SALT LAKE CITY — A biotech company with a big Utah footprint is among the leading innovators of a cutting-edge technology for assessing the genetic footprint of pathogens like COVID-19.
And the tool could become the new frontline defender when, inevitably, a mutated version of SARS-CoV-2 evolves or another pandemic-potential superbug arises.
University of Utah’s Research Park plays host to the lab operations of San Francisco-based IDbyDNA, a clinical metagenomics startup up co-founded by Dr. Robert Schlaberg. While Schlaberg earned his M.D. and Ph.D degrees in Germany and at Columbia University, he has strong Utah ties with a resume that includes teaching pathology at the University of Utah School of Medicine and a directorship at U. Health system’s ARUP Laboratories,
Schlaberg explained that metagenomics takes a sample — say a nasal swab — and breaks down the genetic sequences of every microbe in the sample. These could be viruses, bacteria, fungi or parasites and, unlike previous approaches to diagnostic testing, doesn’t require different methods to weed out whatever nonhuman DNA or RNA is present.
“The strength of this technique is how can you use it,” Schlaberg said. “You don’t have to know what you’re looking for. This has the ability to detect and identify over 50,000 microorganisms and 3,000 known common and rare pathogens.
“In other methods, you have to come with a specific question.”
Schlaberg said a metagenomic test (though not his company’s version) was the method that led to the initial discovery of the SARS-CoV-2 virus and is a technique IDbyDNA has been advancing since it was founded in 2015. (SARS-CoV-2 is the virus responsible for COVID-19.)
The company’s innovative approach combines super-fast next-generation genetic sequencing processes with a machine learning engine that can assess and compare that genetic information against an enormous database.
One of the ways IDbyDNA’s technology is being leveraged in the fight against the novel coronavirus is identifying particular strains that help epidemiologists track its spread.
Schlaberg said an example might be a parent and child who both tested positive for COVID-19. Determining where the virus was contracted — by the parent at work or the child in a school or social setting — is important information for public health officials working to mitigate the pandemic.
Use of the IDbyDNA process in this case would unveil the specific genetic footprint of the virus strain contracted by the parent and child and using that information in comparison with contact tracing data, would determine who brought the virus into that household and from what pathway it came.
“This virus has about 30,000 letters in its genome,” Schlaberg said. “Every time it makes a copy of itself, with every generation, there can be some changes. Though this particular virus doesn’t change that much, there are a couple dozen or so letters and positions that change repeatedly.
“That allows you to generate a fingerprint ... with a particular combination of changed letters that identify a specific strain.”
This strain identification is critical information, Schlaberg said, when it comes to monitoring how the virus is changing as it moves through communities as well as aiding public health officials in tracking infection sources.
This technique can also be used to quickly and efficiently assess whether a sudden cluster of infections is the result of a so-called super-spreader event that tracks back to single modern-day Typhoid Mary or just a group of unrelated positive results.
Physician and researcher Dr. Lauge Farnaes is the assistant medical director at Rady Children’s Institute for Genomic Medicine in San Diego and an attending physician specializing in pediatric infectious diseases.
Farnaes has used the IDbyDNA testing procedure in clinical trials and research projects and said technology that was once out of reach from both a cost and time perspective is now moving toward the realm of everyday diagnostic tools.
“Molecular epidemiology has been something limited to use by hospitals in crisis management situations,” Farnaes said. “IDbyDna could allow you to do molecular epidemiology on everything, all the time.
“With unbiased sequencing, you can find things that you don’t even know you were looking for. ... You see it even before it showed up.”
That power of detection in metagenomics testing is one Farnaes has been exploring in his pursuit of advancing early and accurate detection of infection and pathogens in his young patients.
Farnaes said the combination of fast and accurate gene sequencing melded with the power of a self-evolving database is still in its developmental stages and that a good deal of professional human medical interpretation is still required, But he noted that as the technique continues to evolve, it will have ever growing, and positive impacts on the detection and treatment of infection and disease.
“Like quantum computing, it’s hard to do but it’s possible,” Farnaes said. “Where we are right now is on the cusp of an enormous way to change health care for the entire word.
“You can see the potential,” he said. “A comprehensive diagnostic microbiome lab in a suitcase that could deliver results in, say, four hours. We’re not there yet, but we can see that it is possible.”
IDbyDNA is a venture backed effort that’s raised some $29 million in investment thus far. The company looks set to expand its user base following the March announcement of a strategic partnership with next-generation sequencing innovator Illumina. Following the partnership announcement, IDbyDNA Chief Commercial Officer Jeff Field said the effort could set the worldwide standard for infectious disease diagnosis and surveillance.
“Metagenomic (next-generation sequencing based) testing enables the most comprehensive detection of hundreds to thousands of pathogens, both for routine testing and for emerging public health threats like SARS-CoV-2, the virus responsible for the COVID-19 outbreak,” Field said in a statement.
“Importantly, we are able to determine not only the presence of this emerging virus but also decipher the genetic makeup of individual strains allowing us to compare strains, differentiate them from other coronaviruses and perform surveillance activities right at the time of diagnosis.
“With the increase in global travel and economic integration, the ability to monitor and track the spread of pathogens such as the novel coronavirus is a critical public health challenge. Working with a next-generation sequencing leader, we plan to rapidly make the Explify Platform the new standard for worldwide infectious disease diagnostics and surveillance.”