Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2

  1. Haibo Wu
  2. Na Xing
  3. Kaiwen Meng
  4. Beibei Fu
  5. Weiwei Xue
  6. Pan Dong
  7. Wanyan Tang
  8. Yang Xiao
  9. Gexin Liu
  10. Haitao Luo
  11. Wenzhuang Zhu
  12. Xiaoyuan Lin
  13. Geng Meng
  14. Zhenglin Zhu

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Abstract

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  1. Version published to 10.1016/j.chom.2021.11.005
  2. ScreenIT

    SciScore for 10.1101/2021.05.24.445386: (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
    SentencesResources
    African green monkey kidney epithelial Vero E6 cells (ATCC) and Human lung adenocarcinoma epithelial Calu-3 cells (ATCC) were maintained in a high-glucose Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% FBS (Gibco) at 37⍰°C with 5% CO2.
    Vero E6
    suggested: None
    Calu-3
    suggested: None
    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)
    Recombinant DNA
    SentencesResources
    Seven different DNA fragments spanning the entire genome of SARS-CoV-2 (USA_WA1/2020 SARS-CoV-2 sequence, GenBank accession No. MT020880) were synthesized by Beijing Genomics Institute (BGI, Shanghai, China) and cloned into pUC57 or pCC1 (kindly provided by Dr. Yonghui Zheng) plasmids by standard molecular cloning methods.
    pUC57
    suggested: RRID:Addgene_40306)
    pCC1
    suggested: RRID:Addgene_83007)
    For the generation of R203K/G204R mutant virus, nucleotide substitutions of GGG→AAC were introduced into a subclone of pUC57-F7 containing the nucleocapsid gene of the SARS-CoV-2 wild-type infectious clone by overlap-extension PCR.
    pUC57-F7
    suggested: None
    Software and Algorithms
    SentencesResources
    We assumed the sequence of the strain MN908947, collected in December 201942, as the ancestral state of the SARS-CoV-2 genome and performed genomic alignments between the 884736 SARS-CoV-2 strains and MN908947 by MUSCLE 43,44.
    MUSCLE
    suggested: (MUSCLE, RRID:SCR_011812)
    We processed reads by Bowtie2
    Bowtie2
    suggested: (Bowtie 2, RRID:SCR_016368)
    51, GATK Mark Duplicates 52,53
    GATK
    suggested: (GATK, RRID:SCR_001876)
    and SAMtools 54, requiring the mapping quality > 20 54.
    SAMtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    We calculated Pi, Theta 55 and Tajima’s D 56 by VariScan 2.0 57,58, and the composite likelihood ratio (CLR, step size = 50) 28,29 by SweepFineder2 59.
    VariScan
    suggested: None
    For comparisons of Pi, Theta and Tajima’s D between R203/G204 and 203K/204R, we used the BioPerl PopGen library 60 to perform population genetic calculation within R203/G204 SS and 203K/204R SS, respectively.
    BioPerl
    suggested: (BioPerl, RRID:SCR_002989)
    PopGen
    suggested: (POPGEN, RRID:SCR_007315)
    Then we constructed the phylogenetic tree by FastTree 61.
    FastTree
    suggested: (FastTree, RRID:SCR_015501)
    The curves of the relative infection rates versus the serum dilutions (log10 values) were plotted using GraphPad Prism 8.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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).

    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.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    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.

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

    About SciScore

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  3. Version published to 10.1101/2021.05.24.445386v1 on bioRxiv