Jumpcode Genomics and TGen collaborate on genomic sequencing of SARS-CoV-2

Reviewed by Emily Henderson, B.Sc.Sep 14 2021

Jumpcode Genomics, a genome technology platform company focused on improving the understanding of human biology, announced today a collaboration with the Translational Genomics Research Institute (TGen), an affiliate of City of Hope, to aid investigations into the genomic epidemiology of SARS-CoV-2, the virus that causes COVID-19. Jumpcode Genomics and TGen are validating novel comprehensive solutions and clinical services that leverage meta-genomic sequencing and analysis to facilitate detection of COVID-19 and other infectious diseases; all made very efficient through the use of the Jumpcode Genomics CRISPRclean™ technology.

COVID-19 has led to more than 660,000 deaths in the U.S., and cases caused by new variants are steadily on the rise. Diagnosing SARS-CoV-2 infection, assessing patient risk for COVID illness, and tracking the number and source of infections within a community is important for mitigating and preventing new COVID-19 cases but challenging to do accurately and efficiently. While a national surveillance program to collect COVID-19 case data from state, local, and territorial health departments is ongoing, the cases reported to the Centers for Disease Control and Prevention underestimate the actual number of infections due to asymptomatic and mild cases that do not get tested.

Genomic sequencing of SARS-CoV-2 can play a vital role in diagnosing infection, identifying new variants of the virus and related viruses, and tracking the spread of existing strains, as well as informing public health efforts to prevent future infectious disease outbreaks. Using Jumpcode's CRISPRclean technology for enhancing metagenomic sequencing, we're able to not only detect a SARS-CoV-2 infection, but also any co-infections, and/or associated human host responses to infection."

Nicholas Schork, Ph.D., TGen Distinguished Professor and Director of TGen's Quantitative Medicine and Systems Biology Division

Jumpcode combines CRISPR-based technology with next-generation sequencing to remove unwanted sequences, thereby increasing sensitivity and enabling more efficient and cost-effective sequencing. This approach empowers scientists to obtain better data, extract more relevant information about the nature of an infection, and ultimately identify unique aspects of an infection that would have otherwise been undetected. TGen is testing the potential of Jumpcode's CRISPRclean-mediated depletion reagents in combination with Dr. Schork's laboratory's technologies, including protocols for conducting a diagnostic assay using the CRISPRclean reagents and algorithms for analyzing the resulting metagenomic sequence data. Expanded prospective clinical and epidemiological studies are planned to prove the diagnostic assay's utility in routine patient testing for infectious diseases.

Aspects of the approach taken by Jumpcode and TGen have been recently validated using a set of reference samples in which the infection status and severity of the infection were known. Now, TGen researchers are studying COVID-19 samples previously evaluated by PCR tests to assess the sensitivity and specificity of the metagenomic diagnostic against standard focused PCR-based testing. TGen researchers have also been able to identify possible co-infections in individuals found to have a SARS-CoV-2 infection as well.

"The COVID-19 pandemic has impacted all of our lives in unprecedented ways. Yet there is still much to be learned about the point of infection and how it spreads," said Yaron Hakak, Ph.D., CEO of Jumpcode Genomics. "TGen scientists have been leading some of the most innovative research into COVID-19 testing, diagnosis, and treatment. In addition, TGen is responsible for the majority of state sequencing testing in Arizona, and we're proud to collaborate with them on this metagenomic project. The knowledge gained from these efforts may help public health professionals mitigate the impact of new strains of COVID-19 and prepare for future pandemics."