Detection of potential new SARS-CoV-2 Gamma-related lineage in Tocantins shows the spread and ongoing evolution of P.1 in Brazil
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Abstract
After more than a year of the pandemic situation of COVID-19, the United Kingdom (UK), South Africa, and Brazil became the epicenter of new lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Variants of Concern (VOCs) were identified through a continuous genomic surveillance global effort, the B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and P.1 (Gamma) harboring a constellation set of mutations. This research aims to: (i) report the predominance of the Gamma (P.1) lineage presenting the epidemiological situation of the SARS-CoV-2 genomic surveillance at the state of Tocantins, and (ii) describe the emergence of possible new mutations and viral variants with the potential new lineage (P1-related) represented by 8 genomes from the Tocantins harboring the mutation L106F in ORF3a. At the moment, 6,687 SARS-CoV-2 genomes from GISAID carry this mutation. The whole-genome sequencing has an important role in understanding the evolution and genomic diversity of SARS-CoV-2, thus, the continuous monitoring will help in the control measures and restrictions imposed by the secretary of health of the state to prevent the spread of variants.
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SciScore for 10.1101/2021.06.30.450617: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: The study was approved by the Ethics Committee (33202820.7.1001.5348). Sex as a biological variable Patients were aged between 01 and 80 years old, being 54.2% men and 45.8% women. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources 2.1.2 [16] under the Generalized Time Reversible GRT model of nucleotide substitution with empirical base frequencies (+F) and invariable sites (+I), as selected by the ModelFinder software. ModelFindersuggested: NoneThe final dataset consisting of 851 was aligned using MAFFT v. MAFFTsuggested: (MAFFT, RRID:SCR_011811)A Maximum Likelihood tree was generated using IQ-TREE v. IQ-TREEsugg…SciScore for 10.1101/2021.06.30.450617: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: The study was approved by the Ethics Committee (33202820.7.1001.5348). Sex as a biological variable Patients were aged between 01 and 80 years old, being 54.2% men and 45.8% women. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources 2.1.2 [16] under the Generalized Time Reversible GRT model of nucleotide substitution with empirical base frequencies (+F) and invariable sites (+I), as selected by the ModelFinder software. ModelFindersuggested: NoneThe final dataset consisting of 851 was aligned using MAFFT v. MAFFTsuggested: (MAFFT, RRID:SCR_011811)A Maximum Likelihood tree was generated using IQ-TREE v. IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)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).
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.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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