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SwabExpress: An End-to-End Protocol for Extraction-Free COVID-19 Testing.
Srivatsan, Sanjay; Heidl, Sarah; Pfau, Brian; Martin, Beth K; Han, Peter D; Zhong, Weizhi; van Raay, Katrina; McDermot, Evan; Opsahl, Jordan; Gamboa, Luis; Smith, Nahum; Truong, Melissa; Cho, Shari; Barrow, Kaitlyn A; Rich, Lucille M; Stone, Jeremy; Wolf, Caitlin R; McCulloch, Denise J; Kim, Ashley E; Brandstetter, Elisabeth; Sohlberg, Sarah L; Ilcisin, Misja; Geyer, Rachel E; Chen, Wei; Gehring, Jase; Kosuri, Sriram; Bedford, Trevor; Rieder, Mark J; Nickerson, Deborah A; Chu, Helen Y; Konnick, Eric Q; Debley, Jason S; Shendure, Jay; Lockwood, Christina M; Starita, Lea M.
  • Srivatsan S; Department of Genome Sciences, University of Washington, Seattle, WA.
  • Heidl S; Department of Genome Sciences, University of Washington, Seattle, WA.
  • Pfau B; Department of Genome Sciences, University of Washington, Seattle, WA.
  • Martin BK; Department of Genome Sciences, University of Washington, Seattle, WA.
  • Han PD; Brotman Baty Institute for Precision Medicine, Seattle, WA.
  • Zhong W; Brotman Baty Institute for Precision Medicine, Seattle, WA.
  • van Raay K; Brotman Baty Institute for Precision Medicine, Seattle, WA.
  • McDermot E; Brotman Baty Institute for Precision Medicine, Seattle, WA.
  • Opsahl J; Brotman Baty Institute for Precision Medicine, Seattle, WA.
  • Gamboa L; Brotman Baty Institute for Precision Medicine, Seattle, WA.
  • Smith N; Brotman Baty Institute for Precision Medicine, Seattle, WA.
  • Truong M; Brotman Baty Institute for Precision Medicine, Seattle, WA.
  • Cho S; Brotman Baty Institute for Precision Medicine, Seattle, WA.
  • Barrow KA; Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA.
  • Rich LM; Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA.
  • Stone J; Brotman Baty Institute for Precision Medicine, Seattle, WA.
  • Wolf CR; Department of Allergy and Infectious Disease, University of Washington, Seattle, WA.
  • McCulloch DJ; Department of Allergy and Infectious Disease, University of Washington, Seattle, WA.
  • Kim AE; Department of Allergy and Infectious Disease, University of Washington, Seattle, WA.
  • Brandstetter E; Brotman Baty Institute for Precision Medicine, Seattle, WA.
  • Sohlberg SL; Department of Allergy and Infectious Disease, University of Washington, Seattle, WA.
  • Ilcisin M; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA.
  • Geyer RE; Department of Family Medicine, University of Washington, Seattle, WA.
  • Chen W; Department of Genome Sciences, University of Washington, Seattle, WA.
  • Gehring J; Department of Genome Sciences, University of Washington, Seattle, WA.
  • Kosuri S; Octant, Inc. Emeryville, CA.
  • Bedford T; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA.
  • Rieder MJ; Department of Genome Sciences, University of Washington, Seattle, WA.
  • Nickerson DA; Brotman Baty Institute for Precision Medicine, Seattle, WA.
  • Chu HY; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA.
  • Konnick EQ; Brotman Baty Institute for Precision Medicine, Seattle, WA.
  • Debley JS; Department of Genome Sciences, University of Washington, Seattle, WA.
  • Shendure J; Brotman Baty Institute for Precision Medicine, Seattle, WA.
  • Lockwood CM; Brotman Baty Institute for Precision Medicine, Seattle, WA.
  • Starita LM; Department of Allergy and Infectious Disease, University of Washington, Seattle, WA.
Clin Chem ; 68(1): 143-152, 2021 12 30.
Article in English | MEDLINE | ID: covidwho-20243230
ABSTRACT

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/µL, 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.
Subject(s)

Full text: Available Collection: International databases Database: MEDLINE Main subject: COVID-19 Nucleic Acid Testing / COVID-19 Type of study: Diagnostic study / Experimental Studies / Prognostic study Limits: Humans Language: English Journal: Clin Chem Journal subject: Chemistry, Clinical Year: 2021 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: COVID-19 Nucleic Acid Testing / COVID-19 Type of study: Diagnostic study / Experimental Studies / Prognostic study Limits: Humans Language: English Journal: Clin Chem Journal subject: Chemistry, Clinical Year: 2021 Document Type: Article