SARS-CoV-2 spike D614G change enhances replication and transmission
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SciScore for 10.1101/2020.10.27.357558: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources Supernatants were collected and quantified by western blotting using anti-human IgG secondary antibody (ThermoFisher A-21091). anti-human IgGsuggested: (Thermo Fisher Scientific Cat# A-21091, RRID:AB_2535747)Experimental Models: Cell Lines Sentences Resources Twenty-four hours before electroporation, BHK-SARS-N cells were treated with 1 μg ml−1 doxycyclin to express SARS-CoV N protein. BHK-SARS-Nsuggested: NoneFlow cytometry: A stable clone of BHK cells … SciScore for 10.1101/2020.10.27.357558: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources Supernatants were collected and quantified by western blotting using anti-human IgG secondary antibody (ThermoFisher A-21091). anti-human IgGsuggested: (Thermo Fisher Scientific Cat# A-21091, RRID:AB_2535747)Experimental Models: Cell Lines Sentences Resources Twenty-four hours before electroporation, BHK-SARS-N cells were treated with 1 μg ml−1 doxycyclin to express SARS-CoV N protein. BHK-SARS-Nsuggested: NoneFlow cytometry: A stable clone of BHK cells expressing exogenous hACE2 were pelleted and resuspended in reaction buffer (PBS pH7.4 with 0.02% tween-20 and 4% BSA) at a concentration of 5 × 106 cells/ml. 100 μl/well of the cells were aliquoted into a round-bottom 96-well plate and incubated on ice for at least 5 min. BHKsuggested: NoneTranscribed capped mRNA was electroporated into baby hamster kidney (BHK-21) cells expressing SARS-CoV N protein. BHK-21suggested: ATCC Cat# CRL-6282, RRID:CVCL_1914)In brief, Vero E6 cells were infected with P.1 viruses. Vero E6suggested: RRID:CVCL_XD71)Experimental Models: Organisms/Strains Sentences Resources To determine the ratios of S-614D:S-614G in competition assays in Epithelix and hACE2-KI mice, reverse transcription PCR was performed on extracted RNA using SuperScript™ IV One-step RT-PCR System (Invitrogen). hACE2-KIsuggested: NoneSoftware and Algorithms Sentences Resources After incubation, cells were washed in 200 μl PBST washing solution (PBS pH7.4 with 0.02% tween-20) once and then 100 μl of 1:300 diluted secondary antibody (ThermoFisher Cat # A-21091 for Fc-tag and ThermoFisher Cat # MA1-21315-647 for polyhistidine-tag) was added into each well of cells, mixed, and incubated on ice with shaking for 15 min. ThermoFisher Catsuggested: NoneGeneration of infectious cDNA clones using TAR cloning and rescue of recombinant viruses: To introduce the 614G mutation to the Spike gene, PCR mutagenesis (Supplementary Table 1) was performed on the pUC57 plasmid containing SARS-CoV-2 fragment 1010 using Q5® Site-Directed Mutagenesis Kit (New England BioLab). New England BioLabsuggested: NoneDNA concentration was determined using Qubit dsDNA HS (High Sensitivity) Assay (Thermo Fisher), and subsequently diluted to 200 ng in 50 μl of nuclease-free water for sequencing by Nanopore sequencing MinION. MinIONsuggested: (MinION, RRID:SCR_017985)For data analysis, TrimGalore v0.6.5 was used to remove low-quality reads and adaptors from the raw sequencing files. TrimGaloresuggested: NoneThe resulting trimmed paired-end reads were then aligned to the SARS-CoV-2 genome (GenBank accession MT108784) using Bowtie2 v2.3.5. Bowtie2suggested: (Bowtie 2, RRID:SCR_016368)Finally, a consensus sequence was generated for each virus stock using Samtools v1.10 with the -d option set to 10,000. Samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)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.
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SciScore for 10.1101/2020.10.27.357558: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Eight heterozygous female mice were inoculated intranasally (i.n.) in a competition experiment with a mixture of both viruses, SARS-CoV-2S-614D and SARS-CoV-2S-614G, using 1x105 plaque forming unit (PFU) of each variant (Figure 2A). Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources ( of three replicates (Vero E6) and four replicates (hNE). Vero E6suggested: RRID:CVCL_XD71)Software … SciScore for 10.1101/2020.10.27.357558: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Eight heterozygous female mice were inoculated intranasally (i.n.) in a competition experiment with a mixture of both viruses, SARS-CoV-2S-614D and SARS-CoV-2S-614G, using 1x105 plaque forming unit (PFU) of each variant (Figure 2A). Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources ( of three replicates (Vero E6) and four replicates (hNE). Vero E6suggested: RRID:CVCL_XD71)Software and Algorithms Sentences Resources Data availability Sequencing data from passage 1 virus stocks for recombinant SARS-CoV-2S-614D and SARS- CoV-2S-614G, as well as data from all in vitro and in vivo competition experiments, will be made available on the NCBI Sequence Read Archive (SRA) NCBI Sequence Read Archivesuggested: (NCBI Sequence Read Archive (SRA, RRID:SCR_004891)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.
About SciScore
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