A Novel Strategy for the Detection of SARS-CoV-2 Variants Based on Multiplex PCR-Mass Spectrometry Minisequencing Technology

  1. Fei Zhao
  2. Jinxing Lu
  3. Bing Lu
  4. Tian Qin
  5. Xuemei Wang
  6. Xuexin Hou
  7. Fanliang Meng
  8. Xiaona Xu
  9. Tianyi Li
  10. Haijian Zhou
  11. Jianzhong Zhang
  12. Biao Kan
  13. Ying Huang
  14. Zehui Zhang
  15. Di Xiao

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Abstract

The emergence of SARS-CoV-2 variants is the key factor in the second wave of the COVID-19 pandemic. An all-in-one SARS-CoV-2 variant identification method based on a multiplex PCR-mass spectrometry minisequencing system was developed in this study.

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  1. Version published to 10.1128/spectrum.01267-21
  2. ScreenIT

    SciScore for 10.1101/2021.06.08.21258523: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: All the specimens collected from COVID-19 patients were collected with complete informed consent procedures.
    IRB: This study was approved by the ethics committee of ICDC.
    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:
    However, this method has some limitations. First, the 3’ terminal sequence of MPE prove is fixed, and the quality of the probe is greatly influenced by the base sequence near the detection site, which can lead to the inefficient detection in extreme cases. Second, there is no SARS-CoV-2 variants in this study, and the detection limit of mutant plasmid can only be used as reference. Finally, the number of clinical specimens used in this study is limited, and the number of validation specimens needs to further increased. As a simple screening assay for monitoring the emergence and spread of these SARS-CoV-2 variants, multiplex PCR-MALDI-TOF MS may be helpful for implementing public health strategies to counter these and future mutation strains.

    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.

    Results from scite Reference Check: We found no unreliable references.

    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.

  3. Version published to 10.1101/2021.06.08.21258523v1 on medRxiv