Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines

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1. Version published to 10.1016/j.cell.2021.09.015

   Oct 1, 2021
2. 

   ScreenIT

   Mar 24, 2021

   SciScore for 10.1101/2021.03.15.435528: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: Animal procedures were performed under the approvals of the Institutional Animal Care and Use Committee (IACUC) of University of Washington, Seattle, WA, and University of North Carolina, Chapel Hill, NC. IRB: This study was approved by the University of Washington Human Subjects Division Institutional Review Board (STUDY00000959 and STUDY00003376).
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	HEK293T/17 is a female human embryonic kidney cell line (ATCC).
   Cell Line Authentication	Contamination: Cell lines other than Expi293F were not tested for mycoplasma contamination nor authenticated. Authentication: …

   SciScore for 10.1101/2021.03.15.435528: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: Animal procedures were performed under the approvals of the Institutional Animal Care and Use Committee (IACUC) of University of Washington, Seattle, WA, and University of North Carolina, Chapel Hill, NC. IRB: This study was approved by the University of Washington Human Subjects Division Institutional Review Board (STUDY00000959 and STUDY00003376).
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	HEK293T/17 is a female human embryonic kidney cell line (ATCC).
   Cell Line Authentication	Contamination: Cell lines other than Expi293F were not tested for mycoplasma contamination nor authenticated. Authentication: Cell lines other than Expi293F were not tested for mycoplasma contamination nor authenticated.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Convalescent human sera: Samples collected between 1–60 days post infection from individuals who tested positive for SARS-CoV-2 by PCR were profiled for anti-SARS-CoV-2 S antibody responses and those with anti-S Ab responses were maintained in the cohort 83.	anti-SARS-CoV-2 S suggested: None anti-S suggested: None
   After the antibody incubations, the libraries were secondarily labeled with 1:100 FITC-conjugated anti-MYC antibody (Immunology Consultants Lab, CYMC-45F) to label for RBD expression and and 1:200 Alexa-647-conjugated goat anti-human-IgA+IgG+IgM (Jackson ImmunoResearch 109-605-064) to label for bound serum or plasma antibodies.	anti-MYC suggested: None anti-human-IgA+IgG+IgM suggested: None
   Plates were washed 4 × in TBST, then anti-mouse (Invitrogen), anti-NHP (AlphaDiagnostics), or anti-human (Invitrogen) horseradish peroxidase-conjugated antibodies were diluted 1:5,000 and 25 μL added to each well and incubated at 37°C for 1 h.	anti-mouse suggested: None anti-NHP suggested: None anti-human suggested: None
   Competition ELISA of ---mouse sera and immobilized hACE2 or antibodies for SARS-CoV-2 S2P or SARS-CoV S2P: 384-well Maxisorp plates (Thermo Fisher) were coated overnight at room temperature with 3 µg/mL of hACE2-Fc, CR3022 (Yuan and Wu et al. 2020), or S309 (Pinto et al. 2020) in 20mM Tris pH 8 and 150mM NaCl.	CR3022 suggested: (Imported from the IEDB Cat# CR3022, RRID:AB_2848080)
   Plates were slapped dry and a 30-minute pre-incubated 1:5 serial dilution of mouse sera in TBST, with in initial dilution of 1:50 for hACE2-Fc competition or 1:10 for antibody competition, and a constant concentration of biotinylated (Avidity) SARS-CoV-2 S2P or SARS-CoV 2P at their EC50 values were added.	SARS-CoV-2 suggested: None S2P suggested: None
   Relative luciferase units were plotted and normalized in Prism (GraphPad) using as zero value cells alone or infected with supernatants of non-tranfected cells infected with VSV(G*ΔG-luciferase) VSV(G*ΔG-luciferase) in the presence of anti-VSV-G antibody and as 100% value cells infected with virus alone.	VSV(G*ΔG-luciferase) VSV(G*ΔG-luciferase suggested: None anti-VSV-G suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cell lines: Expi293F cells are derived from the HEK293F cell line (Life Technologies).	Expi293F suggested: RRID:CVCL_D615) HEK293F suggested: RRID:CVCL_6642)
   The HEK-ACE2 adherent cell line was obtained through BEI Resources, NIAID, NIH: Human Embryonic Kidney Cells (HEK293T) Expressing Human Angiotensin-Converting Enzyme 2, HEK293T-hACE2 Cell Line, NR-52511.	HEK293T suggested: None
   Briefly, 293T cells in DMEM supplemented with 10% FBS, 1% PenStrep seeded in 10-cm dishes were transfected with the plasmid encoding for the corresponding S glycoprotein using lipofectamine 2000 (Life Technologies) following manufacturer’s indications.	293T suggested: None
   Pseudovirus Neutralization: HEK-hACE2 cells were cultured in DMEM with 10% FBS (Hyclone) and 1% PenStrep with 8% CO2 in a 37°C incubator (ThermoFisher).	HEK-hACE2 suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Mice: Female BALB/c mice (Stock # 000651, Balb/c cByJ mice) four weeks old were obtained from Jackson Laboratory, Bar Harbor, Maine, and maintained at the Comparative Medicine Facility at the University of Washington, Seattle, WA, accredited by the American Association for the Accreditation of Laboratory Animal Care International (AAALAC).	Balb/c suggested: RRID:IMSR_ORNL:BALB/cRl)
   Software and Algorithms
   Sentences	Resources
   Animals were housed and maintained at the New Iberia Research Center (NIRC) of the University of Louisiana at Lafayette, an AAALAC International accredited institution, in accordance with the rules and regulations of the Guide for the Care and Use of Laboratory Animal Resources.	NIRC suggested: None
   Plates were immediately read at 450 nm on a BioTek plate reader and data plotted and fit in Prism (GraphPad) using nonlinear regression sigmoidal, 4PL, X is log(concentration) to determine EC50 values from curve fits.	Prism suggested: (PRISM, RRID:SCR_005375) GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)

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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: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04742738	Recruiting	Safety and Immunogenicity Study of SARS-CoV-2 Nanoparticle V…
   NCT04750343	Recruiting	Safety and Immunogenicity Study of SARS-CoV-2 Nanoparticle V…

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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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3. 

   Version published to 10.1101/2021.03.15.435528v1 on bioRxiv

   Mar 16, 2021