Real-Time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles
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SciScore for 10.1101/2020.09.10.286948: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Preparations of convalescent plasma from SARS-CoV-2-positive patients: All SARS-CoV-2-postive patient serum work was conducted in accordance with the Declaration of Helsinki in terms of informed consent and approval by an appropriate institutional board (CHUM, 19.381). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources Antibody neutralization assays: In the case of VSVG, SARS-CoV-1, and SARS-CoV-2 parallel neutralization assay (Fig. 4C, and Fig. SARS-CoV-1suggested: NoneExperimental Models: Cell Lines Sentences Re… SciScore for 10.1101/2020.09.10.286948: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement Consent: Preparations of convalescent plasma from SARS-CoV-2-positive patients: All SARS-CoV-2-postive patient serum work was conducted in accordance with the Declaration of Helsinki in terms of informed consent and approval by an appropriate institutional board (CHUM, 19.381). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources Antibody neutralization assays: In the case of VSVG, SARS-CoV-1, and SARS-CoV-2 parallel neutralization assay (Fig. 4C, and Fig. SARS-CoV-1suggested: NoneExperimental Models: Cell Lines Sentences Resources Pelleted viruses were resuspended in above DMEM media and titered on Huh7.5 cells that endogenously express hACE2. Huh7.5suggested: RRID:CVCL_7927)HEK293T cells (not expressing hACE2) infected similarly served as controls to determine basal luciferase activity for obtaining normalized relative light units in infected samples. HEK293Tsuggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)For the preparation of Vpr-HiBiT–containing SARS CoV-2 decorated lentiviruses, a plasmid mixture containing 4 μg of pCMV-S, 4 μg of psPAX2 (Gag-pol, Rev, and Tat expression vector; does not express Vpr), 2 μg of pLL3.7 (packaging reporter to express GFP), and 2 μg of pCMV-Vpr-HiBiT (Vpr-HiBiT expression vector)) was transfected into 60-70 % HEK293 cells using FuGENE 6 (3ul of FuGENE 6 for 1µg of DNA). HEK293suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)Viral capture by any given antibody was visualized by adding 10×104 SARS-CoV-2-resistant Cf2Th cells (not shown) in full DMEM medium per well. Cf2Thsuggested: NIH-ARP Cat# 4662-298, RRID:CVCL_1G50)Flow cytometry analysis of cell-surface staining: Using the standard calcium phosphate method, 10 μg of Spike expressor and 2 μg of a green fluorescent protein (GFP) expressor (pIRES-GFP) was transfected into 2 × 106 293T cells. 293Tsuggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)Software and Algorithms Sentences Resources The full source code of SPARTAN, which was used for analysis of smFRET data, is publicly available. SPARTANsuggested: (SPARTAN, RRID:SCR_014901)The data were processed and plotted using GraphPad Prism 8 v8.4.3. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)Tomograms were reconstructed by weighted back projection and tomographic slices were visualized with IMOD. IMODsuggested: (IMOD, RRID:SCR_003297)Based on visual inspection of traces that revealed direct observations of state-to-state transitions, FRET histograms were fitted into the sum of four Gaussian distributions using the least-squares fitting algorithm in Matlab. Matlabsuggested: (MATLAB, RRID:SCR_001622)Samples were acquired on a LSRII cytometer (BD Biosciences, Mississauga, ON, Canada) and data analysis was performed using FlowJo vX. FlowJosuggested: (FlowJo, RRID:SCR_008520)Results from OddPub: Thank you for sharing your code.
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: We did not find any issues relating to colormaps.
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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