Journal
CLINICAL CHEMISTRY
Volume 68, Issue 1, Pages 143-152Publisher
OXFORD UNIV PRESS INC
DOI: 10.1093/clinchem/hvab132
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Funding
- Gates Ventures
- DARPA [HR001117S0019]
- Bill and Melinda Gates Foundation
- Emergent Ventures
- NHGRI [1RM1HG010461-01]
- NIH/NIAID [K24AI150991-01S1]
- University of Washington
- United States Senate and House of Representative Bill 748, Coronavirus Aid, Relief, and Economic Security Act (CARES Act)
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SwabExpress is a simplified workflow that allows for scaled testing for COVID-19 without compromising test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests in times of critical shortages during pandemics.
BACKGROUND: The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse-transcription PCR (RT-qPCR). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce. To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction. METHODS: We evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral inactivation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance. RESULTS: After optimization, SwabExpress has a low limit of detection at 2-4 molecules/mL, 100% sensitivity, and 99.4% specificity when compared side by side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time. CONCLUSION: SwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics.
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