SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing
SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing
Structured Abstract BackgroundThe 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) (1). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce (2). 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. MethodsWe 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 activation 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. ResultsAfter optimization, SwabExpress has a low limit of detection at 2-4 molecules/uL, 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. ConclusionSwabExpress 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.
Wolf Caitlin R.、Chen Wei、Gehring Jase、Bedford Trevor、Ilcisin Misja、Geyer Rachel E.、Srivatsan Sanjay、Heidl Sarah、Zhong Weizhi、van Raay Katrina、McDermot Evan、Opsahl Jordan、Stone Jeremy、McCulloch Denise J.、Kim Ashley E.、Gamboa Luis、Lockwood Christina M.、Sohlberg Sarah L.、Chu Helen Y.、Debley Jason S.、Pfau Brian、Starita Lea M.、Konnick Eric Q.、Barrow Kaitlyn A.、Martin Beth K.、Shendure Jay、Rieder Mark J.、Cho Shari、Han Peter D.、Truong Melissa、Seattle Flu Study Investigators、Smith Nahum、Kosuri Sriram、Rich Lucille M.、Nickerson Deborah A.、Brandstetter Elisabeth
Department of Allergy and Infectious Disease, University of WashingtonDepartment of Genome Sciences, University of WashingtonDepartment of Genome Sciences, University of WashingtonDepartment of Genome Sciences, University of Washington||Brotman Baty Institute For Precision Medicine||Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research CenterVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research CenterDepartment of Family Medicine, University of Washington, SeattleDepartment of Genome Sciences, University of WashingtonBrotman Baty Institute For Precision MedicineBrotman Baty Institute For Precision MedicineBrotman Baty Institute For Precision MedicineBrotman Baty Institute For Precision MedicineBrotman Baty Institute For Precision MedicineBrotman Baty Institute For Precision MedicineDepartment of Allergy and Infectious Disease, University of WashingtonDepartment of Allergy and Infectious Disease, University of WashingtonBrotman Baty Institute For Precision MedicineDepartment of Genome Sciences, University of Washington||Brotman Baty Institute For Precision Medicine||Department of Laboratory Medicine and PathologyDepartment of Allergy and Infectious Disease, University of WashingtonBrotman Baty Institute For Precision Medicine||Department of Allergy and Infectious Disease, University of WashingtonCenter for Immunity and Immunotherapies, Seattle Children?ˉs Research InstituteBrotman Baty Institute For Precision MedicineDepartment of Genome Sciences, University of Washington||Brotman Baty Institute For Precision MedicineBrotman Baty Institute For Precision Medicine||Department of Laboratory Medicine and PathologyCenter for Immunity and Immunotherapies, Seattle Children?ˉs Research InstituteDepartment of Genome Sciences, University of WashingtonDepartment of Genome Sciences, University of Washington||Brotman Baty Institute For Precision Medicine||Howard Hughes Medical InstituteBrotman Baty Institute For Precision MedicineBrotman Baty Institute For Precision MedicineBrotman Baty Institute For Precision MedicineBrotman Baty Institute For Precision MedicineBrotman Baty Institute For Precision MedicineOctant, Inc. Emeryville CA||Department of Chemistry and Biochemistry, University of CaliforniaCenter for Immunity and Immunotherapies, Seattle Children?ˉs Research InstituteDepartment of Genome Sciences, University of Washington||Brotman Baty Institute For Precision MedicineBrotman Baty Institute For Precision Medicine
医学研究方法基础医学微生物学
Wolf Caitlin R.,Chen Wei,Gehring Jase,Bedford Trevor,Ilcisin Misja,Geyer Rachel E.,Srivatsan Sanjay,Heidl Sarah,Zhong Weizhi,van Raay Katrina,McDermot Evan,Opsahl Jordan,Stone Jeremy,McCulloch Denise J.,Kim Ashley E.,Gamboa Luis,Lockwood Christina M.,Sohlberg Sarah L.,Chu Helen Y.,Debley Jason S.,Pfau Brian,Starita Lea M.,Konnick Eric Q.,Barrow Kaitlyn A.,Martin Beth K.,Shendure Jay,Rieder Mark J.,Cho Shari,Han Peter D.,Truong Melissa,Seattle Flu Study Investigators,Smith Nahum,Kosuri Sriram,Rich Lucille M.,Nickerson Deborah A.,Brandstetter Elisabeth.SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing[EB/OL].(2025-03-28)[2025-06-16].https://www.biorxiv.org/content/10.1101/2020.04.22.056283.点此复制
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