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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.
... the technique also shares all your personal biological data with third parties with implied consent upon usage.
Let's figure out what's wrong with him and get him a cure, STAT.
"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.
So you're saying the labs will no longer be able to gouge us for a two dozen different tests on the same blood sample?
He's got a severely compromised immune system, and yet he goes to a 3rd World country.
What am I missing here?
"I don't know, therefore Aliens" Wafflebox1
Great test if it has good sensitivity and specificity. However, the problem will be that it will yield too much confounding information - the so called 'incedentaloma' but only for viruses. It will lead to people receiving unnecessary treatments for the things that were found. Should only be used for 'house' like cases where 'odd ball' causes are suspected.
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
Exactly. OP is confusing money grubbing tools with the scientifically illiterate.
"I don't know, therefore Aliens" Wafflebox1
USAA is a bunch of crooks. I was walking on a sidewalk when one of their drivers hit me. The adjustor, Vernon Richards at extension 38609, freely admitted that their customer was at fault, but would only offer to pay for 10% of the medical bill. The stupid thing was that they had an agreement with my local hospital and if they had simply paid it directly, they would have paid about a 1/4 of the uninsured bill amount. Instead they fought it and two years later they had to pay the entire billed amount. They could have saved over $30k just by paying the bill they knew they would eventually have to pay.
It makes you indestrucible
https://vimeo.com/96581518
Recycle PCs and build a wireless community network www.hillsborough.org.nz
One step closer to a medical tricorder that tells you exactly what's wrong with your patient. Amazing.
So that all viruses that usually aren't seen in humans are added to the list of those possible to detect.
I wouldn't be surprised if there are viruses that exists and spread without causing symptoms at all as well. It would be a good strategy for spreading - do it silently.
If builders built buildings the way programmers wrote programs, then the first woodpecker would destroy civilization.
The New Technique That Finds All Known Human Viruses In Your Blood
Well, not all, I hope. Otherwise I'm in trouble.
systemd is Roko's Basilisk.
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
The way I've been feeling the last few days, I've probably got all known viruses in my blood.
Slow down, cowboy! It has been 4 hours since you last posted. You must wait another few hours.
They'll still get you with the annual definitions update subscription. Doesn't even have real-time detection - you have to do a full system scan when you suspect a virus.
As an aside (that means off-topic, guys) this looks like part of a fixed-point arithmetic implementation. It may not be as silly as you think.
Bruce Perens.
It is not a Nature or Science paper because it is just a standard target enrichment library. They've been doing this for a long time to profile things like cancer markers, disease panels, etc. These guys just made a library to target viruses. That's all. It can do both RNA and DNA because they do a reverse transcriptase reaction first (required anyway to sequence RNA), and then pull down the resulting cDNA along with DNA and sequence it. Kind of cool, but not really groundbreaking.