Comorbid illnesses are associated with altered adaptive immune responses to SARS-CoV-2

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1. Version published to 10.1172/jci.insight.146242

   Mar 22, 2021
2. 

   ScreenIT

   Nov 30, 2020

   SciScore for 10.1101/2020.11.25.20235150: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: Study Approval: The studies were approved by the University of Washington Human Subjects Institutional Review Board, and all participants, or their legally authorized representatives, completed informed consent. Consent: Study Approval: The studies were approved by the University of Washington Human Subjects Institutional Review Board, and all participants, or their legally authorized representatives, completed informed consent.
   Randomization	not detected.
   Blinding	All experiments were performed in duplicate while operators were blinded to study group assignment, and all cases and controls were run at the same time to avoid batch effects.
   Power Analysis	not …

   SciScore for 10.1101/2020.11.25.20235150: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: Study Approval: The studies were approved by the University of Washington Human Subjects Institutional Review Board, and all participants, or their legally authorized representatives, completed informed consent. Consent: Study Approval: The studies were approved by the University of Washington Human Subjects Institutional Review Board, and all participants, or their legally authorized representatives, completed informed consent.
   Randomization	not detected.
   Blinding	All experiments were performed in duplicate while operators were blinded to study group assignment, and all cases and controls were run at the same time to avoid batch effects.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Antibody titer measurements and FcR binding: In order to measure antigen-specific antibody subclass, isotype, and Fc-receptor (FcR) binding levels, a customized multiplexed Luminex assay was utilized, as previously described(57).	antigen-specific antibody subclass , isotype , suggested: None
   Antigen-specific antibody titers were detected with Phycoerythrin (PE)-coupled antibodies against IgG1, IgG2, IgG3, IgG4, IgA, 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 IgA suggested: None IgM ( SouthernBiotech , Birmingham , AL) suggested: None IgM suggested: None
   Functional antibody measurements: 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 (58–60).	antibody-dependent neutrophil phagocytosis ( ADNP) , suggested: None antibody-dependent complement deposition ( ADCD) suggested: None
   Then, a PacBlue anti-CD66b detection antibody (clone G10F5) (RUO) (BioLegend, San Diego, CA) was used to stain neutrophils.	anti-CD66b suggested: None
   anti-CD56 PE-Cy7 (clone B159), and anti-CD3 PacBlue (clone SP34-2) antibodies (BD Biosciences, San Jose, CA).	PE-Cy7 suggested: (BD Biosciences Cat# 557749, RRID:AB_396855) anti-CD3 suggested: None
   Antibodies included anti-CD3 ECD (clone UCHT1) (Beckman Coulter, Brea, CA)	anti-CD3 ECD suggested: None
   A preparation of anti-CCR7 BV711 antibody (clone 150503) (BD Biosciences, San Jose, CA) in FACS buffer was centrifuged at 10,000xg for 5 minutes and then added to the cells for 30 minutes at 37°C.	anti-CCR7 BV711 suggested: (BD Biosciences Cat# 566752, RRID:AB_2869849)
   Experimental Models: Cell Lines
   Sentences	Resources
   luciferase reporter plasmid pLenti-CMV Puro-Luc (Addgene, Watertown, MA), and spike protein expressing pcDNA3.1-SARS CoV-2 SΔCT were co-transfected into HEK293T cells by lipofectamine 2,000 (Thermo Fisher Scientific, Waltham, MA).	HEK293T suggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)
   The mixture was incubated at 37°C for 1 hour before adding to HEK293T-hACE2 cells.	HEK293T-hACE2 suggested: None
   For measuring monocyte phagocytosis, 2.5×104 THP-1 cells (ATCC, Manassas, VA) were added per well and incubated for 16 hours at 37°C.	THP-1 suggested: None
   Software and Algorithms
   Sentences	Resources
   The supernatant was decanted, and the viable cells were enumerated using the Guava easyCyte (MilliporeSigma, Burlington, MA) with guavaSoft 2.6 software.	guavaSoft suggested: None

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   Results from OddPub: Thank you for sharing your data.

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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: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04338360	Approved for marketing	Expanded Access to Convalescent Plasma for the Treatment of …

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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 10.1101/2020.11.25.20235150v1 on medRxiv

   Nov 30, 2020