Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

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1. Version published to 10.1038/s41564-020-0771-4

   Jul 28, 2020
2. 

   ScreenIT

   Jun 5, 2020

   SciScore for 10.1101/2020.03.30.015008: (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
   A phylogenetic tree – using RAxML v8.2.8 (Stamatakis, 2014, 2006), GTR+Γ model, 100 bootstrap replicates – was inferred for each BFR longer than 500nt.	RAxML suggested: (RAxML, RRID:SCR_006086)
   In order to examine temporal signal in the sequenced data, we plotted root-to-tip divergence against sampling time using TempEst (Rambaut et al., 2016) based on a maximum likelihood tree.	TempEst suggested: (TempEst, RRID:SCR_017304)
   Time-measured phylogenetic reconstruction was performed using a Bayesian approach implemented in BEAST (Suchard et al., 2018).	BEAST suggested: (BEAST, RRID:SCR_010228)
   We used …

   SciScore for 10.1101/2020.03.30.015008: (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
   A phylogenetic tree – using RAxML v8.2.8 (Stamatakis, 2014, 2006), GTR+Γ model, 100 bootstrap replicates – was inferred for each BFR longer than 500nt.	RAxML suggested: (RAxML, RRID:SCR_006086)
   In order to examine temporal signal in the sequenced data, we plotted root-to-tip divergence against sampling time using TempEst (Rambaut et al., 2016) based on a maximum likelihood tree.	TempEst suggested: (TempEst, RRID:SCR_017304)
   Time-measured phylogenetic reconstruction was performed using a Bayesian approach implemented in BEAST (Suchard et al., 2018).	BEAST suggested: (BEAST, RRID:SCR_010228)
   We used TreeAnnotator to summarize the posterior tree distributions and annotated the estimated to a maximum clade credibility tree, which was visualized using FigTree.	FigTree suggested: (FigTree, RRID:SCR_008515)

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   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).

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   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.

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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:

   • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
   • 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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3. 

   Version published to 10.1101/2020.03.30.015008v1 on bioRxiv

   Mar 31, 2020