BARDA announces new partnerships to develop next-gen diagnostics for any respiratory RNA virus


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BARDA’s Division of Research, Innovation, and Ventures (DRIVe) is collaborating with multiple industry and academic partners to advance the ability to quickly respond to public health emergencies with a new diagnostic capability that covers all existing and new respiratory RNA viruses in a single test.

Most of today’s clinical diagnostic tools are designed to detect the presence of a specific and known pathogen. These targeted assays – like the PCR and antigen tests that have become widely used during the COVID-19 pandemic – meet a critical need for diagnostics. Yet targeted diagnostic tests are reactive by design and typically are not available until after an outbreak has begun. Additionally, significant time and effort are needed to develop, verify, and validate such tests and obtain regulatory approval. When faced with a public health emergency of pandemic potential, time is crucial, and having an agnostic diagnostic test – a diagnostic that can identify any known or novel pathogen – can help accelerate public health response.

Next-generation sequencing (NGS) technology is a promising platform for the development of agnostic diagnostic tests. NGS assays can sequence all types of DNA or RNA and can use that information to identify any pathogen that is present, including viruses such as SARS-CoV-2. The technology is already being used for surveillance and COVID-19 variant detection. However, it has not yet been established as a medical diagnostic in the standard of care. Expanding commercial NGS-based agnostic diagnostic capabilities could enable early identification of infections from pathogens of concern and could also provide a broad capability to identify and track variants as they arise.

Well-known pathogenic respiratory infections include those caused by influenza viruses, respiratory syncytial virus (RSV), rhinoviruses, the severe acute respiratory syndrome coronavirus (SARS-CoV), and the Middle East respiratory syndrome coronavirus (MERS-CoV). Many of these pathogens may cause patients to present with a similar set of early onset symptoms. The standard of care currently is grounded in assessing symptoms and then performing targeted testing for individual viruses. NGS-based agnostic diagnostic technology has the potential to change the paradigm of care by leading with a single untargeted diagnostic to detect any and every respiratory pathogen. These assays can also simultaneously detect and distinguish between multiple pathogens present in the same sample, helping to provide information critical to timely, tailored and actionable patient care.

DRIVe is working with multiple partners to bring this innovative technology closer to commercialization, starting with an NGS-based diagnostic that is intended for the detection of all known and unknown respiratory RNA viruses. Partners will optimize their in-house NGS capabilities for commercial clinical use, including by lowering the sample-to-result time to under 24 hours, reducing interference from host RNA, and performing analytical validation of the platform using both contrived and clinical respiratory samples. Each of these optimizations will address some of the most critical constraints on NGS assays, thus yielding faster diagnosis, categorization, and identification of existing, new and emerging pathogens – and potentially, faster time to better, targeted treatment.

DRIVe’s partners all bring unique perspectives and innovative approaches to the program:

  • BugSeq Bioinformatics is a biotech company located in Vancouver, British Columbia. In partnership with the University of British Columbia, they will develop an agnostic diagnostic NGS assay that runs on the Oxford Nanopore technology—a long-read sequencing platform with field-use compatibility.
  • The Center for Infection and Immunity at Columbia University Mailman School of Public Health is based in New York City, New York. They will expand their patented VirCapSeq diagnostic NGS technology, which identifies viruses in blood, to also detect viruses in respiratory samples. VirCapSeq has demonstrated success through numerous government and international research collaborations.
  • Jumpcode Genomics is a genome technology platform company focused on improving the understanding of human biology based will further develop their CRISPRclean technology, a CRISPR-based host RNA depletion strategy, aiming to increase the sensitivity of diagnostic NGS assays.
  • The University of California, Los Angeles’s (UCLA) SwabSeq Laboratory is based in Los Angeles, California, and was created in response to the COVID-19 pandemic. They will turn their NGS-based “Swab-Seq” COVID-19 diagnostic technology—which has been used to process over 1,500,000 COVID-19 tests—into a scalable agnostic assay for identification of any and all respiratory RNA viruses.
  • The University of California San Francisco (UCSF) Clinical Microbiology Laboratory is based in San Francisco, California. Building on their contributions to the NGS-based agnostic diagnostic space, they will broaden their existing cerebrospinal fluid-based NGS assay that was designated a Breakthrough Device by the U.S. Food and Drug Administration (FDA).

Ultimately, partners could potentially pursue appropriate regulatory pathways towards commercialization for their BARDA-funded results. While current applications of this technology are focused on centralized laboratory systems, future applications could include biosurvelliance and testing at the point-of-care and could be expanded to all types of pathogens. These awards have been made under the Easy Broad Agency Announcement (EZ-BAA) area of interest (AOI) #10: NGS-based Agnostic Diagnostic for Respiratory RNA Virus Pathogens.

The emergence of another respiratory RNA virus with pandemic potential is highly likely, and public health and response communities will need comprehensive diagnostic tests to quickly detect the next novel pathogen. Accelerating the development of these NGS-based agnostic diagnostics could help bolster U.S. preparedness for future outbreaks and potentially enable opportunities for infectious disease diagnostics to further integrate across a variety of health care settings.

About BugSeq Bioinformatics:

The following information is provided by the company and does not indicate endorsement by the federal government of the company or its products.

BugSeq is leveraging advanced sequencing technologies to revolutionize infectious disease testing and pathogen surveillance. BugSeq’s analysis suite delivers data analytics and industry-leading expertise to convert sequencing data into actionable results. By profiling tens of thousands of microorganisms and markers of antimicrobial resistance from any specimen, BugSeq enables broad adoption of sequencing to improve health.

About the Center for Infection and Immunity at Columbia University Mailman School of Public Health:

The following information is provided by the company and does not indicate endorsement by the federal government of the company or its products.

The Center for Infection and Immunity (CII) at Columbia University Mailman School of Public Health is dedicated to the discovery of microbes and the characterization of their impact on human and animal health, in partnership with governments worldwide. CII is a leader in pandemic response and has worked on the front lines of numerous outbreaks, including SARS, Nipah, LuJo, H1N1, MERS, Zika and, most recently, SARS-CoV-2. Its scientists have discovered more than 1,800 microbes, pioneered methods for the rapid and accurate detection of pathogens, and reported links between infectious agents and chronic disease. To learn more, please visit https://www.publichealth.columbia.edu/research/center-infection-and-immunity.

Columbia University Mailman School of Public Health Founded in 1922, the Columbia University Mailman School of Public Health pursues an agenda of research, education, and service to address the critical and complex public health issues affecting New Yorkers, the nation and the world. The Columbia Mailman School is the fourth largest recipient of NIH grants among schools of public health. Its nearly 300 multi-disciplinary faculty members work in more than 100 countries around the world, addressing such issues as preventing infectious and chronic diseases, environmental health, maternal and child health, health policy, climate change and health, and public health preparedness. It is a leader in public health education with more than 1,700 graduate students from 56 nations pursuing a variety of master’s and doctoral degree programs. The Columbia Mailman School is also home to numerous world-renowned research centers, including ICAP and the Center for Infection and Immunity.  For more information, please visit publichealth.columbia.edu.


About Jumpcode Genomics:

The following information is provided by the company and does not indicate endorsement by the federal government of the company or its products.

Jumpcode Genomics is changing genomics with technology that allows scientists to break barriers limiting their research. Combining CRISPR-based technology and next-generation sequencing it’s now possible to search for and find novel signals that were previously undetectable. Our technology removes unwanted sequences, allows researchers to extract greater insights, and broadens the understanding of human biology in fields from research to clinical applications. Discover what we can do at www.jumpcodegenomics.com.

About UCLA SwabSeq Laboratory:

The following information is provided by the company and does not indicate endorsement by the federal government of the company or its products.

The University of California, Los Angeles’s (UCLA) SwabSeq Laboratory is a new CLIA-certified laboratory created in response to the COVID-19 pandemic. Starting in April 2020, genomic and computational scientists at UCLA developed a new technology based on next-generation sequencing—the SwabSeq COVID-19 Diagnostic Platform—which obtained FDA EUA approval and was deployed within 6 months. In 2021, the UCLA SwabSeq Laboratory was awarded a contract from NIH's Rapid Acceleration of Diagnostics (RADx) program to leverage automation to expand the lab’s capacity. Since deployment, the UCLA SwabSeq Laboratory has processed over 1,500,000 COVID-19 tests, providing high-throughput low-cost testing to multiple universities, local schools and other partners. For more information, please visit: https://compmed.ucla.edu/content/ucla-swabseq-covid-19-diagnostic-test.

About the UCSF Clinical Microbiology Laboratory:

The following information is provided by the company and does not indicate endorsement by the federal government of the company or its products.

The UCSF Clinical Microbiology is a CLIA-certified, CAP-accredited laboratory in San Francisco, California and occupies over 10,000 square feet of laboratory space. Resources include a biobank repository of over 10,000 specimens and state-of-the-art instrumentation including next-generation sequencers and automated biorobots. The development and validation of novel assays, including metagenomic sequencing tests for diagnosis of neurological infections from cerebrospinal fluid and sepsis/disseminated infection from plasma, are performed in a dedicated molecular area, with all tests run by licensed clinical laboratory scientists. The laboratory has been providing clinical metagenomic testing for hospitals and health centers in the United States and internationally since 2016, serving the diagnostic needs of patients with infections of unknown etiology.


DRIVe EZ-BAA:

BARDA's Division of Research, Innovation, and Ventures (DRIVe) established the Easy Broad Agency Announcement (EZ-BAA) to streamline the application process for the review of transformative products and technologies to protect the U.S. from health security threats. Since its inception in 2018, BARDA DRIVe's EZ-BAA solicitation has received hundreds of abstract submissions annually, with awards made in as few as 30 days. The EZ-BAA has helped transform the solicitation process and provides innovators, entrepreneurs, and organizations with a simplified and rapid mechanism to propose ideas to the U.S. government. The application process is both business-friendly and easy to follow.

Last Updated: May 03, 2022

DRIVe Portfolio

This award is one component of BARDA's expanding DRIVe Portfolio; visit BARDA's DRIVe Portfolio to learn more.