Cryo-electron Microscopy Structure of the Swine Acute Diarrhea Syndrome Coronavirus Spike Glycoprotein Provides Insights into Evolution of Unique Coronavirus Spike Proteins

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1. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2020.03.04.976258: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   The automated software SerialEM was used to collect 1,000 movies at a defocus range of between 1.8 and 2.3 μm.	SerialEM suggested: (SerialEM, RRID:SCR_017293)
   Image processing: Micrograph movie stacks were corrected for beam-induced motion using MotionCor2 [28].	MotionCor2 suggested: (MotionCor2, RRID:SCR_016499)
   The contrast transfer function parameters for each dose weighting image were determined with Gctf [29].	Gctf suggested: (GCTF, RRID:SCR_016500)
   After iterative 2D-class average in RELION, only particles with best-resolved 2D averages were selected for initial model generation and 3D …

   SciScore for 10.1101/2020.03.04.976258: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   The automated software SerialEM was used to collect 1,000 movies at a defocus range of between 1.8 and 2.3 μm.	SerialEM suggested: (SerialEM, RRID:SCR_017293)
   Image processing: Micrograph movie stacks were corrected for beam-induced motion using MotionCor2 [28].	MotionCor2 suggested: (MotionCor2, RRID:SCR_016499)
   The contrast transfer function parameters for each dose weighting image were determined with Gctf [29].	Gctf suggested: (GCTF, RRID:SCR_016500)
   After iterative 2D-class average in RELION, only particles with best-resolved 2D averages were selected for initial model generation and 3D classification using RELION.	RELION suggested: (RELION, RRID:SCR_016274)
   Chimera and PyMOL (https://pymol.org/) were used for graphical visualization [31].	PyMOL suggested: (PyMOL, RRID:SCR_000305)
   Model building: Ab initio modeling of the spike protein was performed in Coot [32], using structure predictions calculated by Phyre2 [33], the partial structure modeled by EMBuilder [34], and the reference model (PDB: 5X58).	Coot suggested: (Coot, RRID:SCR_014222) Phyre2 suggested: None EMBuilder suggested: (EMBuilder, RRID:SCR_018557)

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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: Please consider improving the rainbow (“jet”) colormap(s) used on page 34. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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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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2. Version published to 10.1128/jvi.01301-20

   Oct 27, 2020
3. 

   ScreenIT

   Jun 4, 2020

   SciScore for 10.1101/2020.03.04.976258: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The engagement of the CTDs of SARS S trimer helps it to keep one or more CTDs in the “stand up” position and facilitate the binding of ACE2 or neutralizing antibodies.	ACE2 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Numerous α-CoVs, for example, human CoV (HCoV-229E), utilize aminopeptidase N (APN) as its receptor, SARS-CoV, HCoV-NL63 and SARS-CoV-2 employ angiotensin-converting enzyme 2 (ACE2), and MERSCoV ties to dipeptidyl-peptidase 4 (DPP4).	HCoV-NL63 suggested: CVCL_RW88 …

   SciScore for 10.1101/2020.03.04.976258: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The engagement of the CTDs of SARS S trimer helps it to keep one or more CTDs in the “stand up” position and facilitate the binding of ACE2 or neutralizing antibodies.	ACE2 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Numerous α-CoVs, for example, human CoV (HCoV-229E), utilize aminopeptidase N (APN) as its receptor, SARS-CoV, HCoV-NL63 and SARS-CoV-2 employ angiotensin-converting enzyme 2 (ACE2), and MERSCoV ties to dipeptidyl-peptidase 4 (DPP4).	HCoV-NL63 suggested: CVCL_RW88
   Software and Algorithms
   Sentences	Resources
   Structural evolution of coronavirus spike protein The S protein from all the four different genera of the CoVs packs a crown-like structure by three monomeric subunits, which can be divided into two packing modes: the cross-subunit packing mode and the intra-subunit packing mode [21].	CoVs suggested: None
   The automated software SerialEM was used to collect 1,000 movies at a defocus range of between 1.8 and 2.3 µm.	SerialEM suggested: (SerialEM, SCR_017293)
   Image processing Micrograph movie stacks were corrected for beam-induced motion using MotionCor2 [28].	MotionCor2 suggested: (MotionCor2, SCR_016499)
   The contrast transfer function parameters for each dose weighting image were determined with Gctf [29].	Gctf suggested: (GCTF, SCR_016500)
   Reference-free 2D-class average was performed using RELION [30], and the well-resolved 2D averages were subjected to another iteration particle auto picking as a template with Gautomatch.	RELION suggested: (RELION, SCR_016274)
   Chimera and PyMOL (https://pymol.org/) were used for graphical visualization [31].	PyMOL suggested: (PyMOL, SCR_000305)
   Model building Ab initio modeling of the spike protein was performed in Coot [32], using structure predictions calculated by Phyre2 [33], the partial structure modeled by EMBuilder [34], and the reference model (PDB: 5X58).	Coot suggested: (Coot, SCR_014222) <div style="margin-bottom:8px"> <div><b>Phyre2</b></div> <div>suggested: None</div> </div> <div style="margin-bottom:8px"> <div><b>EMBuilder</b></div> <div>suggested: (EMBuilder, <a href="https://scicrunch.org/resources/Any/search?q=SCR_018557">SCR_018557</a>)</div> </div> </td></tr></table> Results from OddPub: Thank you for sharing your data. 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 10.1101/2020.03.04.976258 on bioRxiv

   Mar 7, 2020