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

View ORCID ProfileSanjay Srivatsan, Sarah Heidl, Brian Pfau, Beth K. Martin, View ORCID ProfilePeter D. Han, Weizhi Zhong, Katrina van Raay, Evan McDermot, Jordan Opsahl, Luis Gamboa, Nahum Smith, Melissa Truong, Shari Cho, Kaitlyn A. Barrow, Lucille M. Rich, Jeremy Stone, Caitlin R. Wolf, View ORCID ProfileDenise J. McCulloch, Ashley E. Kim, View ORCID ProfileElisabeth Brandstetter, Sarah L. Sohlberg, Misja Ilcisin, Rachel E. Geyer, Wei Chen, Jase Gehring, Seattle Flu Study Investigators, View ORCID ProfileSriram Kosuri, Trevor Bedford, Mark J. Rieder, View ORCID ProfileDeborah A. Nickerson, View ORCID ProfileHelen Y. Chu, View ORCID ProfileEric Q. Konnick, Jason S. Debley, View ORCID ProfileJay Shendure, View ORCID ProfileChristina M. Lockwood, View ORCID ProfileLea M. Starita
doi: https://doi.org/10.1101/2020.04.22.056283
Sanjay Srivatsan
1Department of Genome Sciences, University of Washington, Seattle WA, USA
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Sarah Heidl
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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Brian Pfau
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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Beth K. Martin
1Department of Genome Sciences, University of Washington, Seattle WA, USA
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Peter D. Han
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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Weizhi Zhong
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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Katrina van Raay
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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Evan McDermot
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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Jordan Opsahl
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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Luis Gamboa
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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Nahum Smith
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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Melissa Truong
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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Shari Cho
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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Kaitlyn A. Barrow
3Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle WA, USA
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Lucille M. Rich
3Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle WA, USA
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Jeremy Stone
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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Caitlin R. Wolf
4Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
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Denise J. McCulloch
4Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
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Ashley E. Kim
4Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
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Elisabeth Brandstetter
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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Sarah L. Sohlberg
4Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
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Misja Ilcisin
5Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Rachel E. Geyer
6Department of Family Medicine, University of Washington, Seattle, Washington, USA
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Wei Chen
1Department of Genome Sciences, University of Washington, Seattle WA, USA
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Jase Gehring
1Department of Genome Sciences, University of Washington, Seattle WA, USA
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Sriram Kosuri
7Octant, Inc. Emeryville CA, USA
8Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles CA, USA
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Trevor Bedford
1Department of Genome Sciences, University of Washington, Seattle WA, USA
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
5Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Mark J. Rieder
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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Deborah A. Nickerson
1Department of Genome Sciences, University of Washington, Seattle WA, USA
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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Helen Y. Chu
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
4Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
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Eric Q. Konnick
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
9Department of Laboratory Medicine and Pathology, Seattle WA, USA
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Jason S. Debley
3Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle WA, USA
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Jay Shendure
1Department of Genome Sciences, University of Washington, Seattle WA, USA
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
10Howard Hughes Medical Institute. Seattle WA, USA
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Christina M. Lockwood
1Department of Genome Sciences, University of Washington, Seattle WA, USA
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
9Department of Laboratory Medicine and Pathology, Seattle WA, USA
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  • For correspondence: lstarita@uw.edu tinalock@uw.edu
Lea M. Starita
1Department of Genome Sciences, University of Washington, Seattle WA, USA
2Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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  • For correspondence: lstarita@uw.edu tinalock@uw.edu
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Structured 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) (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.

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 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.

Results After 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.

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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • This is a major revision. We have swapped out a stub and idea for a fully validated COVID-19 platform.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 29, 2021.
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SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing
Sanjay Srivatsan, Sarah Heidl, Brian Pfau, Beth K. Martin, Peter D. Han, Weizhi Zhong, Katrina van Raay, Evan McDermot, Jordan Opsahl, Luis Gamboa, Nahum Smith, Melissa Truong, Shari Cho, Kaitlyn A. Barrow, Lucille M. Rich, Jeremy Stone, Caitlin R. Wolf, Denise J. McCulloch, Ashley E. Kim, Elisabeth Brandstetter, Sarah L. Sohlberg, Misja Ilcisin, Rachel E. Geyer, Wei Chen, Jase Gehring, Seattle Flu Study Investigators, Sriram Kosuri, Trevor Bedford, Mark J. Rieder, Deborah A. Nickerson, Helen Y. Chu, Eric Q. Konnick, Jason S. Debley, Jay Shendure, Christina M. Lockwood, Lea M. Starita
bioRxiv 2020.04.22.056283; doi: https://doi.org/10.1101/2020.04.22.056283
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SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing
Sanjay Srivatsan, Sarah Heidl, Brian Pfau, Beth K. Martin, Peter D. Han, Weizhi Zhong, Katrina van Raay, Evan McDermot, Jordan Opsahl, Luis Gamboa, Nahum Smith, Melissa Truong, Shari Cho, Kaitlyn A. Barrow, Lucille M. Rich, Jeremy Stone, Caitlin R. Wolf, Denise J. McCulloch, Ashley E. Kim, Elisabeth Brandstetter, Sarah L. Sohlberg, Misja Ilcisin, Rachel E. Geyer, Wei Chen, Jase Gehring, Seattle Flu Study Investigators, Sriram Kosuri, Trevor Bedford, Mark J. Rieder, Deborah A. Nickerson, Helen Y. Chu, Eric Q. Konnick, Jason S. Debley, Jay Shendure, Christina M. Lockwood, Lea M. Starita
bioRxiv 2020.04.22.056283; doi: https://doi.org/10.1101/2020.04.22.056283

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