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Infectious Diseases

Assessment of a Smartphone-Based Loop-Mediated Isothermal Amplification Assay for Detection of SARS-CoV-2 and Influenza Viruses

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To identify the key insights or developments described in this article

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JAMA Network Open

Published Online: January 28, 2022

Original Investigation

Article Information and Disclosures

Douglas M. Heithoff, PhD^1,2;

Lucien Barnes V, PhD¹;

Scott P. Mahan, BS^1,2,3;

et al

Gary N. Fox, MS⁴;

Katherine E. Arn, MD⁵;

Sarah J. Ettinger, MD⁵;

Andrew M. Bishop, MD⁵;

Lynn N. Fitzgibbons, MD^5,6;

Jeffrey C. Fried, MD^5,7;

David A. Low, PhD^1,2;

Charles E. Samuel, PhD¹;

Michael J. Mahan, PhD^1,2

Author Affiliations

¹Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara
²Institute for Collaborative Biotechnologies, University of California, Santa Barbara, Santa Barbara
³Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis
⁴Department of Materials and Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara
⁵Department of Medical Education, Santa Barbara Cottage Hospital, Santa Barbara, California
⁶Division of Infectious Diseases, Santa Barbara Cottage Hospital, Santa Barbara, California
⁷Department of Pulmonary and Critical Care Medicine, Santa Barbara Cottage Hospital, Santa Barbara, California

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Key Points

Question Can loop-mediated isothermal amplification (LAMP)-based methodology coupled with smartphone detection provide an inexpensive, rapid, sensitive, and reliable platform for COVID-19 and influenza testing?

Findings In this cohort study of saliva samples from 50 community-based patients, the smartphone-based LAMP assay detected SARS-CoV-2 infection and exhibited concordance with reverse transcriptase–quantitative polymerase chain reaction tests.

Meaning These findings suggest that the smartphone-based LAMP assay offers an additional tool to detect COVID-19 that can be readily modified in response to novel SARS-CoV-2 variants and other pathogens with pandemic potential including influenza.

Abstract

Importance A critical need exists in low-income and middle-income countries for low-cost, low-tech, yet highly reliable and scalable testing for SARS-CoV-2 virus that is robust against circulating variants.

Objective To assess whether a smartphone-based assay is suitable for SARS-CoV-2 and influenza virus testing without requiring specialized equipment, accessory devices, or custom reagents.

Design, Setting, and Participants This cohort study enrolled 2 subgroups of participants (symptomatic and asymptomatic) at Santa Barbara Cottage Hospital. The symptomatic group consisted of 20 recruited patients who tested positive for SARS-CoV-2 with symptoms; 30 asymptomatic patients were recruited from the same community, through negative admission screening tests for SARS-CoV-2. The smartphone-based real-time loop-mediated isothermal amplification (smaRT-LAMP) was first optimized for analysis of human saliva samples spiked with either SARS-CoV-2 or influenza A or B virus; these results then were compared with those obtained by side-by-side analysis of spiked samples using the Centers for Disease Control and Prevention (CDC) criterion-standard reverse transcriptase–quantitative polymerase chain reaction (RT-qPCR) assay. Next, both assays were used to test for SARS-CoV-2 and influenza viruses present in blinded clinical saliva samples obtained from 50 hospitalized patients. Statistical analysis was performed from May to June 2021.

Exposures Testing for SARS-CoV-2 and influenza A and B viruses.

Main Outcomes and Measures SARS-CoV-2 and influenza infection status and quantitative viral load were determined.

Results Among the 50 eligible participants with no prior SARS-CoV-2 infection included in the study, 29 were men. The mean age was 57 years (range, 21 to 93 years). SmaRT-LAMP exhibited 100% concordance (50 of 50 patient samples) with the CDC criterion-standard diagnostic for SARS-CoV-2 sensitivity (20 of 20 positive and 30 of 30 negative) and for quantitative detection of viral load. This platform also met the CDC criterion standard for detection of clinically similar influenza A and B viruses in spiked saliva samples (n = 20), and in saliva samples from hospitalized patients (50 of 50 negative). The smartphone-based LAMP assay was rapid (25 minutes), sensitive (1000 copies/mL), low-cost (<$7/test), and scalable (96 samples/phone).

Conclusions and Relevance In this cohort study of saliva samples from patients, the smartphone-based LAMP assay detected SARS-CoV-2 infection and exhibited concordance with RT-qPCR tests. These findings suggest that this tool could be adapted in response to novel CoV-2 variants and other pathogens with pandemic potential including influenza and may be useful in settings with limited resources.

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Article Information

Accepted for Publication: December 3, 2021.

Published: January 28, 2022. doi:10.1001/jamanetworkopen.2021.45669

Corresponding Author: Michael J. Mahan, PhD, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, 2119 Biological Sciences II, Santa Barbara, CA 93106 (mahan@ucsb.edu).

Author Contributions: Dr M. Mahan had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis.

Concept and design: Heithoff, Barnes, S. Mahan, Fox, Ettinger, Fitzgibbons, Fried, Low, Samuel, M. Mahan.

Acquisition, analysis, or interpretation of data: Heithoff, Barnes, S. Mahan, Arn, Ettinger, Bishop, Fitzgibbons, Fried, Low, Samuel, M. Mahan.

Drafting of the manuscript: Heithoff, Barnes, S. Mahan, Ettinger, Fried, Low, Samuel, M. Mahan.

Critical revision of the manuscript for important intellectual content: All authors.

Statistical analysis: Heithoff, Fox, Arn, M. Mahan.

Obtained funding: M. Mahan.

Administrative, technical, or material support: Heithoff, Barnes, S. Mahan, Fox, Ettinger, Fitzgibbons, Fried, Low, Samuel, M. Mahan.

Supervision: Heithoff, Fitzgibbons, Fried, Low, Samuel, M. Mahan.

Conflict of Interest Disclosures: None reported.

Funding/Support: This research was funded by National Institutes of Health (NIH) HL131474 (Drs Fried and M. Mahan), Cottage Health Research Institute (Drs Low and M. Mahan), and U.S. Army Research Office via the Institute for Collaborative Biotechnologies cooperative agreement W911NF-19-2-0026 (Dr M. Mahan) and contract W911NF-19-D-0001-0013 (Drs Low and M. Mahan).

Role of the Funder/Sponsor: The funders had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication.

Additional Contributions: We would like to thank Ken Y. Yoneda, MD, Professor of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of California Davis, for helpful insights regarding patient study design; compensation was not received for this work.

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Assessment of a Smartphone-Based Loop-Mediated Isothermal Amplification Assay for Detection of SARS-CoV-2 and Influenza Viruses

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