Emergence of SARS-CoV-2 through recombination and strong purifying selection
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Abstract
Frequent recombination and strong purifying selection facilitate the cross-species transmission of coronaviruses to humans.
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SciScore for 10.1101/2020.03.20.000885: (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 Pan_SL-CoV_GD/P1La sequence was generated by combining Pan_SL-CoV_GD/P1L (10) with some additional sequences from the NCBI BioProject database PRJNA5732983 (11, 37) to have a maximal coverage of the complete genome sequence for analysis. BioProjectsuggested: (NCBI BioProject, RRID:SCR_004801)The alignments for all coding regions were manually optimized based on the amino acid sequence alignment using SeaView 5.0.1. SeaViewsuggested: (SeaView, RRID:SCR_015059)Selection Analyses: Cumulative plots of the average behavior of each codon for all pairwise comparisons in the input data, for … SciScore for 10.1101/2020.03.20.000885: (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 Pan_SL-CoV_GD/P1La sequence was generated by combining Pan_SL-CoV_GD/P1L (10) with some additional sequences from the NCBI BioProject database PRJNA5732983 (11, 37) to have a maximal coverage of the complete genome sequence for analysis. BioProjectsuggested: (NCBI BioProject, RRID:SCR_004801)The alignments for all coding regions were manually optimized based on the amino acid sequence alignment using SeaView 5.0.1. SeaViewsuggested: (SeaView, RRID:SCR_015059)Selection Analyses: Cumulative plots of the average behavior of each codon for all pairwise comparisons in the input data, for insertions and deletions (indels), synonymous (syn), and nonsynonymous (nonsyn) mutations and values of the ratios of the rate of synonymous nucleotide substitutions per synonymous site and nonsynonymous substitutions per nonsynonymous site (dN/dS, or ω) were obtained using the LANL database tool SNAP (42). SNAPsuggested: (SNAP, RRID:SCR_007936)To investigate the impact of the deletion between residue 473 to 486 to the binding interface between SARS-CoV-2 and human ACE2, a homology model with the deletion was generated using I-TASSER (45). I-TASSERsuggested: (I-TASSER, RRID:SCR_014627)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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