Scientists at the Broad Institute of MIT and Harvard in the US have developed a new computational method called CATCH, which could enable the design of molecular ‘baits’ for any known human virus and all their strains.
The new technique is intended to enable the detection of even low-abundance viruses such as Zika.
Certain existing methods such as metagenomic sequencing and enrichment of clinical samples either miss viral material or are directed at a single microbe.
To address these challenges, the team created a computational method to design probes that could offer a comprehensive analysis of different microbes in clinical samples, as well as enrich for low-abundance microbes.
MIT graduate student Hayden Metsky said: “We wanted to rethink how we were actually designing the probes to do capture. We realised 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.”
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The ‘bait’ design of the CATCH probes facilitates capture of genetic material of any combination of viruses.
Users can run the new computational method by inputting genomes from all forms of human viruses available on GenBank sequence database of the National Center for Biotechnology Information.
The programme establishes the best set of probes depending on what the patient needs to recover, irrespective of all viruses or only a subset.
These probes can be used to identify and study the microbes by capturing desired microbial DNA for sequencing, in turn enriching the samples.
Testing of the probes showed that viral content made up more of the sequencing data after enrichment.
The researchers believe that CATCH can aid small sequencing centres in efficient and cost-effective disease surveillance, delivering the information required to control outbreaks.