Scientists develop an RNA-based breath test to detect COVID-19

The Bubbler, a breathalyzer that reverse-transcribes RNA from airborne SARS-CoV-2 in breath, predicts lower respiratory tract involvement and is less invasive than alternative testing approaches, report researchers in The Journal of Molecular Diagnostics


Philadelphia, December 13, 2021

In a new study in The Journal of Molecular Diagnostics, published by Elsevier, investigators report on the design and testing of a breathalyzer, known as the Bubbler, that relies on viral RNA detection to diagnose SARS-CoV-2. Its name is derived from the bubbling sound that occurs when the patient exhales into the device.

The Bubbler not only reverse transcribes RNA from airborne virus particles into DNA to be tested via PCR but can also barcode that DNA, allowing samples to be linked directly to the patient they have come from and be used for sequencing. It can be used for simultaneous batches of pooled samples and provides additional information such as viral load and strain identity and eliminates the need for stabilizing a sample, potentially allowing the assay to be performed at home.

“Involvement of the lower respiratory tract is often a precursor to severe COVID-19, so there is an argument for a more direct sampling focused on exhaled breath,” explained lead investigator William G. Fairbrother, PhD, professor in the department of molecular biology, cell biology and biochemistry at Brown University in Providence, RI, USA.

Virus detection by the Bubbler is similar to a hospital-swab PCR test; however, it is a better measure of risk of contagion as it detects airborne viral particles. Swab tests can return a positive result for months after infection as they detect viral RNA fragments in cells that persist in previously infected cells. The Bubbler can also be adapted for environmental sampling in hospitals, transportation hubs, and closed environments like offices, ships, and planes, the investigators report.


(Left) Constructing the Bubblers. Breathalyzers were bathed in UV light to maintain sterile field prior to construction of kits prepared for the clinical trial at Rhode Island Hospital; (Right) Bubbler kits were processed in a negative pressure bench top box to prevent contamination of amplicon particles in the laboratory (Credit: William G. Fairbrother).

The study determined that SARS-CoV-2 can be readily detected in the breath and is more predictive of lower respiratory tract involvement. Viral RNA is more enriched in the breath relative to oral samples, while oral samples include cells involved with SARS-CoV-2 replication that breath samples do not. This suggests the viral signal detected in the Bubbler comes from active viral particles.

“The Bubbler is more likely to be a better indicator of current infection than nasopharyngeal swabs,” said Dr. Fairbrother. “Another advantage is the barcoding, which enables high-throughput RNA virus testing at a fraction of the cost of conventional testing. The barcode returns a viral sequence that also supports strain identification, which may prove useful as more information is learned about transmissibility and possible strain-specific treatment decisions.”

The investigators also demonstrated how the Bubbler might be adapted to detect virus in airborne samples. To model the movement of droplets exhaled in human breath, three unique nucleic acid samples were added to three personal humidifiers at different locations at varied distances from the Bubbler in a room with high airflow and a room with low airflow. Although a detailed exploration of this application was beyond the scope of the study, the results demonstrate the potential to use aerosolized nucleic acids to quantitatively map airflow in indoor spaces, and to detect SARS-CoV-2 in the air.

“Such technology could be useful in restoring service to industries such as hotels, cruise ships, and casinos,” Dr. Fairbrother observed. “There is also an epidemiological benefit to routine testing of air at early warning sites such as transportation hubs and hospital emergency departments.”

Tests for COVID-19 usually use samples collected from the upper respiratory tract by saliva or nasopharyngeal swab. Positive samples contain active virus, but viral load in the upper respiratory tract is not correlated with symptoms in the lower respiratory tract, such as pneumonia.

---

Notes for editors
The article is “Efficient Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from Exhaled Breath,” by Chaorui Duan, Luke Buerer, Jing Wang, Samuel Kaplan, Gavin Sabalewski, Gregory D. Jay, Sean Monaghan, Andrea E. Arena, and William G. Fairbrother (https://doi.org/10.1016/j.jmoldx.2021.09.005). It appears in The Journal of Molecular Diagnostics, volume 23, issue 12 (December 2021) published by Elsevier.

This article is openly available at https://www.jmdjournal.org/article/S1525-1578(21)00294-4/fulltext.

This study was supported by NIH National Institute of General Medical Sciences grants Q3 R01GM105681 and R01GM127472, and the Roddy Foundation.

Full text of this study is also available to credentialed journalists upon request; contact Eileen Leahy at +1 732 238 3628 or jmdmedia@elsevier.com. Journalists wishing to interview the authors should contact William G. Fairbrother at william_fairbrother@brown.edu or Corrie Pikul at +1 401 863 1862 or corrie_pikul@brown.edu.

Elsevier’s Novel Coronavirus Information Center provides expert-curated information for researchers, healthcare professionals and public health officials, including clinical guidance and a portal to access all of Elsevier’s COVID-19 research. All resources are freely available. We also have dedicated hubs for healthcare professionals; health educators and students; librarians; and R&D professionals. You can find these in our Coronavirus Resource Directory.

About The Journal of Molecular Diagnostics
The Journal of Molecular Diagnostics, the official publication of the Association for Molecular Pathology, co-owned by the American Society for Investigative Pathology, and published by Elsevier, seeks to publish high quality original papers on scientific advances in the translation and validation of molecular discoveries in medicine into the clinical diagnostic setting, and the description and application of technological advances in the field of molecular diagnostic medicine. The editors welcome review articles that contain: novel discoveries or clinicopathologic correlations, including studies in oncology, infectious diseases, inherited diseases, predisposition to disease, or the description of polymorphisms linked to disease states or normal variations; the application of diagnostic methodologies in clinical trials; or the development of new or improved molecular methods for diagnosis or monitoring of disease or disease predisposition. www.jmdjournal.org

About Elsevier
As a global leader in information and analytics, Elsevier helps researchers and healthcare professionals advance science and improve health outcomes for the benefit of society. We do this by facilitating insights and critical decision-making for customers across the global research and health ecosystems.

In everything we publish, we uphold the highest standards of quality and integrity. We bring that same rigor to our information analytics solutions for researchers, health professionals, institutions and funders.

Elsevier employs 8,100 people worldwide. We have supported the work of our research and health partners for more than 140 years. Growing from our roots in publishing, we offer knowledge and valuable analytics that help our users make breakthroughs and drive societal progress. Digital solutions such as ScienceDirect, Scopus, SciVal, ClinicalKey and Sherpath support strategic research management, R&D performance, clinical decision support, and health education. Researchers and healthcare professionals rely on our 2,500+ digitized journals, including The Lancet and Cell; our 40,000 eBook titles; and our iconic reference works, such as Gray's Anatomy. With the Elsevier Foundation and our external Inclusion & Diversity Advisory Board, we work in partnership with diverse stakeholders to advance inclusion and diversity in science, research and healthcare in developing countries and around the world.

Elsevier is part of RELX, a global provider of information-based analytics and decision tools for professional and business customers. www.elsevier.com.

Media contacts
Eileen Leahy
Elsevier
+1 732 238 3628
jmdmedia@elsevier.com

Chhavi Chauhan, PhD, Director of Scientific Outreach
The Journal of Molecular Diagnostics
+1 240 283 9724
cchauhan@asip.org