SARS-CoV-2 Harnesses Host Translational Shutoff and Autophagy To Optimize Virus Yields: the Role of the Envelope (E) Protein

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1. Version published to 10.1128/spectrum.03707-22

   Feb 14, 2023
2. 

   ScreenIT

   Mar 28, 2022

   SciScore for 10.1101/2022.03.24.485734: (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
   Cells and Viruses: The A549 cells (human lung adenocarcinoma), Caco-2 (human colorectal adenocarcinoma), HEK-293 (human embryonic kidney epithelial cells), and Vero E6 (normal monkey kidney epithelial cells) were obtained through ATCC.	A549 suggested: None Caco-2 suggested: None HEK-293 suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045) Vero E6 suggested: RRID:CVCL_XD71)
   At 48 h after transfection, the supernatant from the cultures was collected, filtered through a …

   SciScore for 10.1101/2022.03.24.485734: (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
   Cells and Viruses: The A549 cells (human lung adenocarcinoma), Caco-2 (human colorectal adenocarcinoma), HEK-293 (human embryonic kidney epithelial cells), and Vero E6 (normal monkey kidney epithelial cells) were obtained through ATCC.	A549 suggested: None Caco-2 suggested: None HEK-293 suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045) Vero E6 suggested: RRID:CVCL_XD71)
   At 48 h after transfection, the supernatant from the cultures was collected, filtered through a 0.45-μm-pore-size filter, and used to infect Vero-E6 cells, as described before (115, 116).	Vero-E6 suggested: None
   Recombinant DNA
   Sentences	Resources
   HEK-293 cells were seeded in a 60 mm dish at 60% confluence and were co-transfected with the pLenti-mCherry-FLAG-γ134.5 plasmid described above, the Gag-Pol-expressing plasmid, and the vesicular stomatitis virus G (VSV-G)-expressing plasmid at a ratio of 7:7:1 (5 μg total amount of DNA) using Lipofectamine 3000 (Invitrogen) according to the manufacturer’s instructions.	pLenti-mCherry-FLAG-γ134.5 suggested: None VSV-G)-expressing suggested: None
   The genes were expressed in the pcDNA3.1 (+) vector.	pcDNA3.1 (+) suggested: RRID:Addgene_80020)
   The pcDNA3.1 (+)-N-eGFP-N plasmid, expressing N from SARS-CoV-2, was obtained from GenScript Biotech (Catalog # MC_0101137).	pcDNA3.1 (+)-N-eGFP-N suggested: None

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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:

   • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
   • No funding statement was detected.
   • 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 10.1101/2022.03.24.485734v1 on bioRxiv

   Mar 25, 2022