Evolutionary Tracking of SARS-CoV-2 Genetic Variants Highlights an Intricate Balance of Stabilizing and Destabilizing Mutations
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Abstract
Since its initial isolation in Wuhan, China, large numbers of SARS CoV-2 genome sequences have been shared in publicly accessible repositories, thus enabling scientists to do detailed evolutionary analysis. We investigated the evolutionarily associated mutational diversity overlaid on the major phylogenetic lineages circulating globally, using 513 representative genomes. We detailed the phylogenetic persistence of key variants facilitating global expansion of the PANGOLIN variant B.1, including the recent, fast-expanding, B.1.1.7 lineage.
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SciScore for 10.1101/2020.12.22.423920: (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 Phylogenetic analysis: Genome sequences were aligned against the original Wuhan-Hu-1 genome (Accession: NC_045512) using multiple genome sequence alignment tool MAFFT (v6.240). MAFFTsuggested: (MAFFT, RRID:SCR_011811)1.6.1 (http://www.iqtree.org/) under the GTR nucleotide substitution model with 1000 bootstrap replicates. http://www.iqtree.org/suggested: (IQ-TREE, RRID:SCR_017254)Mutation Profiling: In order to identify the genetic variants, assembled genomes were mapped against the reference (Wuhan-Hu-1: Accession: NC_045512) using Snippy mapping and variant calling pipeline … SciScore for 10.1101/2020.12.22.423920: (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 Phylogenetic analysis: Genome sequences were aligned against the original Wuhan-Hu-1 genome (Accession: NC_045512) using multiple genome sequence alignment tool MAFFT (v6.240). MAFFTsuggested: (MAFFT, RRID:SCR_011811)1.6.1 (http://www.iqtree.org/) under the GTR nucleotide substitution model with 1000 bootstrap replicates. http://www.iqtree.org/suggested: (IQ-TREE, RRID:SCR_017254)Mutation Profiling: In order to identify the genetic variants, assembled genomes were mapped against the reference (Wuhan-Hu-1: Accession: NC_045512) using Snippy mapping and variant calling pipeline (https://github.com/tseemann/snippy). Mutation Profilingsuggested: NoneResults 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.
- No funding statement was detected.
- No protocol registration statement was detected.
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