Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 lineages Gamma and P.2 in Brazil

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1. Version published to 10.1016/j.isci.2022.104156

   Apr 1, 2022
2. 

   Version published to 10.1101/2021.10.24.21265116v2 on medRxiv

   Nov 9, 2021
3. 

   ScreenIT

   Oct 29, 2021

   SciScore for 10.1101/2021.10.24.21265116: (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
   All files were downloaded and imported into Geneious v10.2.6 for trimming and assembling using a customized workflow employing BBDuk and BBMap tools (v37.25) and the NC_045512.2 RefSeq as a template.	Geneious suggested: (Geneious, RRID:SCR_010519) BBMap suggested: (BBmap, RRID:SCR_016965) RefSeq suggested: (RefSeq, RRID:SCR_003496)
   Analysis of temporal signal: SARS-CoV-2 Gamma and P.2 complete genome sequences were aligned using MAFFT v7.467 21 and subject to maximum likelihood (ML) phylogenetic analysis using IQ-TREE v2.1.2 22 under the general time-reversible (GTR) model of nucleotide …

   SciScore for 10.1101/2021.10.24.21265116: (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
   All files were downloaded and imported into Geneious v10.2.6 for trimming and assembling using a customized workflow employing BBDuk and BBMap tools (v37.25) and the NC_045512.2 RefSeq as a template.	Geneious suggested: (Geneious, RRID:SCR_010519) BBMap suggested: (BBmap, RRID:SCR_016965) RefSeq suggested: (RefSeq, RRID:SCR_003496)
   Analysis of temporal signal: SARS-CoV-2 Gamma and P.2 complete genome sequences were aligned using MAFFT v7.467 21 and subject to maximum likelihood (ML) phylogenetic analysis using IQ-TREE v2.1.2 22 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 23.	IQ-TREE suggested: (IQ-TREE, RRID:SCR_017254) ModelFinder suggested: None
   The temporal signal of the P.1 and P.2 assembled datasets was assessed from the ML tree by performing a regression analysis of the root-to-tip divergence against sampling time using TempEst 24 and excluding outlier sequences that deviate more than 1.5 interquartile ranges from root-to-tip regression line, which included those Gamma and P.2 sequences with the oldest sampling dates.	TempEst suggested: (TempEst, RRID:SCR_017304)
   Markov Chain Monte Carlo (MCMC) was run sufficiently long to ensure convergence (effective sample size> 200) in all parameter estimates as assessed in TRACER v1.7 27.	TRACER suggested: (Tracer, RRID:SCR_019121)
   Alignments were generated using MAFFT v7.475 21 and visually inspected in AliView 29.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   The maximum clade credibility (MCC) tree was summarized with TreeAnnotator v1.10.	TreeAnnotator suggested: (BEAST2, RRID:SCR_017307)
   ML and MCC trees were visualized using FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/).	FigTree suggested: (FigTree, RRID:SCR_008515)
   To do so, ML phylogenetic trees constructed for both Gamma and P.2 datasets as explained above, were inputted in the BEAST xml file as starting and data trees and analyses were performed under a logistic coalescent prior, which outperformed [Bayes Factor (BF) > 3] the exponential prior in a Marginal Likelihood Estimation (MLE) of model fitness, and a strict molecular clock, as specified above.	Gamma suggested: (GAMMA, RRID:SCR_009484)
   Discrete Bayesian phylogeography: A set of 1000 and 900 trees was randomly selected from the posterior distribution of trees resulting from the BEAST analysis of the full Gamma and P.2 datasets, respectively.	BEAST suggested: (BEAST, RRID:SCR_010228)
   Viral migration history between all supported location transitions was then visualized in circular migration flow plots using the package “circlize” 34 available in R software (https://www.r-project.org).	https://www.r-project.org suggested: (R Project for Statistical Computing, RRID:SCR_001905)

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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: We detected the following sentences addressing limitations in the study:

   The most important limitation of our study was the uneven sampling among Brazilian states and throughout the time, which may have introduced some bias in phylogeographic analyses. Although the number of genomes analyzed in this study roughly follows the number of COVID-19 confirmed cases in Brazil (Figure 1A and 1B), the smaller sampling from September and December 2020 limited the potential of our analyzes to identify large state-specific P.2 clusters and to accurate estimates the earliest onset date of communitarian transmission of this variant in several locations. In addition, even though the datasets here analyzed comprise SARS-CoV-2 sequences from 24 out of 27 Brazilian states, the uneven distribution of these genomes among locations might have biased contributions to the overall inter-states’ transmissions. In summary, this molecular epidemiological study showed that the COVID-19 epidemic in Brazil from September 2020 to March 2021 was characterized by the emergence and spread of the lineage P.2 and the VOC Gamma that were the most prevalent SARS-CoV-2 variants at different time periods in the country. The spatial dispersion of these variants in Brazil was driven by short and long-distance viral transmission and both variants circulated cryptically in several locations for some weeks before being detected. The VOC Gamma displayed a higher transmissibility than lineage P.2 which explained the faster rate of spatial spread of this variant and its establishment as the dom...

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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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4. 

   Version published to 10.1101/2021.10.24.21265116v1 on medRxiv

   Oct 26, 2021