New Testing Approach Leverages Metagenomic Sequencing and Analysis to Detect COVID-19 and Identify New SARS-CoV-2 Variants

A new collaboration aims to leverage meta-genomic sequencing and analysis to facilitate detection of COVID-19 and other infectious diseases, as well as identify new SARS-CoV-2 variants.

Jumpcode Genomics (San Diego, CA, USA), a genome technology platform company focused on improving the understanding of human biology, has entered into a collaboration with the Translational Genomics Research Institute (TGen; Phoenix, AZ, USA) to aid investigations into the genomic epidemiology of SARS-CoV-2, the virus that causes COVID-19. Jumpcode 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’s CRISPRclean technology.


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 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.

“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,” said Nicholas Schork, Ph.D., TGen Distinguished Professor and Director of TGen’s Quantitative Medicine and Systems Biology Division. “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.”

Related Links:
Jumpcode Genomics
Translational Genomics Research Institute