SwabExpress: An End-to-End Protocol for Extraction-Free COVID-19 Testing

• Published in: Clinical Chemistry Vol. 68; no. 1; pp. 143 - 152
• Main Authors: 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
• Format: Journal Article Web Resource
• Language: English
• Published: England Oxford University Press 01.01.2022
• Subjects: Clinical Laboratory Techniques; Coronaviruses; COVID-19; COVID-19 - diagnosis; COVID-19 diagnostic tests; COVID-19 Nucleic Acid Testing - methods; Endopeptidase K; Equipment and supplies; Heat treatment; Heat treatments; Humans; Inactivation; Laboratories; Laboratory tests; Molecular diagnostic techniques; Molecular Diagnostics and Genetics; Nucleic acids; Optimization; Pandemics; Proteinase; Protocol; Reagents; Real-Time Polymerase Chain Reaction; RNA, Viral - isolation & purification; SARS-CoV-2 - isolation & purification; Sensitivity and Specificity; Severe acute respiratory syndrome coronavirus 2; Shortages; Specimen Handling; Supply chains; Test procedures; Transport media; Viral diseases; Workflow; United States
• ISSN: 0009-9147; 1530-8561
• DOI: 10.1093/clinchem/hvab132

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.