Infectious disease surveillance

The COVID-19 pandemic has brought intense awareness to zoonotic diseases and the real danger they pose to global human health and welfare. The pandemic highlights how easily an infectious agent can spread through a population, particularly when many affected individuals are asymptomatic or have symptoms easily mistaken for any number of diseases. As such, a sensitive and specific means of detecting the virus has been essential to tracking it and implementing effective public health measures.

The challenge

PCR testing is rapid and sensitive - but has significant limitations:

  1. By its nature, PCR is not available when the initial outbreak occurs, limiting its effectiveness when tracking is most needed to prevent an epidemic.
  2. PCR is of little use for genome surveillance and tracking viral evolution.
  3. PCR does not provide any information on co-infections and the human host response to the infection.

The solution

A single test to provide information on viral genomic data, microbiome composition, information on co-infection, and the transcriptional status of the host immune response.

Testimonial

"The problem [with NGS] is that a lot of the stuff… is not what you're looking for — it's more noise. And most of it will just be human DNA, because it's taken from a human. What one would want to do is find the stuff that's not human, that is… the DNA sequence reflecting the pathogen, and somehow get rid of all the noise. And that's what Jumpcode's technology can do."

Nicholas Schork, Deputy Director and Distinguished Professor of Quantitative Medicine

Read more: TGen, Jumpcode Genomics Marrying NGS, CRISPR to Build a Better COVID-19 Test

The samples and method

Contrived samples spiked with SARS-CoV-2 down to 60 viral copies.

Contrived samples consist of 1 ng of lung-derived total RNA combined with different fractions of Staphylococcus aureus total RNA and a synthetic SARS-CoV-2 control. Both S. aureus and SARS-CoV-2 were added to the samples from 1% down to 0.0001% of total RNA. For SARS-CoV-2, this amounts to a maximum of 600,000 and a minimum of 60 viral copies. 

NEB Ultra II Directional RNA Library Prep Kits were used to prepare libraries and then CRISPRclean Metatranscriptomic rRNA Depletion Kit was applied to samples to remove human and over 200 bacteria ribosomal RNA sequences. Libraries were sequenced on short-read sequencing instrument. Data analysis was performed using Jumpcode proprietary software to measure alignment and depletion rates, the SILVA database for ribosomal RNA read alignment, and the Kraken2 and the CosmosID pipelines for k-mer based metagenomic investigation.

Table1_coverage

The results

When 99% of ribosomal RNA from human and more than 200 bacteria are removed, you can clearly see what's important in your sample.

Fig2_fold enrichment

High sensitivity detection of SARS-CoV-2 down to 0.0001% contrived samples.

Increased number of reads aligning to SARS-CoV-2 from 10,000 to 70,000 reads after CRISPRclean depletion.

A similar increase in reads occurred for S. aureus.

 

Fig3_Readsaligning
Fig4_heatmap

Higher reads aligned to viral genomes.

CosmosID shotgun metagenomics analysis heatmap using k-mer based approach shows more read counts aligning to viral genomes than the control sample.

UID poster

Universal Infectious Disease Assay

TGen, Jumpcode Genomics Marrying NGS, CRISPR to Build a Better COVID-19 Test

In a new article from GenomeWeb, Senior Editor Christie Rizk speaks with Nicholas Schork, Ph.D., Deputy Director and Distinguished Professor of Quantitative Medicine at The Translational Genomics Research Institute, about how Jumpcode’s CRISPRclean™ technology is helping researchers build a better COVID-19 test: While COVID-19 held the world in its grip throughout much of 2020, the […]

With CRISPRclean, you can now acquire viral genomic data, microbiome composition, information on co-infections, and host-immune response in a single workflow.

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