New research demonstrates potential of Jumpcode Genomics rRNA depletion technology to improve pandemic response

New research shows that a CRISPR-based depletion technology overcomes the limitations of past NGS pandemic preparedness strategies by specifically targeting and removing abundant host and microbial ribosomal RNA (rRNA) sequences.

Jumpcode Genomics, a genome technology platform company focused on improving the understanding of human biology, together with the Translational Genomics Research Institute (TGen), part of City of Hope, today announced the results of a new study demonstrating the potential of Jumpcode Genomics depletion technology for improving future large-scale infectious disease testing and pandemic response. The results were published in the journal Cell Reports Methods in an article titled, “A CRISPR-enhanced metagenomic NGS test to improve pandemic preparedness.”

“The massive loss of life due to COVID-19 exposed how underprepared governments and public health institutions are for large-scale pandemics. COVID-19 is likely not the last pandemic we will face and national and international pandemic preparedness plans are essential to ensure the health and wellbeing of people across the globe and prevent another tragedy of this scale,” said Jon Armstrong, lead author and Vice President, Research & Development at Jumpcode Genomics. “These new findings demonstrate the potential for Jumpcode’s depletion technology to provide highly sensitive, pathogen-agnostic next-generation sequencing (NGS) deployable at “Day Zero” to combat any future pathogen outbreak before it progresses to a pandemic.”

In the past, NGS has had limited use for pandemic preparedness strategy due to various factors, including time-consuming workflows, extensive infrastructure needs, and expensive sequencing instruments. However, this new research shows that a CRISPR-based depletion technology and NGS – overcomes these limitations by specifically targeting and removing abundant host and microbial ribosomal RNA (rRNA) sequences.

Researchers from Jumpcode Genomics and TGen conducted a study evaluating the performance of molecular enrichment strategy by removing abundant and uninformative sequences to boost identification of variant strain types, co-infections, and individual human host response assessment in a single workflow. The results demonstrate that SARS-CoV-2 detection sensitivity using the CRISPR-based depletion method is comparable to RT-qPCR based detection for samples with Ct values up to 35.

Additionally, the data show that the CRISPR-NGS strategy enables variant strain typing, detection of co-infecting pathogens, identification of antimicrobial resistance genes, and reporting of human host responses to infection. Furthermore, using contrived samples containing viral nucleic acid, the researchers found that the CRISPR-NGS approach can successfully detect other pathogens, such as Zika virus.

“The flexibility of the proposed test is indeed one of its virtues. Understand that currently one might have to be evaluated with multiple logistically challenging and time-consuming  tests to determine what they have been infected with, whether they might need immediate medical attention, and what their prognosis might be, and the proposed test has the potential to help put aspects of these much needed insights together in a single test,” said Nicholas Schork, Deputy Director of Quantitative Science and Distinguished Professor at TGen and senior author on the paper.

SourcePR Newswire

Chan AP, Siddique A, Desplat Y et al. (2023) A CRISPR-enhanced metagenomic NGS test to improve pandemic preparedness. Cell Rep Meth [Epub ahead of print]. [article]

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