Molecular Characterization, Phylogenetic and Variation Analyzes of SARS-CoV-2 strains in Turkey

  1. Karamese Murat
  2. Ozgur Didem
  3. Tutuncu Emin Ediz

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Abstract

Introduction

We present the sequence analysis for 47 complete genomes for SARS-CoV-2 isolates on Turkish patients. To identify their genetic similarity, phylogenetic analysis was performed by comparing the worldwide SARS-CoV-2 sequences, selected from GISAID, to the complete genomes from Turkish isolates. In addition, we focused on the variation analysis to show the mutations on SARS-CoV-2 genomes.

Methods

Illumina MiSeq platform was used for sequencing the libraries. The raw reads were aligned to the known SARS-CoV-2 genome (GenBank: MN908947.3 ) using the Burrows-Wheeler aligner (v.0.7.1). The phylogenetic tree was constructer using Phylip v.3.6 with Neighbor-Joining and composite likelihood method. The variants were detected by using Genome Analysis Toolkit-HaplotypeCaller v.3.8.0 and were inspected on GenomeBrowse v2.1.2.

Results

All viral genome sequences of our isolates was located in lineage B under the different clusters such as B.1 (n=3), B.1.1 (n=28), and B.1.9 (n=16). According to the GISAID nomenclature, all our complete genomes were placed in G, GR and GH clades. Five hundred forty-nine total and 53 unique variants were detected. All 47 genomes exhibited different kinds of variants. The distinct variants consist of 274 missense, 225 synonymous, and 50 non-coding alleles.

Conclusion

The results indicated that the SARS-CoV-2 sequences of our isolates have great similarity with all Turkish and European sequences. Further studies should be performed for better comparison of strains, after more complete genome sequences will be released. We also believe that collecting and sharing any data about SARS-CoV-2 virus and COVID-19 will be effective and may help the related studies.

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  1. ScreenIT

    SciScore for 10.1101/2020.09.11.293183: (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 both the Republic of Turkey Ministry of Health COVID-19 Scientific Research Evaluation Commission (Approval date: 02/05/2020; number: 2020-05-02T16_13_50) and the Local Ethics Committee of Kafkas University Faculty of Medicine (Approval date: 06/05/2020 number: 80576354-050-99/130).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The quality of the raw data was examined by FastQC v.
    FastQC
    suggested: (FastQC, RRID:SCR_014583)
    0.11.5, and low-quality bases and primers were trimmed using Trimmomatic (version 0.32).
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    The consensus sequences were aligned via multiple sequence alignment using MAFFT v7.450 tool.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    The phylogenetic tree was constructer using Phylip v.
    Phylip
    suggested: (PHYLIP, RRID:SCR_006244)
    The variants were detected by using Genome Analysis Toolkit-HaplotypeCaller (GATK) v.3.8.0 and were inspected on GenomeBrowse v2.1.2 (GoldenHelix).
    Genome Analysis Toolkit-HaplotypeCaller
    suggested: None
    GATK
    suggested: (GATK, RRID:SCR_001876)

    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:
    Our study have some limitations; (I) the number of national genomes available at the time of analysis; and (II) the number of detected variations. These limitations should be eliminated for further studies. In conclusion, the results of present study indicated that the SARS-CoV-2 sequences of our isolates have great similarity with all Turkish and European sequences. Further studies should be performed for better comparison of strains, after more complete genome sequences will be released; however, these data may be useful to understand the dynamics of virus spread and may help the further vaccine and treatment studies. On the other hand, the increase of SARS-CoV-2 cases all over the world is giving more genomes that may present some visibility of populace structure. This study showed the common and new variations in SARS-CoV-2 isolates. The fight against COVID-19 will last long time until the effective vaccine or drug will be developed. However, we believe that collecting and sharing any data about SARS-CoV-2 virus and COVID-19 will be effective and may help the related studies. At that point, we should carry on detecting the new variations.

    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 10.1101/2020.09.11.293183v1 on bioRxiv