Emergence of Two Distinct SARS-CoV-2 Gamma Variants and the Rapid Spread of P.1-like-II SARS-CoV-2 during the Second Wave of COVID-19 in Santa Catarina, Southern Brazil

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1. Version published to 10.3390/v14040695

   Mar 27, 2022
2. 

   Version published to 10.1101/2022.01.13.22268697v3 on medRxiv

   Feb 11, 2022
3. 

   ScreenIT

   Jan 19, 2022

   SciScore for 10.1101/2022.01.13.22268697: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics	IRB: This study was approved by the Federal University of Santa Catarina Ethics Committee (CAAE:
   Sex as a biological variable	not detected.
   Randomization	Briefly, complementary DNA (cDNA) was synthesized from viral RNA using 50 μM random primers and 200 U/μL Superscript IV reverse transcriptase (ThermoFisher Scientific, Waltham, MA, USA).
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Briefly, low-quality bases (Q < 25) and Illumina adapters were trimmed (19), and mapped to the human reference genome (hg19 - GCF_000001405.13) to remove contaminants using BWA v.	BWA suggested: (BWA, RRID:SCR_010910)
   1.3 (21) and mpileup function from …

   SciScore for 10.1101/2022.01.13.22268697: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics	IRB: This study was approved by the Federal University of Santa Catarina Ethics Committee (CAAE:
   Sex as a biological variable	not detected.
   Randomization	Briefly, complementary DNA (cDNA) was synthesized from viral RNA using 50 μM random primers and 200 U/μL Superscript IV reverse transcriptase (ThermoFisher Scientific, Waltham, MA, USA).
   Blinding	not detected.
   Power Analysis	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Briefly, low-quality bases (Q < 25) and Illumina adapters were trimmed (19), and mapped to the human reference genome (hg19 - GCF_000001405.13) to remove contaminants using BWA v.	BWA suggested: (BWA, RRID:SCR_010910)
   1.3 (21) and mpileup function from samtools v.	samtools suggested: (SAMTOOLS, RRID:SCR_002105)
   Mutations, deletions, and insertions were used to assess the dissimilarity of the genomes using the vegan R package v. 2.5.6 (25) with the Jaccard index method.	vegan suggested: (vegan, RRID:SCR_011950)
   The multidimensional scaling (MDS) and the distribution of variants in SC were plotted using the ggplot2 R package v. 3.3.0 (26)	ggplot2 suggested: (ggplot2, RRID:SCR_014601)
   7.310 (27) with default parameters and were manually curated using AliView v.	AliView suggested: (AliView, RRID:SCR_002780)
   A ML tree was constructed using the alignment, with GTR+F+I as the substitution model predicted by ModelFinder (29), 1,000 bootstrap runs using UFBoot tree optimization (30) and SH-like approximate likelihood ratio test (SH-aLRT) (31), using IQ-TREE v.	IQ-TREE suggested: (IQ-TREE, RRID:SCR_017254)
   Spike (S) gene sequence polymorphism and protein structure analysis: For structural analysis of S protein of VOC Gamma, 57 presented full-length S protein coverage of VOC Gamma sequenced in this study with 722 retrieved from GISAID (December 3rd, 2021), including the reference sequence (NC_045512.2) were aligned using MAFFT (27).	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   The mutations were highlighted and colored according to observed frequencies and built with PyMOL version 2.3.3 software (35).	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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   Results from scite Reference Check: We found no unreliable references.

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4. 

   Version published to 10.1101/2022.01.13.22268697v2 on medRxiv

   Jan 17, 2022
5. 

   Version published to 10.1101/2022.01.13.22268697v1 on medRxiv

   Jan 14, 2022