Phylogenetic Analysis of SARS-CoV-2 Genomes in Turkey

  1. Ogün Adebalı
  2. Aylin Bırcan
  3. Defne Çırcı
  4. Burak İşlek
  5. Zeynep Kilinç
  6. Berkay Selçuk
  7. Berk Turhan

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Abstract

COVID-19 has effectively spread worldwide. As of May 2020, Turkey is among the top ten countries with the most cases. A comprehensive genomic characterization of the virus isolates in Turkey is yet to be carried out. Here, we built a phylogenetic tree with globally obtained 15,277 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes. We identified the subtypes based on the phylogenetic clustering in comparison with the previously annotated classifications. We performed a phylogenetic analysis of the first thirty SARS-CoV-2 genomes isolated and sequenced in Turkey. We suggest that the first introduction of the virus to the country is earlier than the first reported case of infection. Virus genomes isolated from Turkey are dispersed among most types in the phylogenetic tree. We find two of the seventeen sub-clusters enriched with the isolates of Turkey, which likely have spread expansively in the country. Finally, we traced virus genomes based on their phylogenetic placements. This analysis suggested multiple independent international introductions of the virus and revealed a hub for the inland transmission. We released a web application to track the global and interprovincial virus spread of the isolates from Turkey in comparison to thousands of genomes worldwide.

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  1. ScreenIT

    SciScore for 10.1101/2020.05.15.095794: (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
    We used Augur toolkit to align whole genome sequences using mafft algorithm (--reorder --anysymbol – nomemsave) (Katoh and Standley 2016).
    Augur
    suggested: None
    For the sample EPI-ISL-428718 we additionally built a separate maximum likelihood phylogenetic tree by using IQ-TREE multicore version 1.6.1 with Ultra-fast Bootstrapping option and 1000 bootstraps.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    The tree was visualized in FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/), and rerooted by selecting EPI_ISL_428718 as an outgroup.
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    The GFF file of the reference genome (GCF_009858895.2) was extracted from NCBI Genome database.
    NCBI Genome
    suggested: (NCBI Genome, RRID:SCR_002474)

    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: We detected the following sentences addressing limitations in the study:
    We aim to eliminate the technical limitations (because of the size) by applying filtering methods without losing any relevant information.

    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.

  2. Version published to 10.1101/2020.05.15.095794 on bioRxiv