Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa
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SciScore for 10.1101/2020.08.24.20176792: (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 The sequences were then aligned to the reference SARS-CoV-2 sequence (accession number: NC_045512) and alignment was conducted using multiple alignment program for amino acid or nucleotide sequences (MAFFT v. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Maximum likelihood phylogenetic analysis: The whole MENA S gene dataset was analyzed phylogenetically using the maximum likelihood (ML) approach in PhyML v3, with selection of the best nucleotide substitution model using Smart Model Selection (SMS), and depending on Akaike Information Criterion (AIK) (Guindon and Gascuel, 2003; Lefort et al., … SciScore for 10.1101/2020.08.24.20176792: (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 The sequences were then aligned to the reference SARS-CoV-2 sequence (accession number: NC_045512) and alignment was conducted using multiple alignment program for amino acid or nucleotide sequences (MAFFT v. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Maximum likelihood phylogenetic analysis: The whole MENA S gene dataset was analyzed phylogenetically using the maximum likelihood (ML) approach in PhyML v3, with selection of the best nucleotide substitution model using Smart Model Selection (SMS), and depending on Akaike Information Criterion (AIK) (Guindon and Gascuel, 2003; Lefort et al., 2017). PhyMLsuggested: (PhyML, RRID:SCR_014629)Samples of trees and parameters were collected every 20,000 steps after discarding a burn-in of 20%, and convergence was analyzed in Tracer v1.6.0 (Rambaut et al., 2015). Tracersuggested: (Tracer, RRID:SCR_019121)The maximum clade credibility (MCC) trees were assembled using TreeAnnotator in BEAST and were visualized using FigTree (Rambaut, 2012). BEASTsuggested: (BEAST, RRID:SCR_010228)FigTreesuggested: (FigTree, RRID:SCR_008515)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: We detected the following sentences addressing limitations in the study:Limitations of this study should be clearly stated and taken into consideration. The most obvious caveat in the study was sampling bias. In spite of reporting COVID-19 in all MENA countries, the following countries did not have S sequences submitted to GISAID: Syria, Libya, Yemen, Sudan and Palestine (Iraq had partial sequences that did not include the S gene). In addition, bias was observed for timing of sequence collection. Furthermore, only two countries (Oman and KSA) had more than 100 sequences available for analysis. Another point that should be considered is related to the molecular clock analysis, where we used a strong informative prior which may have affected our tMRCA estimates for dating the origins of the two large phylogenetic clusters. Sequencing errors should also be taken into account, which can partly explain some sporadic mutations that were found in this study.
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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