Direct RNA sequencing and early evolution of SARS-CoV-2
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Abstract
Fundamental aspects of SARS-CoV-2 biology remain to be described, having the potential to provide insight to the response effort for this high-priority pathogen. Here we describe the first native RNA sequence of SARS-CoV-2, detailing the coronaviral transcriptome and epitranscriptome, and share these data publicly. A data-driven inference of viral genetic features and evolutionary rate is also made. The rapid sharing of sequence information throughout the SARS-CoV-2 pandemic represents an inflection point for public health and genomic epidemiology, providing early insights into the biology and evolution of this emerging pathogen.
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SciScore for 10.1101/2020.03.05.976167: (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
Software and Algorithms Sentences Resources Both signal-space and basecalled read data are available at BioProject PRJNA608224. BioProjectsuggested: (NCBI BioProject, RRID:SCR_004801)Subgenome bins were re-aligned, with coverage calculated in SAMtools [M4], and plotted using ggplot2 [M5] in R [M6]. SAMtoolssuggested: (SAMTOOLS, RRID:SCR_002105)ggplot2suggested: (ggplot2, RRID:SCR_014601)Assessment of publicly available proteomes: Proteomic datasets were downloaded from the PRIDE proteomic database [M11] (Pride accession: PXD017710) and processes using Maxquant (1.6.3.4 [M12]) allowing semi-specific free-N-terminus tryptic as a … SciScore for 10.1101/2020.03.05.976167: (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
Software and Algorithms Sentences Resources Both signal-space and basecalled read data are available at BioProject PRJNA608224. BioProjectsuggested: (NCBI BioProject, RRID:SCR_004801)Subgenome bins were re-aligned, with coverage calculated in SAMtools [M4], and plotted using ggplot2 [M5] in R [M6]. SAMtoolssuggested: (SAMTOOLS, RRID:SCR_002105)ggplot2suggested: (ggplot2, RRID:SCR_014601)Assessment of publicly available proteomes: Proteomic datasets were downloaded from the PRIDE proteomic database [M11] (Pride accession: PXD017710) and processes using Maxquant (1.6.3.4 [M12]) allowing semi-specific free-N-terminus tryptic as a protease specificity. PRIDEsuggested: (Pride-asap, RRID:SCR_012052)SARS-CoV-2 Phylogenetics: In order to estimate the evolutionary rate and time of origin of SARS-CoV-2, we carried out phylogenetic analyses in BEAST v1.101 [M13 on three datasets. BEASTsuggested: (BEAST, RRID:SCR_010228)Results from OddPub: Thank you for sharing your 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:- No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
- No funding statement was detected.
- No protocol registration statement was detected.
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