Replicating RNA platform enables rapid response to the SARS-CoV-2 Omicron variant and elicits enhanced protection in naïve hamsters compared to ancestral vaccine

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1. Version published to 10.1016/j.ebiom.2022.104196

   Sep 1, 2022
2. 

   ScreenIT

   Feb 6, 2022

   SciScore for 10.1101/2022.01.31.478520: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: Animal experiments were approved by the corresponding institutional animal care and use committee and performed by experienced personnel under veterinary oversight.
   Sex as a biological variable	Mouse studies: Six-to-eight-week-old female C57BL/6 mice (Jackson laboratory) received 1μg of each vaccine, as outlined in Figure 2A, via intramuscular injections, in a 50ul volume, on days −52, −24, 0, and 28.
   Randomization	Hamsters were randomly assigned to study groups and acclimatized for several days prior to vaccination.
   Blinding	Sections were scored by a certified pathologist who was blinded to study groups.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   …

   SciScore for 10.1101/2022.01.31.478520: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: Animal experiments were approved by the corresponding institutional animal care and use committee and performed by experienced personnel under veterinary oversight.
   Sex as a biological variable	Mouse studies: Six-to-eight-week-old female C57BL/6 mice (Jackson laboratory) received 1μg of each vaccine, as outlined in Figure 2A, via intramuscular injections, in a 50ul volume, on days −52, −24, 0, and 28.
   Randomization	Hamsters were randomly assigned to study groups and acclimatized for several days prior to vaccination.
   Blinding	Sections were scored by a certified pathologist who was blinded to study groups.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Twenty-four hours later, cell lysates were added to an ELISA plate coated with anti-SARS-CoV2 Spike (S1 domain) monoclonal antibody.	anti-SARS-CoV2 Spike ( S1 domain ) suggested: None
   Following a primary incubation and washes, a polyclonal anti-SARS-CoV2 Spike (full-length S) primary antibody was added.	anti-SARS-CoV2 suggested: None
   The secondary antibody was the Vector Laboratories ImPress VR anti-mouse IgG polymer (cat# MP-7422).	anti-mouse IgG suggested: (Vector Laboratories Cat# MP-7422, RRID:AB_2336527)
   Experimental Models: Cell Lines
   Sentences	Resources
   0.1 ml of the cleaned VTM was used to infect VeroE6 cells ectopically expressing human Ace2and TMPRSS2 (VeroE6-AT cells; a gift from Dr. Barney Graham, National Institutes of Health, Bethesda MD) in a 48-well plate.	VeroE6 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
   The P0 stock was used to produce P1 virus stock, with virus cultures grown in VeroE6/TMPRSS2 cells (JCRB1819).	VeroE6/TMPRSS2 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
   Briefly, serial dilutions of LION/repRNA were incubated on a monolayer of BHK cells in a 96-well plate.	BHK suggested: None
   Serum/virus mixtures were added, along with virus only and mock controls, to Vero E6-TMPRSS2 cells (ATCC) in 12-well plates and incubated for 30 min at 37C.	Vero E6-TMPRSS2 suggested: None
   Infectious virus titration: Infectious virus in swabs or tissues was quantified by tissue-culture infectious dose 50 assay (TCID50) on Vero cells.	Vero suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)
   Experimental Models: Organisms/Strains
   Sentences	Resources
   VeroE6-TMPRSS2 (JCRB1819, JCRB Cell Bank, NIBIOHN) cells were cultured at 37C in DMEM supplemented with 10% FBS, 100U/ml of penicillin-streptomycin, and 1mg/ml G418.	VeroE6-TMPRSS2 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
   Mouse studies: Six-to-eight-week-old female C57BL/6 mice (Jackson laboratory) received 1μg of each vaccine, as outlined in Figure 2A, via intramuscular injections, in a 50ul volume, on days −52, −24, 0, and 28.	C57BL/6 suggested: None
   Recombinant DNA
   Sentences	Resources
   Tiles were then synthesized on the BioXP (CodexDNA) and combined with linearized repRNA plasmid backbone in a four-fragment Gibson assembly reaction followed by transformation of e. coli and selection of clones.	repRNA suggested: None
   Software and Algorithms
   Sentences	Resources
   Statistical Analyses: Statistical analyses as described in the figure legends were performed using Prism 8.4.3 (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 10.1101/2022.01.31.478520 on bioRxiv

   Feb 3, 2022