Emergence and Spread of the SARS-CoV-2 Variant of Concern Delta across Different Brazilian Regions

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1. Version published to 10.1128/spectrum.02641-21

   Oct 26, 2022
2. 

   ScreenIT

   Dec 1, 2021

   SciScore for 10.1101/2021.11.25.21266251: (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 resulting dataset (n = 4,260) was aligned with MAFFT v7.453 (Katoh, 2002) and assigned to PANGO lineages (Rambaut et al., 2020) by the Pangolin algorithm (O’Toole et al., 2021).	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   Identification of Phylogenetic Clusters: An initial dataset of 4,260 sequences was employed in a Maximum Likelihood (ML) phylogenetic reconstruction with IQ-TREE v2.1.3 (Minh et al., 2020), using a GTR + I + F + Г4 nucleotide substitution model as selected by ModelFinder (Kalyaanamoorthy et al., 2017) to identify possible phylogenetic clusters of VOC Delta in Brazilian …

   SciScore for 10.1101/2021.11.25.21266251: (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 resulting dataset (n = 4,260) was aligned with MAFFT v7.453 (Katoh, 2002) and assigned to PANGO lineages (Rambaut et al., 2020) by the Pangolin algorithm (O’Toole et al., 2021).	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   Identification of Phylogenetic Clusters: An initial dataset of 4,260 sequences was employed in a Maximum Likelihood (ML) phylogenetic reconstruction with IQ-TREE v2.1.3 (Minh et al., 2020), using a GTR + I + F + Г4 nucleotide substitution model as selected by ModelFinder (Kalyaanamoorthy et al., 2017) to identify possible phylogenetic clusters of VOC Delta in Brazilian territory.	IQ-TREE suggested: (IQ-TREE, RRID:SCR_017254)
   To trace back their MRCA (Most Recent Common Ancestor) and reconstruct their spatial diffusion pattern, a time-scaled phylogenetic tree was inferred in the Bayesian Markov Chain Monte Carlo (MCMC) approach as implemented in the software package BEAST v1.10.4 (Drummond et al., 2002, Marc A Suchard et al., 2018) with BEAGLE (Suchard & Rambaut, 2009) to improve run-time efficiency.	BEAST suggested: (BEAST, RRID:SCR_010228) BEAGLE suggested: (BEAGLE, RRID:SCR_001789)
   MCMC chains were run for 200 × 106 generations, and convergence and uncertainty of parameter estimates were assessed by calculating the Effective Sample Size (ESS) and 95% Highest Probability Density (HPD) values with Tracer v1.7.1 (Rambaut et al., 2018).	Tracer suggested: (Tracer, RRID:SCR_019121)
   The maximum clade credibility (MCC) trees were summarized with TreeAnnotator v1.10.4 and visualized with FigTree v1.4.4 (Rambaut, 2009).	TreeAnnotator suggested: (BEAST2, RRID:SCR_017307) FigTree suggested: (FigTree, RRID:SCR_008515)
   All non-synonymous substitutions and deletions detected in the majority of sequences (≥ 75%) were represented in a heatmap generated with the ggplot2 package (https://ggplot2.tidyverse.org/reference/ggplot.html).	ggplot2 suggested: (ggplot2, RRID:SCR_014601)

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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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   Results from scite Reference Check: We found no unreliable references.

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3. 

   Version published to 10.1101/2021.11.25.21266251v1 on medRxiv

   Nov 28, 2021