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A Saliva-Based RT-PCR SARS-CoV-2 Detection Assay: Development and Deployment

C.E. Credits: P.A.C.E. CE Florida CE
Speaker
  • NGS Core Manager La Jolla Institute for Immunology
    Biography

      Suzie Alarcon CGMBS, MB(ASCP)CM is the manager of the Next Generation Sequencing Core at the La Jolla Institute for Immunology (LJI) and Team Leader of Team LJI - winner of the XPRIZE Rapid COVID Testing competition. Suzie has 18 years of experience working in molecular biology in taste, nutrition metabolomics, prenatal clinical diagnostics, epigenetics, and immunology. Her current work focuses on driving research endeavors of collaborators across the US and applies her varied experience to advise on technical development and optimization of NGS upstream workflows. She received her BS in Biology from Ursinus College, PA, US and her clinical training at Sequenom, CA, US.


    Abstract

    A One-Step RT-qPCR assay based on the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel has been developed which can effectively detect SARS-CoV-2 particles from saliva samples which undergo both heat inactivation and direct lysis with detergent, eliminating the need to extract RNA. Human RNAseP detection ensures accessibility of challenging saliva samples, acting as a true internal control in a multiplexed reaction. 6ul reactions have been validated with positive clinical samples and perform well with a sensitivity of 94.7% or higher. Low volume testing increases throughput, decreases cost, and decreases total specimen volume requirement to 0.375ul. After the collection process is described in writing and through video instructions accessible online, participants are able to perform the collection at home without oversight, and failure to submit a quality sample is below 1%.

    Learning Objectives:

    1. To describe the relative advantages and disadvantages of a saliva-based assay to detect upper respiratory pathogens, specifically SARS-CoV-2.

    2. To describe the relative advantages and disadvantages of an RNA extraction-free protocol to detect upper respiratory pathogens, specifically SARS-CoV-2.

    3. To explore designing flexible and agile PCR-based protocols


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