Dataset Information

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

ABSTRACT: 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. 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. 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. 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.

SUBMITTER: Srivatsan S

PROVIDER: S-EPMC7263496 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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

Srivatsan Sanjay S Heidl Sarah S Pfau Brian B Martin Beth K BK Han Peter D PD Zhong Weizhi W van Raay Katrina K McDermot Evan E Opsahl Jordan J Gamboa Luis L Smith Nahum N Truong Melissa M Cho Shari S Barrow Kaitlyn A KA Rich Lucille M LM Stone Jeremy J Wolf Caitlin R CR McCulloch Denise J DJ Kim Ashley E AE Brandstetter Elisabeth E Sohlberg Sarah L SL Ilcisin Misja M Geyer Rachel E RE Chen Wei W Gehring Jase J Kosuri Sriram S Bedford Trevor T Rieder Mark J MJ Nickerson Deborah A DA Chu Helen Y HY Konnick Eric Q EQ Debley Jason S JS Shendure Jay J Lockwood Christina M CM Starita Lea M LM

bioRxiv : the preprint server for biology 20210429

<h4>Background</h4>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 ...[more]

PMID: 32511368

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Project description:BackgroundThe SARS-CoV-2 (COVID-19) pandemic may accelerate the adoption of digital, decentralized clinical trials. Conceptual recommendations for digitalized and remote clinical studies and technology are available to enable digitalization. Fully remote studies may break down some of the participation barriers in traditional trials. However, they add logistical complexity and offer fewer opportunities to intervene following a technical failure or adverse event.ObjectiveOur group designed an end-to-end digitalized clinical study protocol, using the Food and Drug Administration (FDA)-cleared Current Health (CH) remote monitoring platform to collect symptoms and continuous physiological data of individuals recently infected with COVID-19 in the community. The purpose of this work is to provide a detailed example of an end-to-end digitalized protocol implementation based on conceptual recommendations by describing the study setup in detail, evaluating its performance, and identifying points of success and failure.MethodsPrimary recruitment was via social media and word of mouth. Informed consent was obtained during a virtual appointment, and the CH-monitoring kit was shipped directly to the participants. The wearable continuously recorded pulse rate (PR), respiratory rate (RR), oxygen saturation (SpO2), skin temperature, and step count, while a tablet administered symptom surveys. Data were transmitted in real time to the CH cloud-based platform and displayed in the web-based dashboard, with alerts to the study team if the wearable was not charged or worn. The study duration was up to 30 days. The time to recruit, screen, consent, set up equipment, and collect data was quantified, and advertising engagement was tracked with a web analytics service.ResultsOf 13 different study advertisements, 5 (38.5%) were live on social media at any one time. In total, 38 eligibility forms were completed, and 19 (50%) respondents met the eligibility criteria. Of these, 9 (47.4%) were contactable and 8 (88.9%) provided informed consent. Deployment times ranged from 22 to 110 hours, and participants set up the equipment and started transmitting vital signs within 7.6 (IQR 6.3-10) hours of delivery. The mean wearable adherence was 70% (SD 19%), and the mean daily survey adherence was 88% (SD 21%) for the 8 participants. Vital signs were in normal ranges during study participation, and symptoms decreased over time.ConclusionsEvaluation of clinical study implementation is important to capture what works and what might need to be modified. A well-calibrated approach to online advertising and enrollment can remove barriers to recruitment and lower costs but remains the most challenging part of research. Equipment was effectively and promptly shipped to participants and removed the risk of illness transmission associated with in-person encounters during a pandemic. Wearable technology incorporating continuous, clinical-grade monitoring offered an unprecedented level of detail and ecological validity. However, study planning, relationship building, and troubleshooting are more complex in the remote setting. The relevance of a study to potential participants remains key to its success.

Dataset Information

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

Publications

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

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