cell derivative adapted for suspension culture that were used for SARS-CoV-2 pseudovirus production.	HEK293 suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)
   Then, 2×104 HEK293T/hACE2 cells treated with DEAE-Dextran (Sigma-Aldrich) were added.	HEK293T/hACE2 suggested: RRID:CVCL_A7UK)
   Recombinant DNA
   Sentences	Resources
   Material availability: The plasmids pcDNA3.4 SARS-CoV-2.SctΔ19 are available upon request to the lead contact.	pcDNA3.4 suggested: RRID:Addgene_131198)
   DETAILS: Pseudovirus generation and neutralization assay: HIV reporter pseudoviruses expressing SARS-CoV-2 S protein and Luciferase were generated. pNL4-3.Luc.R-.	pNL4-3.Luc suggested: None
   E-was obtained from the NIH AIDS Reagent Program.58 SARS-CoV-2.SctΔ19 was generated (GeneArt) from the full protein sequence of SARS-CoV-2 spike with a deletion of the last 19 amino acids in C-terminal,59 human-codon optimized and inserted into pcDNA3.4-TOPO.	pcDNA3.4-TOPO suggested: None
   Software and Algorithms
   Sentences	Resources
   The KING cohort included individuals with a documented positive RT-qPCR result from nasopharyngeal swab and/or a positive serological diagnostic test.	KING suggested: (KING, RRID:SCR_009251)
   The values were normalized, and the ID50 (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 9.0.2 (GraphPad Software, USA)	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   Statistical analyses were performed using R-3.6.3 (R Foundation for Statistical Computing) and Prism 9.0.2 (GraphPad Software)	Prism suggested: (PRISM, RRID:SCR_005375)

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

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3. 

   Version published to 10.1101/2021.08.12.21261921v1 on medRxiv

   Aug 13, 2021