The mNGS test soon became routine at UCSF, with hospitals and clinics nationwide sending samples to be processed by the UCSF Clinical Microbiology Laboratory, of which Chiu is the director.
Between 2016 and 2023, the UCSF team analyzed nearly 5,000 CSF samples with the test, 14.4% of which turned out to have an infection. In those samples, the test accurately identified the pathogen 86% of the time.
“Our mNGS test performs better than any other category of test for neurologic infections,” Chiu said, “The results support its use as a critical part of the diagnostic armamentarium for physicians who are working up patients with infectious diseases.”
To increase access to this technology, Chiu, DeRisi, Wilson and others helped found Delve Bio, which is now the exclusive provider of the mNGS CSF test developed at UCSF.
“These findings support including mNGS as a core tool in the clinical workup for CNS infections,” said Steve Miller, MD, PhD, chief medical officer of Delve Bio. “mNGS offers the single most unbiased, complete and definitive tool for pathogen detection. Thanks to its ability to quickly diagnose an infection, mNGS helps guide management decisions and treatment for patients with meningitis and encephalitis, potentially reducing healthcare costs down the line.”
Preparing for the next pandemic
If it is going to serve as an early-warning system for pandemics, the mNGS test must be fast. Chiu and his colleagues have adapted it to work with respiratory fluid and figured out how to automate it.
Whereas the CSF test entails more than 100 separate steps and can take 2 to 7 days to process, the respiratory test requires just 30 minutes of hands-on time before robots and algorithms can take over.
“Our goal was to have the entire process completed within 12 to 24 hours, giving a same-day or next-day result,” Chiu said.
In the Nature Communications study, the researchers demonstrated that the test could detect respiratory viruses with pandemic potential, including SARS-CoV-2, influenza A and B, and RSV in less than a day, even when there were only small amounts of virus present in a sample.
They also modeled the technology’s ability to detect divergent viruses – or newly-evolved strains – and found that it could hypothetically detect all of them, should they emerge in the future.
Both the CSF and respiratory versions of the mNGS test have received breakthrough device designation from the U.S. Food and Drug Administration (FDA).
Clinical research coordinator Jenna Chui loads DNA samples into a biorobot as Charles Chiu, M.D., Ph.D., looks on. Image by Noah Berger
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