Emergence of a recurrent insertion in the N-terminal domain of the SARS-CoV-2 spike glycoprotein
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
Article activity feed
-
-
-
-
-
SciScore for 10.1101/2021.04.17.440288: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Briefly, nucleotide sequences were aligned with MAFFT [39] and the resulting multiple sequence alignment was used as an input for a maximum likelihood phylogenetic inference analysis, carried out with IQ-TREE [40] under a generalized time reversible (GTR) model of molecular evolution. MAFFTsuggested: (MAFFT, RRID:SCR_011811)IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)Phylogenetic trees were rooted based on the oldest genotype available, which in this case was Wuhan-Hu-1, and graphically rendered using FigTree … SciScore for 10.1101/2021.04.17.440288: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Briefly, nucleotide sequences were aligned with MAFFT [39] and the resulting multiple sequence alignment was used as an input for a maximum likelihood phylogenetic inference analysis, carried out with IQ-TREE [40] under a generalized time reversible (GTR) model of molecular evolution. MAFFTsuggested: (MAFFT, RRID:SCR_011811)IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)Phylogenetic trees were rooted based on the oldest genotype available, which in this case was Wuhan-Hu-1, and graphically rendered using FigTree v.1.1.4. FigTreesuggested: (FigTree, RRID:SCR_008515)The number of non-synonymous mutations, insertions and deletions affecting the spike protein of at least 50% of the genomes belonging to the A.2.5 and B.1.214.2 lineages sampled from February 1st 2021 was calculated with MEGA X [41], compared with the reference genotype Wuhan-Hu-1. MEGAsuggested: (Mega BLAST, RRID:SCR_011920)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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
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.
-