Vaccines elicit highly conserved cellular immunity to SARS-CoV-2 Omicron

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1. Version published to 10.1038/s41586-022-04465-y

   Jan 31, 2022
2. 

   ScreenIT

   Jan 6, 2022

   SciScore for 10.1101/2022.01.02.22268634: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Both studies were approved by the BIDMC institutional review board. Consent: All participants provided informed consent.
   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

   Antibodies
   Sentences	Resources
   The plates were washed with ELISPOT wash buffer and incubated for 2-4 h with Biotinylated mouse anti-human IFN-γ monoclonal antibody from MabTech (1 µg/mL).	anti-human IFN-γ suggested: None
   106 peripheral blood mononuclear cells well were re-suspended in 100 µL of R10 media supplemented with CD49d monoclonal antibody (1 µg/mL) and CD28 monoclonal antibody (1 µg/mL).	CD49d suggest…

   SciScore for 10.1101/2022.01.02.22268634: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Both studies were approved by the BIDMC institutional review board. Consent: All participants provided informed consent.
   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

   Antibodies
   Sentences	Resources
   The plates were washed with ELISPOT wash buffer and incubated for 2-4 h with Biotinylated mouse anti-human IFN-γ monoclonal antibody from MabTech (1 µg/mL).	anti-human IFN-γ suggested: None
   106 peripheral blood mononuclear cells well were re-suspended in 100 µL of R10 media supplemented with CD49d monoclonal antibody (1 µg/mL) and CD28 monoclonal antibody (1 µg/mL).	CD49d suggested: (BD Biosciences Cat# 347690, RRID:AB_647457) CD28 suggested: None
   The next day, the cells were washed twice with DPBS, stained with aqua live/dead dye for 10 mins and then stained with predetermined titers of monoclonal antibodies against CD279 (clone EH12.1, BB700), CD4 (clone L200, BV711), CD27 (clone M-T271, BUV563), CD8 (clone SK1, BUV805), CD45RA (clone 5H9, APC H7) for 30 min.	CD279 suggested: (BD Biosciences Cat# 566460, RRID:AB_2744348) CD4 suggested: None CD27 suggested: (BD Biosciences Cat# 748705, RRID:AB_2873109) CD8 suggested: (Abcam Cat# ab34397, RRID:AB_2291359) CD45RA suggested: None
   Cells were washed twice with 1X Perm Wash buffer (BD Perm/WashTM Buffer 10X in the CytoFix/CytoPerm Fixation/ Permeabilization kit diluted with MilliQ water and passed through 0.22µm filter) and stained with intracellularly with monoclonal antibodies against IFN-γ (clone B27; BUV395), and CD3 (clone SP34.2, Alexa 700), for 30 min.	IFN-γ suggested: (BD Biosciences Cat# 563563, RRID:AB_2738277) CD3 suggested: (BD Biosciences Cat# 556610, RRID:AB_396483)
   Experimental Models: Cell Lines
   Sentences	Resources
   In brief, the packaging construct psPAX2 (AIDS Resource and Reagent Program), luciferase reporter plasmid pLenti-CMV Puro-Luc (Addgene) and spike protein expressing pcDNA3.1-SARS-CoV-2 SΔCT were co-transfected into HEK293T cells (ATCC CRL_3216) with lipofectamine 2000 (ThermoFisher Scientific).	HEK293T suggested: ATCC Cat# CRL-3216, RRID:CVCL_0063)
   To determine the neutralization activity of human serum, HEK293T-hACE2 cells were seeded in 96-well tissue culture plates at a density of 1.75 × 104 cells per well overnight.	HEK293T-hACE2 suggested: RRID:CVCL_A7UK)
   Recombinant DNA
   Sentences	Resources
   In brief, the packaging construct psPAX2 (AIDS Resource and Reagent Program), luciferase reporter plasmid pLenti-CMV Puro-Luc (Addgene) and spike protein expressing pcDNA3.1-SARS-CoV-2 SΔCT were co-transfected into HEK293T cells (ATCC CRL_3216) with lipofectamine 2000 (ThermoFisher Scientific).	psPAX2 suggested: RRID:Addgene_12260) pLenti-CMV Puro-Luc suggested: None pcDNA3.1-SARS-CoV-2 suggested: None
   Software and Algorithms
   Sentences	Resources
   Fixed cells were transferred to 96-well round bottom plate and analyzed by BD FACSymphony(tm) system.	BD FACSymphony(tm suggested: None
   Data were analyzed using FlowJo v9.9.	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Statistical analysis: Descriptive statistics and logistic regression were performed using GraphPad Prism 8.4.3, (GraphPad Software, San Diego, California).	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798) 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: 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
   NCT04436276	Active, not recruiting	A Study of Ad26.COV2.S in Adults (COVID-19)

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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 10.1101/2022.01.02.22268634v1 on medRxiv

   Jan 3, 2022