This also allows the test to look at the quantity of various pathogens in the sample to predict disease severity and help quickly narrow down the target pathogen. The technology was first developed to analyze cerebrospinal fluid (CSF), the fluid surrounding the brain and spinal cord, using a powerful genomic sequencing technique called metagenomic next-generation sequencing (mNGS). Since then, it has been performed on thousands of patients experiencing unexplained neurological symptoms, both at UCSF and other hospitals nationwide.
Since its introduction, the test has demonstrated real-world impact. In one notable case, rapid results helped resolve an undiagnosed infection in a young Wisconsin boy. Between 2016 and 2023, the UCSF team analyzed nearly 5,000 CSF samples.
Over 14 percent of samples were determined to be infections, and the new test identified the pathogen 86 percent of the time. While the current CSF test involves over 100 steps and takes two to seven days to complete, the new respiratory version aims for much faster results. “Our goal was to have the entire process completed within 12 to 24 hours, giving a same-day or next-day result,” Chiu said.
The findings of both studies show that the mNGS test could detect respiratory viruses likely to cause pandemics, including SARS-CoV-2, which caused COVID-19, in about one day—even when with only small quantities of the virus present..