Rapid SARS-CoV-2 Adaptation to Available Cellular Proteases
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Abstract
Recently emerging SARS-CoV-2 variants B.1.1.7 (alpha variant), B.1.617.2 (delta variant), and B.1.1.529 (omicron variant) harbor spike mutations and have been linked to increased virus pathogenesis. The emergence of these novel variants highlights coronavirus adaptation and evolution potential, despite the stable consensus genotype of clinical isolates.
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SciScore for 10.1101/2020.08.10.241414: (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 MATERIALS AND METHODS Cell cultures and Viruses Vero E6 (ATCC CRL-1586) cells were maintained in DMEM medium supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 100 IU/mL penicillin and 100 μg/mL streptomycin. E6suggested: NoneCalu-3 (ATCC HTB-55) and Caco-2 (ATCC HTB-37) were cultured in Eagle's Minimum Essential Medium (EMEM) supplemented with 10% FCS, 2 mM L-glutamine, 100 IU/mL penicillin, 100 μg/mL streptomycin and 1x non-essential amino acid … SciScore for 10.1101/2020.08.10.241414: (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 MATERIALS AND METHODS Cell cultures and Viruses Vero E6 (ATCC CRL-1586) cells were maintained in DMEM medium supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 100 IU/mL penicillin and 100 μg/mL streptomycin. E6suggested: NoneCalu-3 (ATCC HTB-55) and Caco-2 (ATCC HTB-37) were cultured in Eagle's Minimum Essential Medium (EMEM) supplemented with 10% FCS, 2 mM L-glutamine, 100 IU/mL penicillin, 100 μg/mL streptomycin and 1x non-essential amino acid solution (Gibco MEM Calu-3suggested: ATCC Cat# HTB-55, RRID:CVCL_0609)SARS-CoV-2 infection and protease inhibition SARS-CoV-2 cell entry inhibition was tested by seeding Vero E6, Calu-3 or Caco-2 cells in 96well plates, one day before infection. Caco-2suggested: NoneThe virus supernatant was collected at 1 and 2 dpi and titrated on Vero E6 cells as described in SARS-CoV-2 titration section. Vero E6suggested: RRID:CVCL_XD71)Software and Algorithms Sentences Resources The plaque area was measured with help of ZEISS ZEN lite 3.0 (Blue edition), and plotted using GraphPad Prism. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)The resulting sequence reads were aligned with reference (BWA 0.7.8). BWAsuggested: (BWA, RRID:SCR_010910)The alignment file was sorted (SAMtools version 1.10) and realigned (GATK IndelRealigner version 3.7). GATKsuggested: (GATK, RRID:SCR_001876)Finally, pileup file (SAMtools) was created and mutation were detected with VarScan (version 2.3.9). SAMtoolssuggested: (Samtools, RRID:SCR_002105)VarScansuggested: (VARSCAN, RRID:SCR_006849)Mutation frequencies were converted to percent values and plotted with ggplot2 (R/Bioconductor 4.0) ggplot2suggested: (ggplot2, RRID:SCR_014601)For all statistical analyses, the GraphPad Prism 7 software package was used (GraphPad Software). GraphPadsuggested: (GraphPad Prism, RRID:SCR_002798)Results from OddPub: Thank you for sharing your code and data.
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 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
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.
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SciScore for 10.1101/2020.08.10.241414: (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 Calu-3 (ATCC HTB-55) and Caco-2 (ATCC HTB-37) were cultured in Eagle's Minimum Essential Medium (EMEM) supplemented with 10% FCS, 2 mM L-glutamine, 100 IU/mL penicillin, 100 μg/mL streptomycin and 1x non-essential amino acid solution (Gibco MEM Calu-3suggested: ATCC Cat# HTB-55, RRID:CVCL_0609)Caco-2suggested: NoneVero E6 seeded in a well of a 24-well plate were infected with 30 PFU of SARS CoV 2. Vero E6suggested: NoneSoftware and Algorithms Sentences Resources The plaque area was measured with help of ZEISS ZEN lite 3.0 (Blue edition), and plotted using GraphPad Prism. GraphPad Prismsu…SciScore for 10.1101/2020.08.10.241414: (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 Calu-3 (ATCC HTB-55) and Caco-2 (ATCC HTB-37) were cultured in Eagle's Minimum Essential Medium (EMEM) supplemented with 10% FCS, 2 mM L-glutamine, 100 IU/mL penicillin, 100 μg/mL streptomycin and 1x non-essential amino acid solution (Gibco MEM Calu-3suggested: ATCC Cat# HTB-55, RRID:CVCL_0609)Caco-2suggested: NoneVero E6 seeded in a well of a 24-well plate were infected with 30 PFU of SARS CoV 2. Vero E6suggested: NoneSoftware and Algorithms Sentences Resources The plaque area was measured with help of ZEISS ZEN lite 3.0 (Blue edition), and plotted using GraphPad Prism. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)The resulting sequence reads were aligned with reference (BWA 0.7.8). BWAsuggested: (BWA, RRID:SCR_010910)The alignment file was sorted (SAMtools version 1.10) and realigned (GATK IndelRealigner version 3.7). GATKsuggested: (GATK, RRID:SCR_001876)Finally, pileup file (SAMtools) was created and mutation were detected with VarScan (version 2.3.9). SAMtoolssuggested: (SAMTOOLS, RRID:SCR_002105)VarScansuggested: (VARSCAN, RRID:SCR_006849)Mutation frequencies were converted to percent values and plotted with ggplot2 (R/Bioconductor 4.0) ggplot2suggested: (ggplot2, RRID:SCR_014601)Results from OddPub: Thank you for sharing your code and data.
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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