Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil

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1. Version published to 10.1128/spectrum.02366-21

   Feb 23, 2022
2. 

   ScreenIT

   Sep 17, 2021

   SciScore for 10.1101/2021.09.12.21263453: (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
   Subsequently, we evaluated the consensus files for quality using Nextclade tool v1.5.2 (https://clades.nextstrain.org), those with more than 1% of ambiguities “Ns” had the FASTQ files imported into Geneious Prime 2021 for trimming and assembling using a customized workflow employing BBDuk and BBMap tools (v38.84) and the NC_045512.2 RefSeq as a template with carefully visually inspection.	BBMap suggested: (BBmap, RRID:SCR_016965) RefSeq suggested: (RefSeq, RRID:SCR_003496)
   Sequences were aligned using MAFFT v7.475 (28) and then subjected to maximum-likelihood (ML) phylogenetic analysis using …

   SciScore for 10.1101/2021.09.12.21263453: (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
   Subsequently, we evaluated the consensus files for quality using Nextclade tool v1.5.2 (https://clades.nextstrain.org), those with more than 1% of ambiguities “Ns” had the FASTQ files imported into Geneious Prime 2021 for trimming and assembling using a customized workflow employing BBDuk and BBMap tools (v38.84) and the NC_045512.2 RefSeq as a template with carefully visually inspection.	BBMap suggested: (BBmap, RRID:SCR_016965) RefSeq suggested: (RefSeq, RRID:SCR_003496)
   Sequences were aligned using MAFFT v7.475 (28) and then subjected to maximum-likelihood (ML) phylogenetic analysis using IQ-TREE v2.1.2 (29) under the general time-reversible (GTR) model of nucleotide substitution with a gamma-distributed rate variation among sites, four rate categories (G4), a proportion of invariable sites (I) and empirical base frequencies (F) nucleotide substitution model, as selected by the ModelFinder application (30).	MAFFT suggested: (MAFFT, RRID:SCR_011811) IQ-TREE suggested: (IQ-TREE, RRID:SCR_017254)
   The temporal signal of the P.1 and P.1+ sequences was assessed from the ML tree by performing a regression analysis of the root-to-tip divergence against sampling time using TempEst (31).	TempEst suggested: (TempEst, RRID:SCR_017304)
   1.3 to P.1.8 plus P.1+Δ144 sampled in Brazil using the Bayesian Markov Chain Monte Carlo (MCMC) approach implemented in BEAST 1.10.4 (32) with BEAGLE library v3 (33) to improve computational time.	BEAST suggested: (BEAST, RRID:SCR_010228) BEAGLE suggested: (BEAGLE, RRID:SCR_001789)
   MCMC was run sufficiently long to ensure convergence (effective sample size [ESS] > 200) in all parameters estimates as assessed in TRACER v1.7 (37).	TRACER suggested: (Tracer, RRID:SCR_019121)
   The maximum clade credibility (MCC) tree was summarized with TreeAnnotator v1.10 and visualized using FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/).	TreeAnnotator suggested: (BEAST2, RRID:SCR_017307) FigTree suggested: (FigTree, RRID:SCR_008515)
   Graphics and statistical analyses were performed using GraphPad v9.02	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)

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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 10.1101/2021.09.12.21263453 on medRxiv

   Sep 15, 2021