Emergence and fast spread of B.1.1.7 lineage in Lebanon

  1. Mahmoud Younes
  2. Kassem Hamze
  3. Hassan Nassar
  4. Mohamad Makki
  5. Maysaa Ghadar
  6. Paul Nguewa
  7. Fadi Abdel Sater

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Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a rapid spread emerging disease. Recently, a new variant of this virus called SARS-CoV-2 VOC 202012/01 (or B.1.1.7 lineage), described in the United Kingdom (UK), has become highly prevalent in several countries. Its rate of transmission has been estimated to be greatly higher. B.1.1.7 lineage harbors 23 mutations co-existed for the first time in the same variant. Herein, we are interested only by the deletion mutation ΔH69/ΔV70 in the spike protein.

In the UK they were able to identify the increase of this new variant through the increase in the false negative result for the spike target of a three-target RT-PCR assay from Thermo Fisher Scientific (TaqPath kit). Later, the manufacturer announced that this false negative result is because of the deletion ΔH69/ΔV70 in the area targeted by the TaqPath Kit. Furthermore, The European CDC recommended that the use of this kit help to track the new variant.

Genome sequencing is the gold method to confirm the new variant, but observational studies provide also stronger evidence if similar models are observed in multiple countries, especially when randomized studies are not possible. In Lebanon, the highest number of confirmed cases were reported in first week of 2021. In the present study, we show the emergence and the fast spreading of the new variant in Lebanon and a relationship between SARS-CoV-2 transmission intensity and the frequency of the new variant during the first twelve days of January.

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  1. ScreenIT

    SciScore for 10.1101/2021.01.25.21249974: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    All PCR tests were performed using Applied Biosystems™ TaqPath™ COVID-19 assay.
    Applied Biosystems™
    suggested: (Applied Biosystems, RRID:SCR_005039)
    RNA was extracted from the clinical samples on Kingfisher flex purification system Thermo Fisher using MagMAX™ Viral/Pathogen Nucleic Acid Isolation Kit (Thermo fisher).
    Thermo Fisher using MagMAX™
    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:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • 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 10.1101/2021.01.25.21249974 on medRxiv