UCLA Health is joining a new effort to increase the ability to quickly respond to emerging pathogens by creating the capability to detect all existing and new respiratory RNA viruses in a single test. The project is being funded by Biomedical Advanced Research and Development Authority (BARDA)’s Division of Research, Innovation and Ventures (DRIVe), which leverages new authorities given under the 21st Century Cures Act.
DRIVe is funding the UCLA SwabSeq Laboratory to adapt SwabSeq technology to develop scalable sequencing approaches for the detection of novel pathogens. Currently, SwabSeq technology amplifies a portion of the SARS-CoV-2 genome to detect the virus. The new project will extend the SwabSeq technology to develop an “agnostic” test. In this approach, instead of amplifying a specific virus, human RNA is instead depleted in the sample and the remaining RNA is sequenced. This approach has the potential to identify any RNA virus including new and emerging pathogens.
UCLA and others involved in the project will optimize their in-house next generation sequencing 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.
Next generation sequencing, which exists in other areas like oncology and certain genetic disorders, is sorely needed for infectious diseases due to health security threats. The goal is to create an agnostic test to detect any respiratory RNA virus, including new and emerging viruses that can be implemented rapidly and without the need for additional regulatory approvals in future pandemic situations.
In a viral outbreak or pandemic, having agnostic tests that can detect any respiratory RNA virus and can be implemented rapidly without the need for additional regulatory approvals is crucial. Next generation sequencing technology can detect and analyze viral genomes from any existing or emerging viruses in an unbiased manner compared to targeted polymerase chain reaction (PCR) and antigen assays. PCR and antigen assays require a significant effort to develop, verify, validate, as well as earn regulatory approval.
In pandemic situations, next-generation sequencing assays could provide the capability for agnostic detection ability, especially with emerging respiratory pathogens and can be used on day one with appropriate regulatory approval. These tests also provide information crucial to timely and actionable patient care.
UCLA’s SwabSeq Laboratory is a CLIA-certified laboratory created in April 2020 in response to the COVID-19 pandemic. Genomic and computational scientists at UCLA developed the 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 1.5 million COVID-19 tests, providing high-throughput low-cost testing to multiple universities, local schools, and other partners. The UCLA SwabSeq Laboratory is housed in the UCLA Department of Computational Medicine.
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