A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation

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1. Version published to 10.1016/j.cell.2021.07.007

   Aug 1, 2021
2. 

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   Mar 1, 2021

   SciScore for 10.1101/2021.02.13.431090: (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

   Experimental Models: Cell Lines
   Sentences	Resources
   Cell lines: Vero E6, monkey kidney cells (ATCC CRL1586) and Calu-3, human lung epithelial cells (ATCC HTB-55) were purchased from ATCC.	Calu-3 suggested: ATCC Cat# HTB-55, RRID:CVCL_0609)
   We electroporated the RNA transcripts into a mixture of Vero E6 (75%) and BHK-21 (25%) cells containing a total of 2×107 cells per electroporation36.	BHK-21 suggested: NCBI_Iran Cat# C107, RRID:CVCL_1915)
   Virus titers were assessed by plaque assay on Vero E6 cells.	Vero E6 suggested: RRID:CVCL_XD71)
   Software and Algorithms
   Sentences	Resources
   To identify glycosylation propensity and predicted glycosylated …

   SciScore for 10.1101/2021.02.13.431090: (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

   Experimental Models: Cell Lines
   Sentences	Resources
   Cell lines: Vero E6, monkey kidney cells (ATCC CRL1586) and Calu-3, human lung epithelial cells (ATCC HTB-55) were purchased from ATCC.	Calu-3 suggested: ATCC Cat# HTB-55, RRID:CVCL_0609)
   We electroporated the RNA transcripts into a mixture of Vero E6 (75%) and BHK-21 (25%) cells containing a total of 2×107 cells per electroporation36.	BHK-21 suggested: NCBI_Iran Cat# C107, RRID:CVCL_1915)
   Virus titers were assessed by plaque assay on Vero E6 cells.	Vero E6 suggested: RRID:CVCL_XD71)
   Software and Algorithms
   Sentences	Resources
   To identify glycosylation propensity and predicted glycosylated residues of the WT S Protein and the A372T mutant, the NetNGlyc 1.0 Server60 and Schrödinger-Maestro’s BioLuminate (v. 2020-2) Reactive Residue package was used58,61–63.	NetNGlyc suggested: (NetNGlyc, RRID:SCR_001570)
   Structures were visualized using PyMOL.	PyMOL suggested: (PyMOL, RRID:SCR_000305)
   Statistics: Statistical analyses were performed in GraphPad version 9.	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 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).

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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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3. 

   Version published to 10.1101/2021.02.13.431090 on bioRxiv

   Feb 17, 2021