Evolution and genetic diversity of SARS-CoV-2 in Africa using whole genome sequences

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1. Version published to 10.1016/j.ijid.2020.11.190

   Feb 1, 2021
2. 

   ScreenIT

   Jul 30, 2020

   SciScore for 10.1101/2020.07.27.222901: (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
   Maximum likelihood phylogenetic analysis was performed using the general time reversible nucleotide substitution model with gamma distributed rate variation GTR-Γ(Yang et al, 1994) with 1000 bootstrap replicates using IQ-TREE software (Nguyen et al 2015).	IQ-TREE suggested: (IQ-TREE, RRID:SCR_017254)
   ANALYSIS: Temporal clock signal was analyzed among the aligned sequences using TempEst version 1.5 (Rambault et al, 2016).	TempEst suggested: (TempEst, RRID:SCR_017304)
   Phylogenetic trees were generated by Bayesian inference through Markov chain Monte Carlo (MCMC), implemented in BEAST version …

   SciScore for 10.1101/2020.07.27.222901: (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
   Maximum likelihood phylogenetic analysis was performed using the general time reversible nucleotide substitution model with gamma distributed rate variation GTR-Γ(Yang et al, 1994) with 1000 bootstrap replicates using IQ-TREE software (Nguyen et al 2015).	IQ-TREE suggested: (IQ-TREE, RRID:SCR_017254)
   ANALYSIS: Temporal clock signal was analyzed among the aligned sequences using TempEst version 1.5 (Rambault et al, 2016).	TempEst suggested: (TempEst, RRID:SCR_017304)
   Phylogenetic trees were generated by Bayesian inference through Markov chain Monte Carlo (MCMC), implemented in BEAST version 1.10.4 (Suchard et al, 2016).	BEAST suggested: (BEAST, RRID:SCR_010228)
   Results were then visualized with Tracer version 1.8.	Tracer suggested: (Tracer, RRID:SCR_019121)
   E PROTEIN: Complete S protein gene sequence of AfrSARSCoV-2 was aligned along with RaTG13 BtCoV and Pangolin SARSrCoV sequences using MAFFT (Katoh et al, 2015).	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   The alignment was then edited and visualized using BioEdit software.	BioEdit suggested: (BioEdit, RRID:SCR_007361)

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   Results from OddPub: Thank you for sharing your code.

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   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   A major limitation was the rather small number of sequences analyzed and very short study duration; therefore our results may not reflect the exact viral population dynamic of the outbreak in Africa. The AfrSARSCoV-2 sequences were analyzed for the D614-G mutation within the S1 subunit of the spike protein, which has been reported to contribute to increased transmissibility of SARSCoV-2 (Korber et al, 2020). Figure 7 shows a representative amino acid alignment of selected Afr SARSCoV-2 sequences along with reference sequences of BtCoV RaTG13 and PCoV. Our results revealed high prevalence of D614-G mutation among AfrSARSCoV-2 with 12/69 (17.39%). The mutation was recorded in isolates from all African countries analyzed in this study, supplementary figure 2. Prior to this report the D614-G spike mutation was found predominantly in Europe accompanied by high number of cases and significant mortality rate (Pachetti et al, 2020; Korber et al, 2020b). The introduction of this strain in Africa is quite worrisome, considering the population densities of most African cities and the poor state of public health infrastructure to support medical intervention of symptomatic SARSCoV-2 cases. Although more evidence is still required to determine the extent of the effect of the D614-G mutation on the virulence properties of the virus, current evidence from in vitro studies seem to support the hypothesis of increased transmissibility of this variant of the virus (Korber et al, 2020; Hu et al,...

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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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3. 

   ScreenIT

   Jul 30, 2020

   SciScore for 10.1101/2020.07.27.222901: (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
   Maximum likelihood phylogenetic analysis was performed using the general time reversible nucleotide substitution model with gamma distributed rate variation GTR-Γ(Yang et al, 1994) with 1000 bootstrap replicates using IQ-TREE software (Nguyen et al 2015).	IQ-TREE suggested: (IQ-TREE, RRID:SCR_017254)
   EVOLUTIONARY AND TIME SCALED PHYLOGENETIC ANALYSIS Temporal clock signal was analyzed among the aligned sequences using TempEst version 1.5 (Rambault et al, 2016).	…

   SciScore for 10.1101/2020.07.27.222901: (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
   Maximum likelihood phylogenetic analysis was performed using the general time reversible nucleotide substitution model with gamma distributed rate variation GTR-Γ(Yang et al, 1994) with 1000 bootstrap replicates using IQ-TREE software (Nguyen et al 2015).	IQ-TREE suggested: (IQ-TREE, RRID:SCR_017254)
   EVOLUTIONARY AND TIME SCALED PHYLOGENETIC ANALYSIS Temporal clock signal was analyzed among the aligned sequences using TempEst version 1.5 (Rambault et al, 2016).	TempEst suggested: (TempEst, RRID:SCR_017304)
   The relaxed clock with Gausian Markov Random Field Skyride plot (GMRF) coalescent prior was selected for the final analysis, after running different models and comparing them using Bayes factor with marginal likelihood estimated using the path sampling and stepping stone methods implemented in BEAST version 1.10.4 (Suchard et al, 2016).	BEAST suggested: (BEAST, RRID:SCR_010228)
   Bayesian skyride analysis was carried out to visualize the epidemic evolutionary history using Tracer v 1.8. ANALYSIS OF SARSCoV-2 SPIKE PROTEIN Complete S protein gene sequence of AfrSARSCoV-2 was aligned along with RaTG13 BtCoV and Pangolin SARSrCoV sequences using MAFFT (Katoh et al, 2015).	Tracer suggested: (TraCeR , RRID:SCR_016338) MAFFT suggested: (MAFFT, RRID:SCR_011811)
   The alignment was then edited and visualized using BioEdit software.	BioEdit suggested: (BioEdit, RRID:SCR_007361)

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   Results from OddPub: Thank you for sharing your code.

   ---

   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 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.

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   About SciScore

   SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

   Read the original source
4. 

   ScreenIT

   Jul 28, 2020

   SciScore for 10.1101/2020.07.27.222901: (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
   Maximum likelihood phylogenetic analysis was performed using the general time reversible nucleotide substitution model with gamma distributed rate variation GTR-Γ(Yang et al, 1994) with 1000 bootstrap replicates using IQ-TREE software (Nguyen et al 2015).	IQ-TREE suggested: (IQ-TREE, SCR_017254)
   PHYLOGENETIC ANALYSIS Temporal clock signal was analyzed among the aligned sequences using TempEst version 1.5 (Rambault et al, 2016).	TempEst suggested: (TempEst, SCR_017304) …

   SciScore for 10.1101/2020.07.27.222901: (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
   Maximum likelihood phylogenetic analysis was performed using the general time reversible nucleotide substitution model with gamma distributed rate variation GTR-Γ(Yang et al, 1994) with 1000 bootstrap replicates using IQ-TREE software (Nguyen et al 2015).	IQ-TREE suggested: (IQ-TREE, SCR_017254)
   PHYLOGENETIC ANALYSIS Temporal clock signal was analyzed among the aligned sequences using TempEst version 1.5 (Rambault et al, 2016).	TempEst suggested: (TempEst, SCR_017304)
   Phylogenetic trees were generated by Bayesian inference through Markov chain Monte Carlo (MCMC), implemented in BEAST version 1.10.4 (Suchard et al, 2016).	BEAST suggested: (BEAST, SCR_010228)
   Bayesian skyride analysis was carried out to visualize the epidemic evolutionary history using Tracer v 1.8	Tracer suggested: (TraCeR , SCR_016338)
   PROTEIN Complete S protein gene sequence of AfrSARSCoV-2 was aligned along with RaTG13 BtCoV and Pangolin SARSrCoV sequences using MAFFT (Katoh et al, 2015).	MAFFT suggested: (MAFFT, SCR_011811)
   The alignment was then edited and visualized using BioEdit software.	BioEdit suggested: (BioEdit, SCR_007361)

   Data from additional tools added to each annotation on a weekly basis.

   About SciScore

   SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.

   Read the original source
5. 

   Version published to 10.1101/2020.07.27.222901v1 on bioRxiv

   Jul 27, 2020