Spike mutation D614G alters SARS-CoV-2 fitness

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1. Version published to 10.1038/s41586-020-2895-3

   Oct 26, 2020
2. 

   ScreenIT

   Sep 9, 2020

   SciScore for 10.1101/2020.09.01.278689: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: The protocol was approved by the Institutional Animal Care and Use Committee (IACUC) at UTMB.
   Randomization	Statistics: Male hamsters were randomly allocated into different groups.
   Blinding	The investigators were not blinded to allocation during the experiments or to the outcome assessment.
   Power Analysis	not detected.
   Sex as a biological variable	Hamster infection: Four-to five-week-old male golden Syrian hamsters, strain HsdHan:AURA (Envigo, Indianapolis, IN), were inoculated intranasally with 2×104 PFU SARS-CoV-2 in a 100-μl volume.
   Cell Line Authentication	Contamination: All cell lines were verified and tested negative for mycoplasma.

   Table 2: Resources

   Antibodies

   SciScore for 10.1101/2020.09.01.278689: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: The protocol was approved by the Institutional Animal Care and Use Committee (IACUC) at UTMB.
   Randomization	Statistics: Male hamsters were randomly allocated into different groups.
   Blinding	The investigators were not blinded to allocation during the experiments or to the outcome assessment.
   Power Analysis	not detected.
   Sex as a biological variable	Hamster infection: Four-to five-week-old male golden Syrian hamsters, strain HsdHan:AURA (Envigo, Indianapolis, IN), were inoculated intranasally with 2×104 PFU SARS-CoV-2 in a 100-μl volume.
   Cell Line Authentication	Contamination: All cell lines were verified and tested negative for mycoplasma.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The purified virions were analyzed by Western blot using polyclonal antibodies against spike protein and nucleocapsid as described previously32.	antibodies against spike protein suggested: None
   On the following day, sera or monoclonal antibodies were serially diluted from 1/20 starting dilution and nine 2-fold dilutions to the final dilution of 1/5,120 and incubated with D614 or G614 mNeonGreen SARS-CoV-2 at 37°C for 1 h.	D614 suggested: (GenWay Biotech Inc. Cat# GWB-A5D614, RRID:AB_10285218)
   Experimental Models: Cell Lines
   Sentences	Resources
   For recovering the mutant viruses, the RNA transcripts were electroporated into Vero E6 cells.	Vero E6 suggested: RRID:CVCL_XD71)
   Viral infection on cells: Approximately 3×105 Vero E6 or Calu-3 cells were seeded onto each well of 12-well plates and cultured at 37°C, 5% CO2 for 16 h.	Calu-3 suggested: None
   Virion purification and spike protein cleavage analysis: Vero E6 or Calu-3 2B4 cells were infected with D614 or G614 viruses at an MOI of 0.01.	Calu-3 2B4 suggested: RRID:CVCL_YZ47)
   The virus-serum mixture was transferred to the Vero cell plate with the final MOI of 2.0.	Vero suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)
   Software and Algorithms
   Sentences	Resources
   The sequencing reactions were purified using a 96-well plate format (EdgeBio, San Jose, CA, USA) and analyzed on a 3500 Genetic Analyzer (Applied Biosystems, Foster City, CA).	EdgeBio suggested: (EdgeBio, RRID:SCR_000183)
   The curves of the relative infection rates versus the serum dilutions (log10 values) were plotted using Prism 8 (GraphPad).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   Analysis was performed in Prism version 7.03 (GraphPad, San Diego, CA).	Prism suggested: (PRISM, RRID:SCR_005375)

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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.
   • 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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   Read the original source
3. 

   Version published to 10.1101/2020.09.01.278689v1 on bioRxiv

   Sep 2, 2020