Profiling of the most reliable mutations from sequenced SARS-CoV-2 genomes scattered in Uzbekistan

  1. Mirzakamol S. Ayubov
  2. Zabardast T. Buriev
  3. Mukhammadjon K. Mirzakhmedov
  4. Abdurakhmon N. Yusupov
  5. Dilshod E. Usmanov
  6. Shukhrat E. Shermatov
  7. Khurshida A. Ubaydullaeva
  8. Ibrokhim Y. Abdurakhmonov

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Abstract

Due to rapid mutations in the coronavirus genome over time and re-emergence of multiple novel variants of concerns (VOC), there is a continuous need for a periodic genome sequencing of SARS-CoV-2 genotypes of particular region. This is for on-time development of diagnostics, monitoring and therapeutic tools against virus in the global pandemics condition. Toward this goal, we have generated 18 high-quality whole-genome sequence data from 32 SARS-CoV-2 genotypes of PCR-positive COVID-19 patients, sampled from the Tashkent region of Uzbekistan. The nucleotide polymorphisms in the sequenced sample genomes were determined, including nonsynonymous (missense) and synonymous mutations in coding regions of coronavirus genome. Phylogenetic analysis grouped fourteen whole genome sample sequences (1, 2, 4, 5, 8, 10–15, 17, 32) into the G clade (or GR sub-clade) and four whole genome sample sequences (3, 6, 25, 27) into the S clade. A total of 128 mutations were identified, consisting of 45 shared and 83 unique mutations. Collectively, nucleotide changes represented one unique frameshift mutation, four upstream region mutations, six downstream region mutations, 50 synonymous mutations, and 67 missense mutations. The sequence data, presented herein, is the first coronavirus genomic sequence data from the Republic of Uzbekistan, which should contribute to enrich the global coronavirus sequence database, helping in future comparative studies. More importantly, the sequenced genomic data of coronavirus genotypes of this study should be useful for comparisons, diagnostics, monitoring, and therapeutics of COVID-19 disease in local and regional levels.

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  1. Version published to 10.1371/journal.pone.0266417
  2. ScreenIT

    SciScore for 10.1101/2022.02.10.479714: (What is this?)

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

    Table 1: Rigor

    EthicsField Sample Permit: The research study has been approved by the Ethics Committee under the Ministry of Health of the Republic of Uzbekistan (#6/20-1582).
    IRB: The research study has been approved by the Ethics Committee under the Ministry of Health of the Republic of Uzbekistan (#6/20-1582).
    Consent: We received a verbal consent for a voluntary participation from all patients involved for sample collection.
    Sex as a biological variableAmong all tested patients, 32 PCR-positive samples (18 females and 14 males) were selected for further studies, which were randomly selected.
    RandomizationBiological samples were collected randomly from PCR-positive patients after laboratory testing for SARS-CoV-2.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The filtered variants were used for sample clustering with Maximum Likelihood Tree in Molecular Evolutionary Genetics Analysis (MEGA, https://www.megasoftware.net) software.
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)

    Results from OddPub: Thank you for sharing your 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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    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

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  3. Version published to 10.1101/2022.02.10.479714v1 on bioRxiv