Survey of SARS-CoV-2 genetic diversity in two major Brazilian cities using a fast and affordable Sanger sequencing strategy

  1. Erick Gustavo Dorlass
  2. Karine Lima Lourenço
  3. Rubens Daniel Miserani Magalhães
  4. Hugo Sato
  5. Alex Fiorini
  6. Renata Peixoto
  7. Helena Perez Coelho
  8. Bruna Larotonda Telezynski
  9. Guilherme Pereira Scagion
  10. Tatiana Ometto
  11. Luciano Matsumiya Thomazelli
  12. Danielle Bruna Leal Oliveira
  13. Ana Paula Fernandes
  14. Edison Luiz Durigon
  15. Flavio Guimarães Fonseca
  16. Santuza Maria Ribeiro Teixeira

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

No abstract available

Article activity feed

  1. Version published to 10.1016/j.ygeno.2021.10.015
  2. ScreenIT

    SciScore for 10.1101/2021.07.02.21259802: (What is this?)

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

    Table 1: Rigor

    EthicsIACUC: Ethical Statement: Part of study involving samples from São Paulo city was approved by Instituto de Ciências Biomédicas ethical committee.
    IRB: The study involving samples from Belo Horizonte was approved by the UFMG Ethics Committee, CAAE-35074720.3.0000.5149. 2.2.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Sequence Analyses: Assembling of Sanger contigs were performed with the GeneStudio software [19].
    GeneStudio
    suggested: None
    These sequences were aligned by the MAFFT tool [20,21] with default parameters: 0 “Offset”, 1.53 “gap open penalty”, 0 “Maximum number of iterative refinements”.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Benchling platform[22] and AliView software [23] were used for visualization of alignments.
    Benchling
    suggested: (Benchling, RRID:SCR_013955)
    AliView
    suggested: (AliView, RRID:SCR_002780)
    Stacked Bar Plots were constructed with the R ggplot2 package.
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)
    Sequencing analysis was performed on Torrent server with IRMA plugin for read assembly and SnpEff for variant annotation.
    SnpEff
    suggested: (SnpEff, RRID:SCR_005191)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    When tailored to focus in genomic regions bearing signature mutations, the sequence length limitation of the Sanger sequencing strategy ceases to be a problem and become an advantage, as a much larger number of samples can be sequenced in a shorter period of time. The data present here showed that the method was able to accurately detect the appearance of the P.1 VOC in two of the largest Brazilian cities and was also able to unveil the strong capacity of the P.1 variant to disseminate and quickly replace the P.2 variant, which was prevalent lineage in both cities. Although beyond the scope of this study, a better understanding of the molecular mechanism behind the increased dissemination capacity as well as the implications of the spreading of distinct variants regarding vaccination and other methods for the control of the pandemic are certainly necessary. Further efforts towards mitigation of new COVID-19 waves may include studies that rely on a broad implementation of Sanger sequencing genotyping strategy such as the one described here.

    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.

    Results from scite Reference Check: We found no unreliable references.

    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 10.1101/2021.07.02.21259802v1 on medRxiv