Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

  1. Ronaldo da Silva Francisco Jr
  2. L. Felipe Benites
  3. Alessandra P. Lamarca
  4. Luiz G.P. de Almeida
  5. Alana Witt Hansen
  6. Juliana Schons Gularte
  7. Meriane Demoliner
  8. Alexandra L. Gerber
  9. Ana Paula de C Guimarães
  10. Ana Karolina Eisen Antunes
  11. Fagner Henrique Heldt
  12. Larissa Mallmann
  13. Bruna Hermann
  14. Ana Luiza Ziulkoski
  15. Vyctoria Goes
  16. Karoline Schallenberger
  17. Micheli Fillipi
  18. Francini Pereira
  19. Matheus Nunes Weber
  20. Paula Rodrigues de Almeida
  21. Juliane Deise Fleck
  22. Ana Tereza R. Vasconcelos
  23. Fernando Rosado Spilki

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Abstract

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  1. Version published to 10.1016/j.virusres.2021.198345
  2. ScreenIT

    SciScore for 10.1101/2021.01.21.21249764: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: This study was approved by the National Committee of Research Ethics and the Institutional Ethical Review Board of the Universidade de Feevale (protocol number: 33202820.7.1001.5348), following Brazilian regulations and international ethical standards.
    RandomizationWe included 180 genomes from the state of Rio de Janeiro containing sequences from C5, which had been observed in our genomes, as well as randomly selected genomes from other Brazilian states (n=201).
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Briefly, FastQC (v0.11.4) and trimmomatic v0.39 (Bolger et al., 2014) was used for quality control analysis and bad quality reads filtration, respectively.
    FastQC
    suggested: (FastQC, RRID:SCR_014583)
    trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    Pre-processed reads were mapped with BWA 0.7.17 software (Li and Durbin, 2009) to the Wuhan-Hu-1 reference genome (NC_045512.2).
    BWA
    suggested: (BWA, RRID:SCR_010910)
    To further sort, filter reads by mapping quality, and remove duplicates we used samtools v1.10 (Li et al., 2009) and picard v2.17.0 (http://broadinstitute.github.io/picard/).
    samtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    http://broadinstitute.github.io/picard/
    suggested: (Picard, RRID:SCR_006525)
    We then performed variant calling using GATK v4.1.7.0 (DePristo et al., 2011) for high-frequency variants and LoFreq v 2.1.5 (Wilm et al., 2012) for low-frequency genetic variants.
    GATK
    suggested: (GATK, RRID:SCR_001876)
    LoFreq
    suggested: (LoFreq, RRID:SCR_013054)
    We annotated the features of each variant with snpEff v4.5 (Cingolani et al., 2012).
    snpEff
    suggested: (SnpEff, RRID:SCR_005191)
    Whole genomic sequences were aligned with MAFFT v7.123b (Katoh and Standley, 2013) using the FFT-NS-2 algorithm.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Maximum Likelihood (ML) phylogenetic trees were inferred with IQ-TREE v2.0.3 (Nguyen et al., 2015) using the GTR+F+R2 nucleotide substitution model, which was selected by ModelTest algorithm built in IQ-TREE (Kalyaanamoorthy et al., 2017).
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    Finally, we assessed the clocklikeness of the inferred tree using TempEst v1.5.3 (Rambaut et al., 2016) to generate the root-to-tip regression against sampling dates (correlation coefficient=0.79, R2=0.63; detail of newly sequenced samples in Supplementary Figure S1).
    TempEst
    suggested: (TempEst, RRID:SCR_017304)

    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.
    • 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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.01.21.21249764v1 on medRxiv