Rapid detection of SARS CoV-2 N501Y mutation in clinical samples

  1. Sirwan M.A. Al-Jaf
  2. Sherko Subhan Niranji

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Abstract

Severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) variants poses major threats in increasing infectivity, transmission, mortality of Coronavirus Disease 2019 (Covid-19). Additionally, SARS CoV-2 variants resist antibody neutralizations or may abolish vaccine efficacies. Researches to develop economical and fast methods will support the developing or poor countries to challenge the Covid-19 pandemic via tracking common mutations that may help to deploy the vaccination programs and control the virus. Current study has developed a novel low-cost rapid technique, exploiting real time PCR probes and conventional PCR specific primers, to identify N501Y mutation, which was independently emerged in the UK, South African and Brazilian variants. Currently, these variants tend to spread to all over the world and seem to be more infectious, transmissible and fatal. This study helps tracking the N501Y mutation for understanding its clinical and epidemiological characteristics, in those countries where sequencing facilities are lacking or expensive. Further study should focus on other common mutations in the variants of concerns of SARS CoV-2.

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  1. ScreenIT

    SciScore for 10.1101/2021.04.17.21255656: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Consent forms were filled by the participants and the study was approved by an ethical committee at the Department of Biology, University of Garmian that follow the rules adhered to the Declaration of Helsinki for human and animal research.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    No key resources detected.

    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:
    The limitation of the current work was that we can only explore the N501 mutation. Development of this method is required to identify other mutations such as K417N mutation, which co-occurred with N501Y in the South African B.1.351 variant, and K417T mutation, which is present in the Brazil variant. However, our sequencings found A570D and D614G mutations as well. Absence of K417N/T but presence of A570D in our sequences, suggested that the N501Y mutant samples are potentially the UK B.1.1.7 variant, not the South Africa or Brazil variants. Further study to find other common mutations such as K417N/T, E484K, P681H and Del69/70 residues of the spike protein should be taken into considerations.

    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 10.1101/2021.04.17.21255656v1 on medRxiv