RG203KR Mutations in SARS-CoV-2 Nucleocapsid: Assessing the Impact Using a Virus-Like Particle Model System

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1. Version published to 10.1128/spectrum.00781-22

   Aug 31, 2022
2. 

   ScreenIT

   Jan 6, 2022

   SciScore for 10.1101/2022.01.02.473343: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: Animal immunization: Approval for animal experiments was taken from ‘Institutional Animal Ethics Committee’.
   Sex as a biological variable	24 female BALB/c mice, 6 weeks old, were grouped into four groups and immunization was given intra peritoneal (i.p.).
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After permeabilization by 0.1 % Triton X-100 for 2 min at room temperature, cells were incubated with 3 % BSA at 37 °C for 1 h followed by incubation with the indicated antibody for 2 h at 4 °C and then detected by Alexa-633-conjugated anti-mouse or Alexa-488 conjugated anti-rabbit …

   SciScore for 10.1101/2022.01.02.473343: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: Animal immunization: Approval for animal experiments was taken from ‘Institutional Animal Ethics Committee’.
   Sex as a biological variable	24 female BALB/c mice, 6 weeks old, were grouped into four groups and immunization was given intra peritoneal (i.p.).
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After permeabilization by 0.1 % Triton X-100 for 2 min at room temperature, cells were incubated with 3 % BSA at 37 °C for 1 h followed by incubation with the indicated antibody for 2 h at 4 °C and then detected by Alexa-633-conjugated anti-mouse or Alexa-488 conjugated anti-rabbit secondary antibody for 30 min (Invitrogen).	anti-mouse suggested: None anti-rabbit suggested: None
   Samples were then analyzed by western blot using the desired antibodies, anti-SARS-CoV-2 S protein (Cat. No.-40591-T62), anti-SARS-CoV-2 N protein (Cat. No.-40143-MM05)	anti-SARS-CoV-2 S protein suggested: None anti-SARS-CoV-2 N protein suggested: None
   , Immunized mice sera followed by the respective secondary antibodies (horseradish peroxidase-conjugated anti-mouse or anti-rabbit IgG; Sigma).	anti-rabbit IgG suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Isolation of VLP: The Baculovirus infected Sf21 cells were lysed with TEN buffer [10 mM Tris (pH 7.5), 1.0 mM EDTA, 1.0 M NaCl, 0.1% Triton X100, 1 mM PMSF].	Sf21 suggested: None
   Vero cells (5×105) were added to the mixture of SARS-CoV-2-VLPs and antibody in DMEM and 25 mM of HEPES buffer (100 µl) and incubated for 2 h at room temperature.	Vero suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   24 female BALB/c mice, 6 weeks old, were grouped into four groups and immunization was given intra peritoneal (i.p.).	BALB/c suggested: RRID:IMSR_ORNL:BALB/cRl)
   Recombinant DNA
   Sentences	Resources
   Vector DNA pBacPAK9 containing the target gene was transfected into Spodoptera frugiperda cells, along with Bsu36 I-digested BacPAK6 Viral DNA as described earlier (Takara Bio Inc., USA).	pBacPAK9 suggested: None
   Software and Algorithms
   Sentences	Resources
   Images were taken using Zeiss microscope and image analysis was done using the Zeiss LSM or ZEN software tools.	ZEN suggested: None
   Statistical analyses were performed using Graph Pad Prism version 8.0.	Graph Pad 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 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 9. 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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   Results from scite Reference Check: We found no unreliable references.

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3. 

   Version published to 10.1101/2022.01.02.473343v1 on bioRxiv

   Jan 3, 2022