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SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing.

Sanjay Srivatsan1, Sarah Heidl2, Brian Pfau2

  • 1Department of Genome Sciences, University of Washington, Seattle WA, USA.

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|June 9, 2020
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Summary

SwabExpress simplifies severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing by bypassing nucleic acid extraction, using anterior nares swabs for direct-to-RT-qPCR. This streamlined protocol reduces costs and hands-on time while maintaining high accuracy for scaled COVID-19 diagnostics.

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Area of Science:

  • Clinical diagnostics
  • Molecular biology
  • Infectious disease research

Background:

  • The COVID-19 pandemic highlighted the need for scalable SARS-CoV-2 testing.
  • Global supply chain disruptions created shortages of critical testing reagents and materials.
  • Conventional RT-qPCR protocols require extensive sample processing, including nucleic acid extraction.

Approach:

  • Developed SwabExpress, a simplified end-to-end protocol for SARS-CoV-2 detection.
  • Utilized anterior nares swabs transported dry, bypassing the need for viral transport media.
  • Integrated heat treatment and proteinase K digestion for direct-to-RT-qPCR analysis.

Key Points:

  • SwabExpress achieved a low limit of detection (2-4 molecules/uL) with 100% sensitivity and 99.4% specificity.
  • The protocol demonstrated superior performance compared to an automated extraction system on real-world specimens.
  • Reduced costs and hands-on time were achieved without compromising test accuracy.

Conclusions:

  • SwabExpress offers a simplified workflow for scaled COVID-19 testing.
  • The protocol maintains high test performance, crucial during reagent shortages.
  • This approach can serve as a model for simplifying other PCR-based clinical tests during pandemics.