Low-Cost Manually Assembled Open Source Reader for Isothermal Pathogen Detection from Saliva using RT-LAMP: SARS-CoV-2 Use Case

  1. John C. Bramley
  2. Jason E. Waligorski
  3. Colin L. Kremitzki
  4. Mariel J. Liebeskind
  5. Alex L. Yenkin
  6. Xinyuan E. Xu
  7. Matthew A. Lalli
  8. Jane A. O’Halloran
  9. Philip A. Mudd
  10. Stacey L. House
  11. Robi D. Mitra
  12. Jeffrey D. Milbrandt
  13. William J. Buchser

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Abstract

Distributed “Point-of-Care” or “at-Home” testing is an important component for a complete suite of testing solutions. This manuscript describes the construction and operation of a platform technology designed to meet this need. The ongoing COVID-19 pandemic will be used as the proof-of-concept for the efficacy and deployment of this platform. The technology outlined consists of a one-pot, reverse-transcription loop-mediated isothermal amplification (RT-LAMP) chemistry coupled with a low-cost and user-assembled reader using saliva as input. This platform is readily adapted to a wide range of pathogens due to the genetic basis of the reaction. A complete guide to the construction of the reader as well as the production of the reaction chemistry are provided here. Additionally, analytical limit of detection data and the results from saliva testing of SARS-CoV-2, are presented. The platform technology outlined here demonstrates a rapid, distributed, molecular point-of-care solution for pathogen detection using crude sample input.

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  1. ScreenIT

    SciScore for 10.1101/2020.10.19.20215319: (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

    No key resources detected.

    Results from OddPub: Thank you for sharing your code.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    The current reporting delays and supply chain limitations in COVID-19 diagnostics experienced by centralized laboratory testing platforms demonstrates the need for distributed, accessible, and more rapid testing solutions. Antigen tests provide one alternative to meet these criteria, however, while offering both a cost savings and turnaround speed advantage, they suffer from lower sensitivity and specificity. Here we present a distributed extraction-free saliva-based molecular testing platform with a less than 30-minute run time. This solution consists of an isothermal LAMP reaction coupled with a low cost, heated fluorescence reader. The results of this are a one-pot, genetic, real time, point of care platform technology for pathogen detection. The development of this reader was driven by the idea of creating a platform technology that could be readily and rapidly deployed across a wide range of use cases. As a result, the reader only occupies a small footprint and is compatible with both AC and battery power. Battery power allows the user to perform field testing and deploy the solution in under-resourced environments. The AC power option allows for repetitive testing in areas where central laboratory-based testing is insufficient or unavailable. To achieve a simple reader design, the chemistry constituting the reaction needed to require little to no sample manipulation as well as minimally invasive conditions. As a result, the isothermal nature of RT-LAMP provided an adequ...

    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

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  2. Version published to 10.1101/2020.10.19.20215319 on medRxiv