Room Temperature Isothermal Colorimetric Padlock Probe Rolling Circle Amplification for Viral DNA and RNA Detection

  1. Wilson Huang
  2. Joyce Ting
  3. Matthew Fang
  4. Hannah Hsu
  5. Jimmy Su
  6. Tsuyoshi Misaki
  7. Derek Chan
  8. Justin Yang
  9. Ting-Yu Yeh
  10. Kelly Yang
  11. Vera Chien
  12. Tiffany Huang
  13. Andrew Chen
  14. Claire Wei
  15. Jonathan Hsu
  16. Jude C. Clapper

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Abstract

Seasonal flu and pandemics, which account for millions of infections and hundreds of thousands of deaths, require rapid and reliable detection mechanisms to implement preventive and therapeutic measures. Current detection methods of viral infections have limitations in speed, accuracy, accessibility, and usability. This project presents a novel, widely applicable viral diagnostic test that uses a modified version of rolling circle amplification (RCA) to be sensitive, specific, direct RNA targeted, colorimetric and operable at room temperature. We are specifically detecting the following high-impact viruses: SARS-CoV-2, Influenza A (H1N1pdm09), and Influenza B (Victoria Lineage), although our test can be adapted to any viral infection. Results using synthetic viral DNA and RNA sequences show that our diagnostic test takes approximately one hour, detects femtomolar concentrations of RNA strands, and differentiates between virus strains. We believe implementing our diagnostic test will provide faster responses to future viral-related outbreaks for quicker societal recovery.

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  1. Version published to 10.1101/2020.06.12.128876v3 on bioRxiv
  2. Version published to 10.1101/2020.06.12.128876v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.06.12.128876: (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
    Synthetic Viral Targets, Probes and Primers: Both DNA and RNA targets were designed with BioEdit through SARS-CoV-2, Influenza A (H1N1pdm09), and Influenza B (Victoria Lineage) sequences provided in NCBI GenBank.
    BioEdit
    suggested: (BioEdit, RRID:SCR_007361)

    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.

  4. Version published to 10.1101/2020.06.12.128876v1 on bioRxiv