Mosaic RBD nanoparticles protect against multiple sarbecovirus challenges in animal models

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   Mar 31, 2022

   SciScore for 10.1101/2022.03.25.485875: (What is this?)

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

   Table 1: Rigor

   Ethics

   Field Sample Permit: This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. IACUC: K18-hACE2 mice: The Institutional Animal Care and Use Committee at Rocky Mountain Laboratories provided animal study approvals, which were conducted in an Association for Assessment and Accreditation of Laboratory Animal Care-accredited facility, following the basic principles and guidelines in the Guide for the Care and Use of Laboratory Animals eighth edition, the Animal Welfare Act, U.S. Department of Agriculture, and the U.S. Public Health …

   SciScore for 10.1101/2022.03.25.485875: (What is this?)

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

   Table 1: Rigor

   Ethics	Field Sample Permit: This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. IACUC: K18-hACE2 mice: The Institutional Animal Care and Use Committee at Rocky Mountain Laboratories provided animal study approvals, which were conducted in an Association for Assessment and Accreditation of Laboratory Animal Care-accredited facility, following the basic principles and guidelines in the Guide for the Care and Use of Laboratory Animals eighth edition, the Animal Welfare Act, U.S. Department of Agriculture, and the U.S. Public Health Service Policy on Humane Care and Use of Laboratory Animals.
   Sex as a biological variable	Male and female macaques per group were balanced.
   Randomization	not detected.
   Blinding	All slides were examined by a board-certified veterinary anatomic pathologist who was blinded to study group allocations.
   Power Analysis	not detected.
   Cell Line Authentication	Contamination: Mycoplasma testing is performed at monthly intervals, and no mycoplasma was detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Raw Illumina sequencing data for the antibody-escape mapping experiments are available on the NCBI Short Read Archive (SRA) at BioProject PRJNA770094, BioSample SAMN26315988.	antibody-escape suggested: None
   Half-maximal inhibitory dilutions (ID50 values) were derived using 4-parameter nonlinear regression in AntibodyDatabase (87).	AntibodyDatabase ( 87 suggested: None
   The libraries were washed and secondarily labeled for 1 hour with 1:100 fluorescein isothiocyanate-conjugated anti-MYC antibody (Immunology Consultants Lab, CYMC-45F) to label for RBD expression and 1:200 Alexa Fluor-647-conjugated goat anti-human-IgG Fc-gamma (Jackson ImmunoResearch 109-135-098) to label for bound NHP antibodies or Alexa Fluor-647-conjugated goat anti-mouse-IgG Fc-gamma (Jackson ImmunoResearch 115-605-008) to label for bound mouse antibodies.	anti-MYC suggested: None anti-human-IgG Fc-gamma suggested: None anti-mouse-IgG Fc-gamma suggested: None
   /, version 0.8.10) to process Illumina sequences into counts of each barcoded RBD variant in each pre-selection and antibody-escape population.	antibody-escape population. suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cells and virus for K18-hACE2 mouse studies: Virus propagation was performed in VeroE6 cells in DMEM containing 2% FBS, 1 mM L-glutamine, penicillin (50 U/mL), and streptomycin (50 μg/mL (DMEM2).	VeroE6 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
   The TCID50 assay was conducted by addition of 10-fold graded dilutions of samples to Vero/TMPRSS2 cell monolayers.	Vero/TMPRSS2 suggested: JCRB Cat# JCRB1818, RRID:CVCL_YQ48)
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Mosaic-8b RBD-mi3 and homotypic SARS-2 RBD-mi3 were compared by negative-stain EM.	Mosaic-8b RBD-mi3 suggested: None
   K18-hACE2 mice: The Institutional Animal Care and Use Committee at Rocky Mountain Laboratories provided animal study approvals, which were conducted in an Association for Assessment and Accreditation of Laboratory Animal Care-accredited facility, following the basic principles and guidelines in the Guide for the Care and Use of Laboratory Animals eighth edition, the Animal Welfare Act, U.S. Department of Agriculture, and the U.S. Public Health Service Policy on Humane Care and Use of Laboratory Animals.	K18-hACE2 suggested: RRID:IMSR_GPT:T037657)
   Immunizations of mosaic-8b or homotypic SARS-2 Beta (5 µg each based on RBD content, 11.4 µg of total RBD-mi3) in 100 µL of 50% v/v AddaVaxTM adjuvant (InvivoGen) were done using intramuscular (IM) injections of 7-8-week-old female BALB/c mice (Envigo) (8 animals per cohort).	BALB/c suggested: RRID:IMSR_ORNL:BALB/cRl)
   Recombinant DNA
   Sentences	Resources
   Preparation of RBD-mi3 nanoparticles: SpyCatcher003-mi3 nanoparticles (78) were expressed in BL21 (DE3)-RIPL E coli (Agilent) transformed with the pET28a His6-SpyCatcher003-mi3 gene (Addgene) as described (34, 84).	pET28a suggested: RRID:Addgene_139598)
   Software and Algorithms
   Sentences	Resources
   Raw Illumina sequencing data for the antibody-escape mapping experiments are available on the NCBI Short Read Archive (SRA) at BioProject PRJNA770094, BioSample SAMN26315988.	NCBI Short Read Archive suggested: None
   Curves were plotted and analyzed to obtain midpoint titers (EC50 values) using Graphpad Prism 9.3.1 (Graphpad Softwatre, San Diego, CA) assuming a one-site binding model with a Hill coefficient.	Graphpad Prism suggested: (GraphPad Prism, RRID:SCR_002798) Graphpad suggested: (GraphPad, RRID:SCR_000306)
   Raw sequencing data are available on the NCBI SRA under BioProject PRJNA770094, BioSample SAMN26315988.	BioProject suggested: (NCBI BioProject, RRID:SCR_004801)

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   Results from OddPub: Thank you for sharing your code and data.

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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 10.1101/2022.03.25.485875 on bioRxiv

   Mar 28, 2022