SARS-CoV-2 in the Republic of Guinea: Fragment and Whole-Genome Sequencing, Phylogenetic Analysis

  1. A.A. Kritsky
  2. Ya.M. Krasnov
  3. M. Keita
  4. S. Keita
  5. A.V. Fedorov
  6. A.P. Shevtsova
  7. N.P. Guseva
  8. E.V. Kazorina
  9. E.A. Sosedova
  10. A.D. Katyshev
  11. E.A. Naryshkina
  12. E.V. Kolomoets
  13. S.A. Shcherbakova
  14. A.Yu. Popova
  15. V.V. Kutyrev

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Abstract

Genetic diversity of SARS-CoV-2 isolates circulating in the Republic of Guinea in May and June 2020, as well as in March 2021, has been demonstrated using fragment (S gene) and whole genome sequencing of 14 strains. Analysis of nucleotide sequences and phylogenetic constructs make it possible to divide the studied strains into 3 groups. Comparison of the obtained data with the already available epidemiological data proves the initial importation of COVID-19 from Western European countries, and also demonstrates four independent import routes in two time periods (March 2020 and no later than March 2021).

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  1. ScreenIT

    SciScore for 10.1101/2021.07.28.454098: (What is this?)

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

    Table 1: Rigor

    EthicsField Sample Permit: Specimens – nasopharyngeal swabs were collected from suspected cases and contact persons as part of the public health emergency response of the Ministry of Health in the Republic of Guinea. Isolation of RNA from specimens was carried out using a kit for the isolation of nucleic acids “RiboPrep” (“InterLabService”, Russia).
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The genome was assembled through mapping the filtered reads to the reference genome (Wuhan-Hu-1 (NC_045512.2)) using the BWA software version 07.17.
    BWA
    suggested: (BWA, RRID:SCR_010910)
    Alignment of the nucleotide sequences of both complete genomes and the S gene was carried out using the MAFFT v.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Comparative phylogenetic analysis was conducted using the BioNumerics 7.6 software package (Applied Maths NV, Belgium) and the Maximum Parsimony algorithm.
    BioNumerics
    suggested: None

    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.

    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.

  2. Version published to 10.1101/2021.07.28.454098v1 on bioRxiv