Homologous and Heterologous Vaccine Boost Strategies for Humoral and Cellular Immunologic Coverage of the SARS-CoV-2 Omicron Variant

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1. 

   ScreenIT

   Dec 8, 2021

   SciScore for 10.1101/2021.12.02.21267198: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: The BIDMC institutional review board approved this study (2020P000361). 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
   Enzyme-linked immunosorbent assay (ELISA): SARS-CoV-2 spike receptor-binding domain (RBD)-specific binding antibodies in serum were assessed by ELISA as described previously.6,7 96-well plates were coated with 2 μg/mL of SARS-CoV-2 WA1/2020, B.1.617.2 (delta), and B.1.351 (beta) RBD protein in 1× Dulbecco phosphate-buffered saline (DPBS) and incubated at 4 °C overnight.	B…

   SciScore for 10.1101/2021.12.02.21267198: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: The BIDMC institutional review board approved this study (2020P000361). 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
   Enzyme-linked immunosorbent assay (ELISA): SARS-CoV-2 spike receptor-binding domain (RBD)-specific binding antibodies in serum were assessed by ELISA as described previously.6,7 96-well plates were coated with 2 μg/mL of SARS-CoV-2 WA1/2020, B.1.617.2 (delta), and B.1.351 (beta) RBD protein in 1× Dulbecco phosphate-buffered saline (DPBS) and incubated at 4 °C overnight.	B.1.351 suggested: None
   The plates were again washed 3 times and 50 μL of SULFO-Tagged anti-Human IgG detection antibody diluted to 1x in Diluent 100 was added to each well and incubated shaking at 700 rpm at room temperature for at least 1 h.	anti-Human IgG suggested: (RevMAb Biosciences Cat# 31-1019-MK, RRID:AB_2783627)
   6 106 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 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)
   RBD-specific B cell staining: PBMCs were stained with Aqua live/dead dye for 20 min, washed with 2% FBS/DPBS buffer, and cells were suspended in 2% FBS/DPBS buffer with Fc Block (BD) for 10 min, followed by staining with monoclonal antibodies against CD45 (clone HI30, BV786), CD3 (clone UCHT1, APC-R700), CD16 (clone 3G8, BUV496), CD14 (clone M5E2, BV605), CD19 (clone SJ25C, BUV615), CD20 (clone 2H7, PE-Cy5), IgM (clone G20-127, BUV395), IgD (clone IA6-2, PE), CD95 (clone DX2, BV711), CD27 (clone M-T271, BUV563), CD21 (clone B-ly4, PE-CF594), CD38 (clone HB7, BUV805), CD71 (clone M-A712, BV750) and staining with SARS-CoV-2 antigens including biotinylated SARS-CoV-2 (WA1/2020) RBD proteins (Sino Biological), SARS-CoV-2 (WA1/2020) RBD proteins (Sino Biological) labeled with FITC, at 4 °C for 30 min.	CD45 suggested: (Nanostring Cat# 121300104, RRID:AB_2893077) CD3 suggested: (BD Biosciences Cat# 565119, RRID:AB_2744385) CD16 suggested: (BD Biosciences Cat# 751323, RRID:AB_2875332) CD14 suggested: (BD Biosciences Cat# 564054, RRID:AB_2687593) CD19 suggested: (Agilent Cat# TC67401, RRID:AB_579635) CD20 suggested: (BD Biosciences Cat# 740204, RRID:AB_2739954) PE-Cy5), IgM suggested: (Bioss Cat# bs-0336R-PE-Cy5, RRID:AB_10893125) IgD suggested: (Thermo Fisher Scientific Cat# 24-5093-51, RRID:AB_469565) CD95 suggested: (BD Biosciences Cat# 741292, RRID:AB_2870823) CD27 suggested: (BD Biosciences Cat# 751679, RRID:AB_2875665) CD21 suggested: (BD Biosciences Cat# 748726, RRID:AB_2873130) CD38 suggested: (BD Biosciences Cat# 742074, RRID:AB_2871359) CD71 suggested: (BD Biosciences Cat# 746857, RRID:AB_2871661)
   Experimental Models: Cell Lines
   Sentences	Resources
   Pseudovirus neutralizing antibody assay: The SARS-CoV-2 pseudoviruses expressing a luciferase reporter gene were used to measure pseudovirus neutralizing antibodies as described previously.6,7 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)
   The mixture was incubated at 37 °C for 1 h before adding to HEK293T-hACE2 cells.	HEK293T-hACE2 suggested: RRID:CVCL_A7UK)
   Recombinant DNA
   Sentences	Resources
   Pseudovirus neutralizing antibody assay: The SARS-CoV-2 pseudoviruses expressing a luciferase reporter gene were used to measure pseudovirus neutralizing antibodies as described previously.6,7 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™ system.	BD FACSymphony™ suggested: None
   Subsequent analyses were performed using FlowJo software (BD Bioscience, v.9.9.6).	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Statistical analysis: Descriptive statistics were calculated 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
   NCT04999111	Recruiting	A Study of Ad26.COV2.S Administered as Booster Vaccination i…

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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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2. 

   Version published to 10.1101/2021.12.02.21267198 on medRxiv

   Dec 5, 2021