A single dose of recombinant VSV-∆G-spike vaccine provides protection against SARS-CoV-2 challenge

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1. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2020.06.18.160655: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: All animal experiments involving SARS-CoV-2 were conducted in a BSL3 facility in accordance with the guideline of the Israel Institute for Biological Research (IIBR) animal experiments committee.
   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
   After washing with PBS, cells were incubated with Alexa Fluor 488 conjugated anti-rabbit, anti-human and anti-hamster antibodies, respectively.	anti-rabbit , anti-human and anti-hamster antibodies , respectively . suggested: None
   Immuno-gold labeling was performed using …

   SciScore for 10.1101/2020.06.18.160655: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: All animal experiments involving SARS-CoV-2 were conducted in a BSL3 facility in accordance with the guideline of the Israel Institute for Biological Research (IIBR) animal experiments committee.
   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
   After washing with PBS, cells were incubated with Alexa Fluor 488 conjugated anti-rabbit, anti-human and anti-hamster antibodies, respectively.	anti-rabbit , anti-human and anti-hamster antibodies , respectively . suggested: None
   Immuno-gold labeling was performed using polyclonal antibody (pAB RBD SBF40150-T62) directed at the receptor binding domain (RBD) of the spike, followed by washing (x3) with PBS and then labeling with gold-conjugated goat anti-rabbit secondary antibody (Sigma, G3779).	anti-rabbit suggested: (Sigma-Aldrich Cat# G3779, RRID:AB_259862) G3779 suggested: None
   Sera was collected two weeks post-vaccination for titration of SARS-CoV-2 neutralizing antibodies.	SARS-CoV-2 neutralizing antibodies. suggested: None
   Sections were then permiabilized for 10 minutes (0.2% Triton X-100 in PBS), blocked for 1 hour (10% NGS in PBS containing 0.05% Triton X-100), incubated in 100 μg/ml of rabbit SARS-CoV-2 primary antibody (in-house preparation of rabbit polyclonal anti-RBD) in antibody cocktail solution (50% blocking solution, 0.05% Triton X-100 in PBS) for 24 hours at 4°C.	SARS-CoV-2 suggested: None anti-RBD suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   48 hours following primary transfection the supernatant containing the recovered VSV-spike was collected, centrifuged at 1300g X 5min to remove cell debris, and filtered twice using 0.22μM filter to remove residual MVA-T7 virus. pCAGGS-VSV-G transfected BHK-21 cells were then infected with the total amount of the filtered supernatant.	BHK-21 suggested: ATCC Cat# CRL-6282, RRID:CVCL_1914)
   Immunofluorescence analysis (IFA): Monolayers of Vero E6 cells were seeded in 8 chamber LabTek (Nunc) (1.5×105 cells/well) and infected with WT-VSV, SARS-CoV-2 or rVSV-ΔG-spike for 24 hours.	Vero E6 suggested: None
   Software and Algorithms
   Sentences	Resources
   The number of plaques in each well was determined, and the serum dilution that neutralizes 50% of the virions (NT50) was calculated using Prism software.	Prism suggested: (PRISM, RRID:SCR_005375)
   FastQC [15] was used for quality control of the data.	FastQC suggested: (FastQC, RRID:SCR_014583)
   Reads originated from Vero E6 host cells were filtered out using Bowtie 2 [16], resulting in 1,070,483 reads originated from rVSV-ΔG-spike.	Bowtie suggested: (Bowtie, RRID:SCR_005476)
   Mapping of the reads against the rVSV-ΔG-spike was performed using Bowtie 2 followed by variant calling using Samtools [17], both with default parameters, resulting in a 3,178x average coverage and several variants.	Samtools suggested: (SAMTOOLS, RRID:SCR_002105)
   Tissue/Air space ratio calculation: Briefly, tissue/air space ratio was determined using Image J free software analysis (particle analysis algorithm).	Image J suggested: (ImageJ, RRID:SCR_003070)
   Statistical analysis: Data was analyzed with GraphPad Prism 5 software (GraphPad software inc.).	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798) GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)

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   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).

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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.
   • No funding statement was detected.
   • No protocol registration statement was detected.

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   Read the original source
2. Version published to 10.1038/s41467-020-20228-7

   Dec 16, 2020
3. 

   ScreenIT

   Jun 21, 2020

   SciScore for 10.1101/2020.06.18.160655: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement

   All animal experiments involving SARS-CoV-2 were conducted in a BSL3 facility in accordance with the guideline of the Israel Institute for Biological Research ( IIBR ) animal experiments committee.

   Randomization

   not detected.

   Blinding

   not detected.

   Power Analysis

   not detected.

   Sex as a biological variable

   not detected.

   Cell Line Authentication

   Transmission electron microscopy ( TEM ) was performed to analyze the ultrastructure of the rVSV-

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After washing with PBS , cells were incubated with Alexa Fluor 488 conjugated anti-rabbit , anti-human and anti-hamster antibodies , respectively .	anti…

   SciScore for 10.1101/2020.06.18.160655: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement

   All animal experiments involving SARS-CoV-2 were conducted in a BSL3 facility in accordance with the guideline of the Israel Institute for Biological Research ( IIBR ) animal experiments committee.

   Randomization

   not detected.

   Blinding

   not detected.

   Power Analysis

   not detected.

   Sex as a biological variable

   not detected.

   Cell Line Authentication

   Transmission electron microscopy ( TEM ) was performed to analyze the ultrastructure of the rVSV-

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After washing with PBS , cells were incubated with Alexa Fluor 488 conjugated anti-rabbit , anti-human and anti-hamster antibodies , respectively .	anti-rabbit , anti-human and anti-hamster antibodies , respectively . suggested: None
   Immuno-gold labeling was performed using polyclonal antibody ( pAB RBD SBF40150-T62 ) directed at the receptor binding domain ( RBD ) of the spike , followed by washing ( x3 ) with PBS and then labeling with gold-conjugated goat anti-rabbit secondary antibody ( Sigma , G3779) .	anti-rabbit suggested: (Sigma-Aldrich Cat# G3779, AB_259862) <div style="margin-bottom:8px"> <div><b>G3779</b></div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Sera was collected two weeks post-vaccination for titration of SARS-CoV-2 neutralizing antibodies .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>SARS-CoV-2 neutralizing antibodies .</b></div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">To evaluate the expression of rVSV-ΔG-spike , we performed immunofluorescence analysis ( IFA ) using anti-SARS-CoV-2 antibodies .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>anti-SARS-CoV-2</b></div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The rVSV-ΔG-spike resembles the SARS-CoV-2 in spike expression properties , antigenicity , and ability to induce neutralizing antibody production .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>antigenicity ,</b></div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">( B ) B ) Immunofluorescence images of Vero E6 cells infected with early passage ( P5)-rVSV-∆G-spike , or late te passage ( P13)-rVSV-∆G-spike , stained with a SARS-CoV-2 antibody ( green ) and DAPI for nuclei staining ng ( blue) .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>P5)-rVSV-∆G-spike</b></div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2"><b>Experimental Models: Cell Lines</b></td></tr><tr><td style="min-width:100px;text=align:center"><i>Sentences</i></td><td style="min-width:100px;text-align:center"><i>Resources</i></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Materials and methods Cell lines and viruses Baby hamster kidney cells (BHK-21, ATCC® CCL-10) and African green monkey kidney clone E6 cells (Vero E6, ATCC® CRL-1586™) were grown in Dulbecco's modified Eagle's medium (DMEM) containing 10</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>BHK-21</b></div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Their occurrence and development , coinciding with a reduction in the VSV-G , a change in the appearance of CPE and increased viral titers suggest that these mutations may be crucial for the adaptation of rVSV-ΔG-spike to replicate in Vero E6 cells .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>Vero E6</b></div> <div>suggested: <a href="https://scicrunch.org/resources/Any/search?q=CVCL_XD71">CVCL_XD71</a></div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Indeed , spike protein was detected by COVID-19 human convalescent sera in both rVSV-ΔGspike and SARS-CoV-2 infected Vero-E6 cells at 24 hours post-infection ( Fig . 3A) .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>Vero-E6</b></div> <div>suggested: None</div> </div> </td></tr><tr><td style="min-width:100px;text-align:center; padding-top:4px;" colspan="2"><b>Software and Algorithms</b></td></tr><tr><td style="min-width:100px;text=align:center"><i>Sentences</i></td><td style="min-width:100px;text-align:center"><i>Resources</i></td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">The number of plaques in each well was determined , and the serum dilution that neutralizes 50 % of the virions ( NT50 ) was calculated using Prism software.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>Prism</b></div> <div>suggested: (PRISM, <a href="https://scicrunch.org/resources/Any/search?q=SCR_005375">SCR_005375</a>)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">FastQC [ 15 ] was used for quality control of the data .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>FastQC</b></div> <div>suggested: (FastQC, <a href="https://scicrunch.org/resources/Any/search?q=SCR_014583">SCR_014583</a>)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Reads originated from Vero E6 host cells were filtered out using Bowtie 2 [ 16] , resulting in 1,070,483 reads originated from rVSV-ΔG-spike.</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>Bowtie</b></div> <div>suggested: (Bowtie, <a href="https://scicrunch.org/resources/Any/search?q=SCR_005476">SCR_005476</a>)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Mapping of the reads against the rVSV-ΔG-spike was performed using Bowtie 2 followed by variant calling using Samtools [ 17] , both with default parameters , resulting in a 3,178x average coverage and several variants .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>Samtools</b></div> <div>suggested: (Samtools, <a href="https://scicrunch.org/resources/Any/search?q=SCR_002105">SCR_002105</a>)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Tissue/Air space ratio calculation Briefly , tissue/air space ratio was determined using Image J free software analysis ( particle analysis algorithm) .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>Image J</b></div> <div>suggested: (ImageJ, <a href="https://scicrunch.org/resources/Any/search?q=SCR_003070">SCR_003070</a>)</div> </div> </td></tr><tr><td style="min-width:100px;vertical-align:top;border-bottom:1px solid lightgray">Statistical analysis Data was analyzed with GraphPad Prism 5 software ( GraphPad software inc . ) .</td><td style="min-width:100px;border-bottom:1px solid lightgray"> <div style="margin-bottom:8px"> <div><b>GraphPad Prism</b></div> <div>suggested: (GraphPad Prism, <a href="https://scicrunch.org/resources/Any/search?q=SCR_002798">SCR_002798</a>)</div> </div> <div style="margin-bottom:8px"> <div><b>GraphPad</b></div> <div>suggested: (GraphPad Prism, <a href="https://scicrunch.org/resources/Any/search?q=SCR_002798">SCR_002798</a>)</div> </div> </td></tr></table> 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 Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015). Results from OddPub: We did not find a statement about open data. We also did not find a statement about open code. Researchers are encouraged to share open data when possible (see Nature blog). About SciScore SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

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4. 

   Version published to 10.1101/2020.06.18.160655v1 on bioRxiv

   Jun 19, 2020