Two-component spike nanoparticle vaccine protects macaques from SARS-CoV-2 infection

Article activity feed

1. Version published to 10.1016/j.cell.2021.01.035

   Mar 1, 2021
2. 

   ScreenIT

   Nov 9, 2020

   SciScore for 10.1101/2020.11.07.365726: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: All animals were housed in IDMIT infrastructure facilities (CEA, Fontenay-aux-roses), under BSL-2 and BSL-3 containment when necessary (Animal facility authorization #D92-032-02, Prefecture des Hauts de Seine, France) and in compliance with European Directive 2010/63/EU, the French regulations and the Standards for Human Care and Use of Laboratory Animals, of the Office for Laboratory Animal Welfare (OLAW, assurance number #A5826-01, US).
   Randomization	Animals and study designs: Cynomolgus macaques were randomly assigned in two experimental groups.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Female New Zealand White rabbits of …

   SciScore for 10.1101/2020.11.07.365726: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: All animals were housed in IDMIT infrastructure facilities (CEA, Fontenay-aux-roses), under BSL-2 and BSL-3 containment when necessary (Animal facility authorization #D92-032-02, Prefecture des Hauts de Seine, France) and in compliance with European Directive 2010/63/EU, the French regulations and the Standards for Human Care and Use of Laboratory Animals, of the Office for Laboratory Animal Welfare (OLAW, assurance number #A5826-01, US).
   Randomization	Animals and study designs: Cynomolgus macaques were randomly assigned in two experimental groups.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Female New Zealand White rabbits of 2.5-3 kg from multiple litters were used.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   BLI assay: SARS-CoV-2 S-I53-50A.1NT1 and SARS-CoV-2 S-I53-50NP were diluted to 100 nM and 5nM, respectively, in BLI running buffer (PBS/0.1% bovine serum albumin/0.02% Tween20) and antibody binding was assessed using a ForteBio Octet K2.	SARS-CoV-2 suggested: None S-I53-50NP suggested: None
   Pilot experiments determined the optimal dilution for detection of SARS-CoV-2 S protein-specific IgG, IgA and IgM antibodies in serum to be 1:50,000, for the detection of antibody binding to FcyRIIa, FcyRIIIa and C1q in serum at 1:500 and for detection of S protein-specific IgG and IgA in saliva and nose fluid at 1:20.	IgM suggested: None
   Next, the following antibodies and viability dye were incubated with PBMCs at RT for 20 min: anti-CD3 BUV395 (clone SP34-2; BD Biosciences)	anti-CD3 suggested: None
   5×106 cells were stained for 30 min at 4°C with the fluorescent probes, a viability marker (LiveDead-eF780, eBiosciences) and the following B cell-specific antibodies: anti-CD20-PE-CF594 (2H7; BD Biosciences), anti-IgG-PE-Cy7 (G18-145;BD Biosciences), anti-CD27-PE (M-T271; BD Biosciences), and anti-IgM-BV605 (MHM-88; Biolegend).	anti-CD20-PE-CF594 suggested: None anti-IgG-PE-Cy7 suggested: None anti-CD27-PE suggested: (Sigma-Aldrich Cat# SAB4700134, RRID:AB_10896453) anti-IgM-BV605 suggested: None
   Plates were incubated for 42 h at 37°C in an atmosphere containing 5% CO2, then washed 5 times with PBS and incubated for 2 h at 37°C with a biotinylated anti-IFNy antibody.	anti-IFNy suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Protein expression and purification: All constructs were expressed by transient transfection of HEK 293F cells (Invitrogen) maintained in Freestyle medium (Life Technologies) at a density of 0.8-1.2 million cells/mL.	HEK 293F suggested: RRID:CVCL_6642)
   Two days post transfection, IgM-negative Ramos B cells cultured in RPMI (Gibco) supplemented with 10% fetal calf serum, streptomycin (100 μg/mL) and penicillin (100 U/mL) (RPMI++) were transduced with filtered (0.45 μm) and concentrated (100 kDa molecular weight cutoff, GE Healthcare)	Ramos B suggested: RRID:CVCL_JL65)
   B cell activation assay: B cell activation experiments of SARS-CoV-2 S protein-specific Ramos B cells were performed as previously described (Brouwer et al., 2019; Sliepen et al., 2019).	Ramos suggested: None
   Briefly, HEK 293T cells (ATCC, CRL-11268) were transfected with a pHIV-1NL43ΔENV-NanoLuc reporter virus plasmid and a SARS-CoV-2-SΔ19 plasmid.	HEK 293T suggested: ATCC Cat# CRL-11268G-1, RRID:CVCL_UE07)
   To determine the neutralization activity in serum, saliva or nasopharyngeal samples, HEK 293T/ACE2 cells were first seeded in 96-well plates coated with 50 μg/mL poly-l-lysine at a density of 2×104/well in the culture medium described above but with GlutaMax (Gibco) added.	HEK 293T/ACE2 suggested: None
   After incubation, the mixtures were put on Vero-E6 cells (ATCC CRL-1586) and incubated for 1 h.	Vero-E6 suggested: None
   Virus stocks used in vivo were produced by two passages on Vero E6 cells in DMEM (Gibco) without FBS, supplemented with penicillin at 100 U/mL, streptomycin at 100 μg/mL, and 1 μg/mL TPCK-trypsin at 37°C in a humidified CO2 incubator and titrated on Vero E6 cells.	Vero E6 suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Female Balb/c mice were housed at the Animal Research Institute Amsterdam under BSL-2 conditions.	Balb/c suggested: RRID:IMSR_ORNL:BALB/cRl)
   Software and Algorithms
   Sentences	Resources
   Protein concentrations were determined by the Nanodrop method using the proteins peptidic molecular weight and extinction coefficient as determined by the online ExPASy software (ProtParam).	ExPASy suggested: None
   Data was analyzed using ImageQuant TL 8.2 image analysis software (GE Healthcare)	ImageQuant suggested: (ImageQuant, RRID:SCR_014246)
   Afterwards, the beads were washed with TBST and resuspended in 110 μL Bioplex sheath fluid (Bio-Rad).	Bioplex suggested: (BioPlex, RRID:SCR_016144)
   Analysis was performed on FlowJo v.10.7.1.	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   Reads were then filtered by Nanoplot v1.28.1 based on length and quality to select high quality reads.	Nanoplot suggested: None
   Finally, variant calling was performed with Longshot v0.4.1.	Longshot suggested: None
   Statistical analysis: Binding titers (endpoint titers and concentrations) and midpoint neutralization titers were determined using Graphpad Prism 7.0.	Graphpad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   Comparisons between two experimental groups were made using a Mann-Whitney U test (Excel 2016, Graphpad Prism 7.0).	Graphpad suggested: (GraphPad, RRID:SCR_000306)

   ---

   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).

   ---

   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.

   ---

   Results from TrialIdentifier: No clinical trial numbers were referenced.

   ---

   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

   ---

   Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 14 and 31. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

   ---

   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.

   ---

   Read the original source
3. 

   Version published to 10.1101/2020.11.07.365726v1 on bioRxiv

   Nov 8, 2020