Nucleocapsid 203 mutations enhance SARS-CoV-2 immune evasion

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   ScreenIT

   Dec 27, 2021

   SciScore for 10.1101/2021.12.20.473471: (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
   Human lung adenocarcinoma epithelial Calu-3 cells (ATCC) and African green monkey kidney epithelial Vero E6 cells (ATCC) were maintained at 37⍰°C with 5% CO2 in high-glucose Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% FBS (Gibco).	Calu-3 suggested: None
   Then, full-length genomic RNA was obtained via in vitro transcription, followed by electroporation into Vero E6 cells.	Vero E6 suggested: RRID:CVCL_XD71)
   Recombinant DNA
   Sentences	Resources
   Using standard molecular cloning methods, seven different DNA fragments spanning the entire genome of SARS-CoV-2, were …

   SciScore for 10.1101/2021.12.20.473471: (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
   Human lung adenocarcinoma epithelial Calu-3 cells (ATCC) and African green monkey kidney epithelial Vero E6 cells (ATCC) were maintained at 37⍰°C with 5% CO2 in high-glucose Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% FBS (Gibco).	Calu-3 suggested: None
   Then, full-length genomic RNA was obtained via in vitro transcription, followed by electroporation into Vero E6 cells.	Vero E6 suggested: RRID:CVCL_XD71)
   Recombinant DNA
   Sentences	Resources
   Using standard molecular cloning methods, seven different DNA fragments spanning the entire genome of SARS-CoV-2, were synthesized by Beijing Genomics Institute (BGI, Shanghai, China) and cloned into the pCC1 or pUC57 plasmid.	pCC1 suggested: RRID:Addgene_83007) pUC57 suggested: RRID:Addgene_40306)
   Software and Algorithms
   Sentences	Resources
   We performed simulations of the strains from January 2021 to June 2021 in an exponential growth model by using BEAST v1.10.4 36 with an HYK substitution model and a strict clock type and a chain length of 1000000.	BEAST suggested: (BEAST, RRID:SCR_010228)
   We used FastTree 37 (the parameters are -gtr -nt -boot 1000) to build the phylogenetic tree of the R203M/L452R and L452R variants, respectively.	FastTree suggested: (FastTree, RRID:SCR_015501)
   We performed analyses of the simulation data and built figures with the R packages gdata, ggplot2 and dplyr.	ggplot2 suggested: (ggplot2, RRID:SCR_014601)
   GraphPad Prism 8 was used to plot the curves of the relative infection rates versus the serum dilutions (log10 values).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)

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   Results from OddPub: Thank you for sharing your data.

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   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   Limitations of the study: The limitations of our work are mostly attributed to the lack of mechanistic studies of the N protein mutation. We demonstrated a positive contribution of the R203M mutation to the transmission and resistance to neutralization of Delta. However, the clarification of the detailed mechanism requires more extensive biochemical and structural research. Detailed biochemistry and structural studies would be helpful to characterize the biological function of the N mutation. We did not observe an increased virulence associated with the R203M/L452R variant relative to that of the L452R-only variant. These results do not indicate that there is no contribution of the R203M mutation to the disease severity of Delta. Hence, a more comprehensive survey and in-depth investigation are needed.

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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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   Results from scite Reference Check: We found no unreliable references.

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   Read the original source
2. 

   Version published to 10.1101/2021.12.20.473471 on bioRxiv

   Dec 23, 2021