Biomechanical Dependence of SARS-CoV-2 Infections

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1. Version published to 10.1021/acsabm.2c00143

   Apr 29, 2022
2. 

   ScreenIT

   Feb 20, 2022

   SciScore for 10.1101/2022.02.17.479764: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   Generation of HEK293T cells with stable expression of human ACE-2: HEK293T cells were transduced with a lentiviral vector (pHAGE2-EF1aInt-ACE-2-WT) that expresses human ACE-2 under an EF1a promoter.	HEK293T suggested: None
   Generation of (SARS-CoV-2) S protein Pseudotyped Lentivirus: PVs were prepared by co-transfecting 293T cells with plasmids for (1) lentiviral backbone containing fluorescent reporter (pHAGE2-CMV-ZsGreen-W), (2) HIV virion formation proteins under …

   SciScore for 10.1101/2022.02.17.479764: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   Generation of HEK293T cells with stable expression of human ACE-2: HEK293T cells were transduced with a lentiviral vector (pHAGE2-EF1aInt-ACE-2-WT) that expresses human ACE-2 under an EF1a promoter.	HEK293T suggested: None
   Generation of (SARS-CoV-2) S protein Pseudotyped Lentivirus: PVs were prepared by co-transfecting 293T cells with plasmids for (1) lentiviral backbone containing fluorescent reporter (pHAGE2-CMV-ZsGreen-W), (2) HIV virion formation proteins under CMV promoters (HDM-Hgpm2, pRC-CMV-Rev1b, and HDM-tat1b; and (3) viral entry proteins SARS-CoV-2 S protein (WT, D614G mutant) or VSV G as a positive control for infectivity.	293T suggested: None
   Calu-3 cells were maintained in EMEM (with EBSS and L-glutamine, BioWhittaker, Lonza) supplemented with 20% FBS (heat-inactivated, Gibco), 0.1 mM MEM non-essential amino acids (Gibco), and 10 mM HEPES (Gibco) at pH 7.4.	Calu-3 suggested: None
   ACE-2 HEK 293T cells were cultured in DMEM + GlutaMax™-I medium (Gibco) supplemented with 10% FBS.	ACE-2 HEK 293T suggested: RRID:CVCL_A7UK)
   Recombinant DNA
   Sentences	Resources
   Plasmids for lentiviral backbone expressing fluorescent reporter under CMV promoter (pHAGE2-CMV-ZsGreen-W) or human ACE-2 gene (GenBank ID NM_021804) under an EF1a promoter (pHAGE2-EF1aInt-ACE-2-WT) were obtained from BEI resources as NR-52520 and NR52512, respectively [35].	pHAGE2-EF1aInt-ACE-2-WT suggested: None
   The envelope vector expressing VSV-G (vesicular stomatitis virus glycoprotein) was obtained from Cell Biolabs (pCMV-VSV-G, Part No. RV-110).	VSV-G suggested: RRID:Addgene_138479) pCMV-VSV-G suggested: RRID:Addgene_8454)
   Generation of (SARS-CoV-2) S protein Pseudotyped Lentivirus: PVs were prepared by co-transfecting 293T cells with plasmids for (1) lentiviral backbone containing fluorescent reporter (pHAGE2-CMV-ZsGreen-W), (2) HIV virion formation proteins under CMV promoters (HDM-Hgpm2, pRC-CMV-Rev1b, and HDM-tat1b; and (3) viral entry proteins SARS-CoV-2 S protein (WT, D614G mutant) or VSV G as a positive control for infectivity.	pHAGE2-CMV-ZsGreen-W suggested: None pRC-CMV-Rev1b suggested: RRID:Addgene_164443)
   Software and Algorithms
   Sentences	Resources
   The ZsGreen expression area was quantified and normalized to the cell area estimated from the DRAQ5 staining using a custom ImageJ script.	ImageJ suggested: (ImageJ, RRID:SCR_003070)
   Statistical analysis: Statistical differences were analyzed using GraphPad Prism.	GraphPad Prism 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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   Results from scite Reference Check: We found no unreliable references.

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   Read the original source
3. 

   Version published to 10.1101/2022.02.17.479764v1 on bioRxiv

   Feb 17, 2022