Genomic and phylogenetic analyses of SARS-CoV-2 strains isolated in the city of Gwangju, South Korea

  1. Ji-eun Lee
  2. Jae Keun Chung
  3. Tae sun Kim
  4. Jungwook Park
  5. Mi hyeon Lim
  6. Da jeong Hwang
  7. Jin Jeong
  8. Kwang gon Kim
  9. Ji-eun Yoon
  10. Hye young Kee
  11. Jin jong Seo
  12. Min Ji Kim

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Abstract

Since the first identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China in late December 2019, the coronavirus disease 2019 (COVID-19) has spread fast around the world. RNA viruses, including SARS-CoV-2, have higher gene mutations than DNA viruses during virus replication. Variations in SARS-CoV-2 genome could contribute to efficiency of viral spread and severity of COVID-19. In this study, we analyzed the locations of genomic mutations to investigate the genetic diversity among isolates of SARS-CoV-2 in Gwangju. We detected non-synonymous and frameshift mutations in various parts of SARS-CoV-2 genome. The phylogenetic analysis for whole genome showed that SARS-CoV-2 genomes in Gwangju isolates are clustered within clade V and G. Our findings not only provide a glimpse into changes of prevalent virus clades in Gwangju, South Korea, but also support genomic surveillance of SARS-CoV-2 to aid in the development of efficient therapeutic antibodies and vaccines against COVID-19.

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  1. ScreenIT

    SciScore for 10.1101/2020.12.16.423178: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Sampling and viral RNA isolation: This study was approved by the Institutional Review Board (approval no. P01-202008-31-004) of Public Institutional Bioethics Committee designated by the Ministry of Health of Welfare (MOHW).
    IACUC: Sampling and viral RNA isolation: This study was approved by the Institutional Review Board (approval no. P01-202008-31-004) of Public Institutional Bioethics Committee designated by the Ministry of Health of Welfare (MOHW).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Inoculated monolayers of Vero cells were incubated in MEM supplemented with 2% FBS at 37°C in the presence of 5% CO2.
    Vero
    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:
    • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
    • No funding statement was detected.
    • 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 10.1101/2020.12.16.423178v1 on bioRxiv