Detection of a SARS-CoV-2 variant of concern in South Africa

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1. Version published to 10.1038/s41586-021-03402-9

   Mar 9, 2021
2. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2020.12.21.20248640: (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
   Mutations were confirmed visually with bam files using Geneious software (Biomatters Ltd, New Zealand).	Geneious suggested: (Geneious, RRID:SCR_010519)
   This was selected from the Nextstrain global reference dataset, plus the five most similar sequences to each of the South African sequences as defined by a local BLAST search.	BLAST suggested: (BLASTX, RRID:SCR_001653)
   The pipeline contains several python scripts that manage the analysis workflow.	python suggested: (IPython, RRID:SCR_001658)
   We extracted this cluster and constructed a preliminary maximum likelihood (ML) tree in IQ-tree, together …

   SciScore for 10.1101/2020.12.21.20248640: (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
   Mutations were confirmed visually with bam files using Geneious software (Biomatters Ltd, New Zealand).	Geneious suggested: (Geneious, RRID:SCR_010519)
   This was selected from the Nextstrain global reference dataset, plus the five most similar sequences to each of the South African sequences as defined by a local BLAST search.	BLAST suggested: (BLASTX, RRID:SCR_001653)
   The pipeline contains several python scripts that manage the analysis workflow.	python suggested: (IPython, RRID:SCR_001658)
   We extracted this cluster and constructed a preliminary maximum likelihood (ML) tree in IQ-tree, together with eight basal sequences from the region sampled June-September 2020.	IQ-tree suggested: (IQ-TREE, RRID:SCR_017254)
   We inspected this ML tree in TempEst v1.5.3 for the presence of a temporal (i.e. molecular clock) signal.	TempEst suggested: (TempEst, RRID:SCR_017304)
   As above, MCMC chains were run in duplicate for 100 million generations and sampled every 10 000 steps, with convergence assessed using Tracer v1.7.1.	Tracer suggested: (Tracer, RRID:SCR_019121)
   Selection analysis: To identify which, if any, of the observed mutations in the spike protein was most likely to increase viral fitness, we used the natural selection analysis of SARS-CoV-2 pipeline (https://observablehq.com/@spond/revised-sars-cov-2-analytics-page).	SARS-CoV-2 suggested: (Active Motif Cat# 91351, RRID:AB_2847848)
   We used the Pymol program (The PyMOL Molecular Graphics System, Version 2.2.0, Schrödinger, LLC.) for visualization.	PyMOL suggested: (PyMOL, RRID:SCR_000305)

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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:

   • 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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3. 

   Version published to 10.1101/2020.12.21.20248640 on medRxiv

   Dec 22, 2020