Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa

  1. Olayinka Sunday Okoh
  2. Nicholas Israel Nii-Trebi
  3. Abdulrokeeb Jakkari
  4. Tosin Titus Olaniran
  5. Tosin Yetunde Senbadejo
  6. Anna Aba Kafintu-kwashie
  7. Emmanuel Oluwatobi Dairo
  8. Tajudeen Oladunni Ganiyu
  9. Ifiokakaninyene Ekpo Akaninyene
  10. Louis Odinakaose Ezediuno
  11. Idowu Jesulayomi Adeosun
  12. Michael Asebake Ockiya
  13. Esther Moradeyo Jimah
  14. David J. Spiro
  15. Elijah Kolawole Oladipo
  16. Nídia S. Trovão

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Abstract

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  1. Version published to 10.1016/j.isci.2022.103880
  2. ScreenIT

    SciScore for 10.1101/2021.05.17.21257341: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The aligned sequences were manually edited and cleaned in AliView version 1.26 (Larsson,
    AliView
    suggested: (AliView, RRID:SCR_002780)
    This dataset was subjected to multiple iterations of phylogeny reconstruction using IQ-TREE multicore software version v1.6.12 (Nguyen et al., 2015) with parameters -m GTR+G -nt 50
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    A similar approach to that described above (including alignment using MAFFT, manual inspection using AliView, phylogenetic tree reconstruction with IQ-TREE and exclusion of root-to-tip outliers using TempEst) was employed, resulting in a dataset with 5002 sequences with 29796 nucleotide base pairs.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    TempEst
    suggested: (TempEst, RRID:SCR_017304)
    Trees were rooted in the Wuhan-Hu-1 (accession number: MN908947.3) reference genome and visualized in FigTree version 1.4.4.
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    We conducted the analyses using the Molecular Evolutionary Genetics Analysis software version 10 (MEGA X) (Kumar et al., 2018, Stecher et al., 2020) and applied the maximum composite likelihood mode (Tamura et al., 2004).
    Molecular Evolutionary Genetics Analysis
    suggested: None
    The R packages used were maptools (Bivand et al., 2021), RColorBrewer (Neuwirth, 2014), maps (Becker et al., 2018), mapdata (Becker et al., 2018), readxl (Wickham and Bryan, 2019), ggplot2 (Kassambara, 2019), qwraps2 (DeWitt, 2021), dplyr (Wickham and Wickham, 2020), gridExtra (Auguie, 2017), ggcorrplot (Kassambara, 2019), ggpubr (Kassambara, 2020), gridExtra (Auguie, 2017), tidyr (Wickham and Henry, 2020), scatterpie (Yu, 2018), ggmap (Kahle and Wickham, 2013), and mapproj (McIlroy et al., 2020).
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)
    Detection of repeat patterns and motifs: The retrieved SARS-CoV-2 sequences from Africa were annotated using GLAM2 (http://meme-suite.org/tools/glam2).
    GLAM2
    suggested: (Glam2, RRID:SCR_016129)
    The Wuhan isolate with accession number NC_045512.2 was annotated for novel motifs, and the Biostrings R package from Bioconductor was used to find the motifs’ appearance in the retrieved African SARS-CoV-2 sequences.
    Biostrings
    suggested: (Biostrings, RRID:SCR_016949)
    Bioconductor
    suggested: (Bioconductor, RRID:SCR_006442)

    Results from OddPub: Thank you for sharing your code and data.

    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.

    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 10.1101/2021.05.17.21257341v1 on medRxiv