Since mid-January, the Translational Genomics Research Institute (TGen), an affiliate of City of Hope, has been part of the worldwide effort to conduct testing for the SARS-CoV-2 virus causing COVID-19 disease. Acting as genomic first responders, Arizona-based TGen is using advanced biomedical technologies to study this disease while also working to help establish a statewide tracking network for COVID-19.
In early March — after receiving Emergency Use Authorization (EUA) from the Food and Drug Administration for its genomic-based test — TGen began working with federal, state, county and tribal governments, private health care providers and others to expand testing for COVID-19 in Arizona, part of a concerted effort to get out in front of this global health threat.
TGen's testing uses RNA analysis to confirm the existence of the virus and, if present, TGen scientists then sequence the genome to identify the particular strain, where it came from and how it's moving and mutating.
“These types of tests are essentially what the Centers for Disease Control developed and what others are developing around the world, and they look at respiratory samples, the nasal swabs that people have been hearing about,” David Engelthaler, Ph.D., co-director of TGen’s Pathogen and Microbiome Division (infectious diseases) in Flagstaff, explained in a late-March podcast. “If the virus is present in that patient, it's usually picked up in that sample type, and the TGen test can definitively determine whether or not the virus is in that sample.”
Processing hundreds of samples daily
“We can actually take that swab, extract the genetic material — that takes about half an hour to an hour to process — and then we get it into our polymerase chain reaction machines, which can give us results back in about 45 minutes. The whole process takes less than an hour and a half,” he explained. But because TGen is testing up to hundreds of samples at a time, the current turnaround time is 24 hours, he added. As of mid-April , TGen’s Clinical Laboratory Improvement Amendments (CLIA)-certified lab has scaled up to process up to 600 samples a day, he said.
TGen is also conducting analyses of samples from suspected and symptomatic individuals for COVID-19 from select communities, including Native American communities; and special populations, such as long-term health care centers and jail populations, to help provide support to these often-underserved groups who are most in need.
In collaboration with City of Hope physician Laura Goetz, M.D., M.P.H., assistant clinical professor in the Department of Medical Oncology & Therapeutics Research, work has also been done to introduce a protocol to the City of Hope institutional review board in hopes of soon beginning comprehensive testing for high-risk health care workers on the first line of defense in combating this pandemic.
“We're trying to find the virus where it's present before it's starting to cause the severe cases, so we better understand where it is and where to focus public health resources,” Engelthaler said. “We've developed a high throughput laboratory capacity that allows us to scale up. Now we can do hundreds of samples a day and we can move to thousands of samples a day in pretty short order as the need evolves.”
Finally, TGen’s informatics teams have joined forces with City of Hope and myriad other institutions to study the whole genome sequence of SARs-CoV-2, using samples from hundreds of infected patients. All positive cases in Arizona, more than 600 so far, have been provided to TGen for genomic sequencing of the virus.
“The great thing about TGen is the ‘Gen’ in TGen, the genomics,” Engelthaler said. “We can look to see where the virus strains are coming from, how they're moving around the community, which ones are more related to others, and watch and understand this new pathogen as it evolves in front of us.”
This approach — think of it as the “Ancestry.com of the virus” — has many advantages and could benefit the health care system by determining how widespread COVID-19 is within Arizona and beyond, identifying emerging hotspots as they occur and assisting in efforts to contain and prevent the disease.
California licensure received
Importantly, TGen is analyzing samples from public health and health care entities. Working with the Arizona Department of Health Services, it is taking both a defensive and offensive approach: doing direct testing of patients who are high risk for possible coronavirus disease, as well as doing community testing to identify hidden pockets of COVID-19 across Arizona.
Finally, in addition to TGen’s FDA-EUA test, the team completed and recently received permanent CLIA certification for virology testing in a high-complexity laboratory by the California Department of Public Health.