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The New Technique That Finds All Known Human Viruses In Your Blood
schwit1 writes with this story at the Atlantic that profiles Ian Lipkin and his new method for quickly detecting all known human viruses in a sample: Ian Lipkin, a virus hunter from Columbia University, recently received a blood sample from colleagues at the National Institutes of Health. They came from a man who had received a bone-marrow transplant and had fallen mysteriously ill, with evidence of severely inflamed blood vessels. In analyzing a similar case a few years back, Lipkin had discovered a new polyomavirus, part of a family that can cause disease in people with compromised immune systems. Perhaps this new case would yield another new virus. It didn't. Instead, when Lipkin's team ran the sample through a system that they had devised to detect human viruses, they found that the man was infected with dengue virus. In hindsight, that made sense-he had recently returned from Vietnam, where dengue is prevalent. But the thing is: The team wasn't looking for dengue virus.
"It wasn't what we anticipated, but we didn't have to make a priori decisions about what we planned to find," Lipkin says. "When people analyze samples from people who are ill, they have some idea in mind. This is probably an enterovirus, or maybe it's a herpesvirues. They then do a specific assay for that particular agent. They don't usually have the capacity to look broadly." The new system, known as VirCapSeq-VERT, barrels past this limitation. Lipkin, together with fellow Columbia professors Thomas Briese and Amit Kapoor, designed it to detect all known human viruses, quickly, efficiently, and sensitively. By searching for thousands, perhaps millions, of viruses at once, it should take a lot of the (educated) guesswork out of viral diagnosis.
"It wasn't what we anticipated, but we didn't have to make a priori decisions about what we planned to find," Lipkin says. "When people analyze samples from people who are ill, they have some idea in mind. This is probably an enterovirus, or maybe it's a herpesvirues. They then do a specific assay for that particular agent. They don't usually have the capacity to look broadly." The new system, known as VirCapSeq-VERT, barrels past this limitation. Lipkin, together with fellow Columbia professors Thomas Briese and Amit Kapoor, designed it to detect all known human viruses, quickly, efficiently, and sensitively. By searching for thousands, perhaps millions, of viruses at once, it should take a lot of the (educated) guesswork out of viral diagnosis.
"You have a virus, specifically a bargoburomyopolyfluenza 2 virus."
"That's great doc, what do we do to treat it?"
"Take two aspirin, call me in the morning."
Faster! Faster! Faster would be better!
Trying to figure out the tech, reference was made to this
http://www.google.com/patents/...
whereby for this particular application they have put "probes" for specific sequences of all known viruses on "tiles" of a rectangular area. In general, the tech could be used for RNA, DNA, proteins, and more
In slightly more technical terms, they've designed a system that selectively targets & amplifies ~2 million DNA sites; chosen from the genomes of all known infectious viruses. The scientists basically apply this assay to the infected cells (I'm assuming they take a blood sample or something), leaving them with DNA that matches those targets. Then, they run those DNA fragments through a sequencer, and see what they got. From there, they can deduce which virus was present in the original sample.
My understanding from a very quick skim of the paper (open access, here) is that they are not using microarrays. They have a mixture of a very large (2 million) number of probes to match DNA/RNA sequences of all known viruses which infect vertebrates. They use these to amplify viral sequences and then use normal high throughput DNA sequencing (Illumina, in this case) to see what they've got. They claim that it is sensitive to both DNA and RNA viruses (and all the variations - double, single stranded etc.) Being able to detect both DNA and RNA in a single test mildly surprises me, but I'm only slightly familiar with DNA sequencing technology, so maybe it isn't a big deal.
They do say "A biotinylated oligonucleotide library was synthesized on the NimbleGen cleavable array platform and used for solution-based capture of viral nucleic acids present in complex samples containing variable proportions of viral and host nucleic acids." Perhaps that translates to say the microarray you talk about was used to make the 2 million probes.
As a complete aside, I'm a little surprised this isn't a Nature or Science paper.
Quattuor res in hoc mundo sanctae sunt: libri, liberi, libertas et liberalitas.
If this system finds all known human viruses in a person's blood, my guess is it has to put them there. How else can one person get all human viruses at once?
God spoke to me
The hypothesized cost of $25 per sample was bandied about as feasible by the similar (same?) process VirScan.
I wish them luck. We may eventually be able to figure out just how widespread things like lyme disease really are.
Someone had to do it.
Availability of $13 generics for drugs that cost $750 here?
Someone had to do it.
Since we have very few antivirals, it isn't much of a problem.
"Go home and wash your hands. Don't kiss anybody you like." And that's pretty much it.
Faster! Faster! Faster would be better!
They have a mixture of a very large (2 million) number of probes to match DNA/RNA sequences of all known viruses which infect vertebrates. They use these to amplify viral sequences and then use normal high throughput DNA sequencing (Illumina, in this case) to see what they've got.
Yep, that seems a fair explanation. I liken it to trying to hit an ant with a minigun. It's probably not higher profile because probe capture has been done before (e.g. for ribosomal enrichment / exclusion); this is just taking it to the extreme. I wouldn't be surprised if someone follows this up later on with a 1 billion probe capture design for bacterial sequencing -- there'll always be more probes that can be added into the mix.
Ask me about repetitive DNA