Lineage-mosaic and mutation-patched spike proteins for broad-spectrum COVID-19 vaccine

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1. Version published to 10.1016/j.chom.2022.10.011

   Dec 1, 2022
2. 

   ScreenIT

   Jan 30, 2022

   SciScore for 10.1101/2022.01.25.477789: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: The mouse and hamster studies were carried out in strict accordance with the recommendations of the Guide for the Care and Use of Laboratory Animals under the approval of the Institutional Animal Care and Use Committee of Xiamen University.
   Sex as a biological variable	Rhesus monkey immunizations: Ten rhesus monkeys were allocated randomly into two groups (three females and two males per group).
   Randomization	Rhesus monkey immunizations: Ten rhesus monkeys were allocated randomly into two groups (three females and two males per group).
   Blinding	Microscopic evaluation of pathological lung lesions was performed blindly by pathologists following a semiquantitative scoring system with the …

   SciScore for 10.1101/2022.01.25.477789: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: The mouse and hamster studies were carried out in strict accordance with the recommendations of the Guide for the Care and Use of Laboratory Animals under the approval of the Institutional Animal Care and Use Committee of Xiamen University.
   Sex as a biological variable	Rhesus monkey immunizations: Ten rhesus monkeys were allocated randomly into two groups (three females and two males per group).
   Randomization	Rhesus monkey immunizations: Ten rhesus monkeys were allocated randomly into two groups (three females and two males per group).
   Blinding	Microscopic evaluation of pathological lung lesions was performed blindly by pathologists following a semiquantitative scoring system with the inclusion of three indicators (49): (i) alveolar septum thickening and consolidation; (ii) hemorrhage, exudation, pulmonary edema, and mucous; and (iii) recruitment and infiltration of inflammatory immune cells.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Two weeks after boosting, serum samples were collected for antibody analyses, including measurement of anti-spike IgG, anti-RBD IgG, pseudovirus neutralizing antibody, and authentic neutralizing antibody titers.	anti-spike IgG suggested: None anti-RBD IgG suggested: None
   In brief, single-cell suspensions were obtained from mouse spleen (106 cells per well) through grinding in 70 μm cell strainers and were seeded in anti-mouse IFN-γ antibody precoated ELISpot plates.	anti-mouse IFN-γ suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   The mixtures (150 μL per well) were added to a monolayer of Vero cells in a 96-well plate and incubated at 37 °C supplying with 5% CO2.	Vero suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Experimental animals: BALB/c and C57BL/6 mice were purchased from Shanghai SLAC Laboratory Animal Co.	C57BL/6 suggested: None
   Mouse immunizations: Six to eight-week-old BALB/c mice (n=6 per group) were immunized with STFK vaccines at 0.01, 0.1, 1, or 10 μg per dose in 150 μL through intramuscular injection following a two-dose schedule at weeks 0 and 3.	BALB/c suggested: None
   Recombinant DNA
   Sentences	Resources
   The tag-free STFK and STFK variants were constructed into a pGS01b vector, modified from the pCGS3 vector containing glutamine synthetase (GS) selection marker (Sigma Aldrich).	pGS01b suggested: None pCGS3 suggested: None
   Software and Algorithms
   Sentences	Resources
   Data were acquired using the SerialEM software on an FEI Tecnai F30 transmission electron microscope (ThermoFisher Scientific) operated at 300 kV and equipped with a Gatan K3 direct detector.	SerialEM suggested: (SerialEM, RRID:SCR_017293)
   Image processing and 3D reconstruction: Drift and beam-induced motion correction were performed with MotionCor2 (38) to produce a micrograph from each movie.	MotionCor2 suggested: (MotionCor2, RRID:SCR_016499)
   We initially fitted the templates into the corresponding final cryo-EM maps using Chimera (43), and further corrected and adjusted them manually by real-space refinement in Coot (44).	Coot suggested: (Coot, RRID:SCR_014222)
   The resulting models were then refined with phenix.real_space_refine in PHENIX (45).	PHENIX suggested: (Phenix, RRID:SCR_014224)
   The final atomic models were validated with Molprobity (46, 47).	Molprobity suggested: (MolProbity, RRID:SCR_014226)
   All statistical analyses were conducted in GraphPad Prism 8 software.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

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   Results from OddPub: Thank you for sharing your 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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3. 

   Version published to 10.1101/2022.01.25.477789v1 on bioRxiv

   Jan 26, 2022