Immunization with recombinant accessory protein-deficient SARS-CoV-2 protects against lethal challenge and viral transmission

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   ScreenIT

   Mar 17, 2022

   SciScore for 10.1101/2022.03.13.484172: (What is this?)

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

   Table 1: Rigor

   Ethics	Field Sample Permit: Biosafety: All in vitro and in vivo experiments with infectious natural isolate or rSARS-CoV-2 were conducted under appropriate biosafety level 3 (BSL3) and animal BSL3 (ABSL3) laboratories, respectively, at Texas Biomedical Research Institute. IACUC: Biosafety (IBC) and Animal Care and Use Committees (IACUC) Euthanasia Agents: Animal infection was performed by intranasally inoculation after being anesthetized following gaseous sedation in an isoflurane chamber.
   Sex as a biological variable	Five-week-old female K18 hACE2 transgenic mice were purchased from The Jackson Laboratory and five-week-old female golden Syrian hamsters were purchased from Charles River Laboratories.
   Ran…

   SciScore for 10.1101/2022.03.13.484172: (What is this?)

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

   Table 1: Rigor

   Ethics	Field Sample Permit: Biosafety: All in vitro and in vivo experiments with infectious natural isolate or rSARS-CoV-2 were conducted under appropriate biosafety level 3 (BSL3) and animal BSL3 (ABSL3) laboratories, respectively, at Texas Biomedical Research Institute. IACUC: Biosafety (IBC) and Animal Care and Use Committees (IACUC) Euthanasia Agents: Animal infection was performed by intranasally inoculation after being anesthetized following gaseous sedation in an isoflurane chamber.
   Sex as a biological variable	Five-week-old female K18 hACE2 transgenic mice were purchased from The Jackson Laboratory and five-week-old female golden Syrian hamsters were purchased from Charles River Laboratories.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Authentication: Multiplex cytokines and chemokines assay: Multiple cytokines and chemokines (IFN-α, IFN-γ, IL-6, IL-10, IL-17A, MCP-1, RANTES, and TNF-α) were measured using a custom 8-plex panel mouse ProcartaPlex assay (ThermoFisher Scientific, catalog# PPX-08-MXGZGFX), following the manufacturer’s instructions.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Cells, peptides, proteins, antibodies and viruses: African green monkey kidney epithelial cells (Vero E6, CRL-1586) were obtained from the American Type Culture Collection (ATCC, Bethesda, MD) and a Vero E6 cell line expressing hACE2 and TMPRSS2 (Vero AT) was obtained from BEI Resources (NR-54970).	TMPRSS2 suggested: None
   The cross-reactive mouse monoclonal antibody against SARS-CoV N protein, 1C7C7, was kindly provided by Dr. Thomas Moran at the Icahn School of Medicine at Mount Sinai.	SARS-CoV N protein , 1C7C7 suggested: None
   After 2 h incubation, plates were washed 3 time with PBST, then incubated with HRP-conjugated goat anti-mouse secondary antibody (ThermoFisher Scientific, catalog# 31430) at 25°C.	anti-mouse suggested: (Thermo Fisher Scientific Cat# 31430, RRID:AB_228307)
   Experimental Models: Cell Lines
   Sentences	Resources
   After incubation at 37°C for 1 h with constant rotation, mixtures were transferred to confluent monolayers (4×105 cells/well, quadruplicates) of Vero E6 cells (Vero AT cells for o), as previously described 42.	Vero E6 suggested: None Vero AT suggested: None
   Multiplex cytokines and chemokines assay: Multiple cytokines and chemokines (IFN-α, IFN-γ, IL-6, IL-10, IL-17A, MCP-1, RANTES, and TNF-α) were measured using a custom 8-plex panel mouse ProcartaPlex assay (ThermoFisher Scientific, catalog# PPX-08-MXGZGFX), following the manufacturer’s instructions.	MCP-1 suggested: None
   Software and Algorithms
   Sentences	Resources
   Raw reads were quality filtered using Trimmomatic v0.39 37 and mapped to a SARS-CoV-2 USA-WA1/2020 strain reference genome (Genbank Accession No. MN985325) with Bowtie2 v2.4.1 38.	Trimmomatic suggested: (Trimmomatic, RRID:SCR_011848) Bowtie2 suggested: (Bowtie 2, RRID:SCR_016368)
   We genotyped each sample for low frequency variants with LoFreq* v2.1.3.1 40 and filtered sites with less than 100x read depth or minor allele frequencies less than 1%.	LoFreq* suggested: None
   Finally, we used SnpEff v4.3t 41 to identify the impact of potential variants on the protein coding regions in the SARS-CoV-2 reference genome.	SnpEff suggested: (SnpEff, RRID:SCR_005191)
   Data were analyzed using FlowJo v10 (Tree Star)	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Evaluation of lung pathological lesions: Macroscopic pathology scoring was evaluated using ImageJ software to determine the percentage of the total surface area of the lung (dorsal and ventral view) affected by consolidation, congestion, and atelectasis, as previously described 43.	ImageJ suggested: (ImageJ, RRID:SCR_003070)

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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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   Version published to 10.1101/2022.03.13.484172v1 on bioRxiv

   Mar 14, 2022