FEB 10, 2019 4:29 AM PST

A New Way to Detect Any Human Virus

WRITTEN BY: Carmen Leitch

Some viruses, like Zika, can be challenging to study when they suddenly cause outbreaks because they can be tough to detect in blood samples. Now, scientists in the lab of Pardis Sabeti at there Broad Institute have created a way to design molecular baits that can grab viral particles. The new tool, called CATCH, will enable researchers to study viruses that are only present at low levels in clinical samples. The work has been reported in Nature Biotechnology. Sabeti discussess how we monitor and respond to infectious disease outbreaks in the video.

"As genomic sequencing becomes a critical part of disease surveillance, tools like CATCH will help us and others detect outbreaks earlier and generate more data on pathogens that can be shared with the wider scientific and medical research communities," said the co-senior author of the study Christian Matranga, who now works with a biotech startup.

Viral particles can be captured, even at low levels, with metagenomic techniques, which aim to sequence all of the genetic material in a sample. But those low-level viruses can get lost in the huge amount of genetic information from other sources, like microbes and patient DNA.

Scientists in the Sabeti lab needed a way to use probes they had already made for detecting pieces of viral DNA, while also enriching the microbes that were present at low levels, like Zika.

"We wanted to rethink how we were actually designing the probes to do capture," said MIT graduate student Hayden Metsky. "We realized that we could capture viruses, including their known diversity, with fewer probes than we'd used before. To make this an effective tool for surveillance, we then decided to try targeting about 20 viruses at a time, and we eventually scaled up to the 356 viral species known to infect humans."

They developed CATCH (Compact Aggregation of Targets for Comprehensive Hybridization), which enables a user to design probes that grab genetic material from microbial species, including viruses that infect people. The probes are based on any human virus that's in the GenBank database (from the National Center for Biotechnology Information) and can be made by any number of commercial probe-synthesis companies.

In this work, the researchers used CATCH to design probes for Zika and chikungunya and were able to detect the presence of Zika viruses in several regions before other scientists were able to. This demonstrates that this strategy could help control outbreaks in the future.

A digitally colorized transmission electron microscopic (TEM) image of Zika virus, a member of the  Flaviviridae family. Virus particles (red) are 40nm in diameter, with outer envelope, and inner dense core. / Credit: CDC/ Cynthia Goldsmith

Ideally, this approach would be used in locations where viral outbreaks are common. "We'd like our partners in Nigeria to be able to efficiently perform metagenomic sequencing from diverse samples, and CATCH helps them boost the sensitivity for these pathogens," explained postdoctoral researcher Katie Siddle.

The method can also help clinicians who encounter fevers that may be caused by a virus, but are difficult to diagnose. "We're excited about the potential to use metagenomic sequencing to shed light on those cases and, in particular, the possibility of doing so locally in affected countries," said Siddle.

CATCH can also easily be used when new viral sequences are discovered. The probes designed by Metsky and Siddle have also been made available for public use. 

This work may not only improve our ability to watch for viral outbreaks, but it could also aid in large-scale studies of microbiomes or become a diagnostic tool.


Sources: AAAS/Eurekalert! Via Broad Institute of MIT and Harvard, Nature Biotechnology

About the Author
  • Experienced research scientist and technical expert with authorships on 28 peer-reviewed publications, traveler to over 60 countries, published photographer and internationally-exhibited painter, volunteer trained in disaster-response, CPR and DV counseling.
You May Also Like
MAY 20, 2020
Cell & Molecular Biology
Researchers Detect a Vulnerability in Viruses
MAY 20, 2020
Researchers Detect a Vulnerability in Viruses
Myriad organisms share this planet, and there is an ongoing evolutionary arms race between competing traits or species, ...
JUN 07, 2020
Drug Discovery & Development
Repurposing An Antibiotic To Defeat a Deadly Superbug
JUN 07, 2020
Repurposing An Antibiotic To Defeat a Deadly Superbug
A recent study published in Nature Microbiology describes how an old antibiotic used for Tuberculosis can be powerful tr ...
JUL 03, 2020
Cell & Molecular Biology
A Gut Pathogen Moves With Help From Its Environment
JUL 03, 2020
A Gut Pathogen Moves With Help From Its Environment
Campylobacter jejuni is a foodborne bacterial pathogen that causes millions of cases of food poisoning each year.
JUL 26, 2020
Microbiology
Ongoing Salmonella Outbreak Rapidly Spreads to 23 States
JUL 26, 2020
Ongoing Salmonella Outbreak Rapidly Spreads to 23 States
The CDC has announced that an outbreak of infections related to a strain of the bacterium Salmonella is "rapidly growing ...
JUL 31, 2020
Cell & Molecular Biology
To Outsmart Salmonella, Cells Can Commit Suicide in Different Ways
JUL 31, 2020
To Outsmart Salmonella, Cells Can Commit Suicide in Different Ways
When cells are infected with some strains of the Salmonella bacterium, it can cause typhoid fever, which causes the deat ...
AUG 13, 2020
Immunology
Antibiotics Now, Inflammatory Bowel Disease Later
AUG 13, 2020
Antibiotics Now, Inflammatory Bowel Disease Later
Taking a course of antibiotics as a baby has been linked to a spiked risk of developing inflammatory bowel disease in ad ...
Loading Comments...