Omicron-specific mRNA vaccine elicits potent immune responses in mice, hamsters, and nonhuman primates

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1. Version published to 10.1038/s41422-022-00706-x

   Aug 1, 2022
2. 

   ScreenIT

   Mar 4, 2022

   SciScore for 10.1101/2022.03.01.481391: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	Mouse immunizations: Female BALB/c mice (8–12 weeks old) were randomly allocated to groups.
   Randomization	Mouse immunizations: Female BALB/c mice (8–12 weeks old) were randomly allocated to groups.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The cells were stained with an anti-rabbit fluorescent IgG secondary antibody, and nucleus DNA was stained with DAPI (Sigma-Aldrich).	anti-rabbit fluorescent IgG suggested: None
   Cells were blocked by Fc-receptor blockade with anti-CD16/CD32 (BD Biosciences), and then stained for 30 minutes at 4℃ with the following antibody panel each …

   SciScore for 10.1101/2022.03.01.481391: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	Mouse immunizations: Female BALB/c mice (8–12 weeks old) were randomly allocated to groups.
   Randomization	Mouse immunizations: Female BALB/c mice (8–12 weeks old) were randomly allocated to groups.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The cells were stained with an anti-rabbit fluorescent IgG secondary antibody, and nucleus DNA was stained with DAPI (Sigma-Aldrich).	anti-rabbit fluorescent IgG suggested: None
   Cells were blocked by Fc-receptor blockade with anti-CD16/CD32 (BD Biosciences), and then stained for 30 minutes at 4℃ with the following antibody panel each diluted in PBS: APC/Cyanine7 anti-mouse CD45 antibody (Biolegend) or FITC anti-mouse CD45.2 antibody (Biolegend), APC anti-mouse CD4 antibody (Biolegend),	anti-mouse CD45 suggested: None anti-mouse CD45.2 suggested: None anti-mouse CD4 suggested: None
   anti-mouse CD19 antibody (Biolegend), PE anti-mouse CD8a antibody (Biolegend) or PE anti-mouse/human CD45R/B220 antibody (Biolegend), PerCP/Cyanine5.5	CD19 suggested: None anti-mouse CD8a suggested: None anti-mouse/human CD45R/B220 suggested: None
   anti-mouse/human CD44 antibody (Biolegend)	anti-mouse/human CD44 suggested: None
   APC anti-mouse CD138 (Syndecan-1) antibody (Biolegend), Brilliant Violet 510™ anti-mouse CD62L antibody (Biolegend), FITC anti-mouse CD107a (LAMP-1) antibody (Biolegend),	anti-mouse CD138 suggested: None Syndecan-1 suggested: None anti-mouse CD62L suggested: None anti-mouse CD107a suggested: None LAMP-1 suggested: None
   Then samples were blocked by anti-CD16/CD32 blockade as above, stained for 30 minutes at 4℃ with the following antibody: APC/Cyanine7 anti-mouse CD45 antibody (Biolegend),	anti-CD16/CD32 suggested: None
   anti-mouse CD4 antibody (Biolegend),	CD4 suggested: None
   anti-mouse CD8a antibody (Biolegend).	CD8a suggested: None
   Cells were washed and fixed and permeabilized using Foxp3/Transcription factor staining buffer set (Invitrogen), and stained intracellularly for 30 minutes in PBS with antibodies including: PE anti-mouse IL-4 antibody (Biolegend) or PE anti-mouse IFN-γ antibody (Biolegend)	anti-mouse IL-4 suggested: None
   , APC anti-mouse IL-2 antibody (Biolegend) and FITC anti-human/mouse Granzyme B recombinant antibody (Biolegend).	anti-mouse IL-2 suggested: None anti-human/mouse suggested: None
   After incubation at 37℃, 5% CO2 for 18 h, the plates were washed, and biotinylated anti-mouse IFN-γ, IL-2, or IL-4 antibody was added to each well, following incubation of detection second antibodies.	anti-mouse IFN-γ suggested: None IL-2 suggested: None IL-4 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Vaccine antigen detection by immunofluorescence: Transfected HEK293T cells were fixed in 4% paraformaldehyde (PFA) and permeabilized in PBS/0.1% Triton X-100.	HEK293T suggested: None
   Briefly, virus samples were serially 10-fold diluted with DMEM with 2.5% FBS, and inoculated to Vero cells or Vero E6 seeded overnight at 1.5 × 105 /well in 24-well plates; after incubated at 37°C for 1 h, the inoculate was replaced with DMEM containing 2.5% FBS and 0.9% carboxymethyl-cellulose.	Vero suggested: None Vero E6 suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Mouse immunizations: Female BALB/c mice (8–12 weeks old) were randomly allocated to groups.	BALB/c suggested: RRID:IMSR_ORNL:BALB/cRl)
   Software and Algorithms
   Sentences	Resources
   RNA integrity was assessed by microfluidic capillary electrophoresis (Fragment Analyzer systems 5200, Agilent), and the concentration, pH, residual DNA, proteins, and dsRNA impurities of the solution were determined.	Agilent suggested: (Agilent Bravo NGS, RRID:SCR_019473)
   RLUs of sample wells were normalized with positive control wells, and NT50 was calculated as EC50 by a normalized four-parameter sigmoid curve fit with constrains of EC50 > 0 and hillslope > 0 in Prism 8.0 (GraphPad)	Prism suggested: (PRISM, RRID:SCR_005375) 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: 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 10.1101/2022.03.01.481391v1 on bioRxiv

   Mar 1, 2022