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The New Technique That Finds All Known Human Viruses In Your Blood

Posted by samzenpus on from the got-to-get-them-all dept.

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.

111 comments

  1. Unfortunately ... by Anonymous Coward · · Score: 1, Insightful

    ... the technique also shares all your personal biological data with third parties with implied consent upon usage.

    1. Re:Unfortunately ... by ooshna · · Score: 1

      Weighed against dying of some unknown illness sign me up.

    2. Re:Unfortunately ... by Anonymous Coward · · Score: 0

      I think the OP was ripping on AVG's new "privacy" policy.

  2. Someone please test APK by Anonymous Coward · · Score: 1

    Let's figure out what's wrong with him and get him a cure, STAT.

  3. Doctor what's wrong with me? by ColdWetDog · · Score: 2

    "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!
    1. Re:Doctor what's wrong with me? by Anonymous Coward · · Score: 1

      "Take two aspirin, call me in the morning."

      Of course, this is important for individual diagnosis. But it's the longer term implications on the epidemiology side that are absolutely huge.

      In another decade or two it will be possible to check everyone for contagious illness in all public spaces (in developed countries, at least) and to then quarantine anyone who is infected. Basically, infectious disease will become a distant ugly memory. And, of course, vaccines will be obsolete (again, for everyone in developed countries).

      Back in the late '80s and early '90s, there were a handful of tech savvy people who could foresee the rise of the internet. But most people were oblivious. Well, now we're at a similar place with DNA sequencing. The writings on the wall but most people don't see it.

    2. Re:Doctor what's wrong with me? by viperidaenz · · Score: 1

      Except the people that refuse to be checked, because with the vaccines gone, it will be these scans that cause autism

      Then there will be people who have never been exposed to a vast array of illnesses and because of that have underdeveloped immune systems. They'll take a trip someone (an undeveloped country) and die a few hours after getting off the plane.

    3. Re:Doctor what's wrong with me? by Bruce+Perens · · Score: 5, Insightful

      What about the human beings who have virus DNA incorporated into their genome? That's pretty much all of us.

      --
      Bruce Perens.
    4. Re:Doctor what's wrong with me? by tsotha · · Score: 1

      "Treat you? We don't really know what this one does. It might not be bad for you at all. Or it might kill you in some new and interesting way. Hard to tell."

    5. Re:Doctor what's wrong with me? by Anonymous Coward · · Score: 0

      Even the smallest viruses have genomes that are thousands of base pairs long. 4^1000 is a lot of different viral sequences. And most viruses mutate fairly quickly. Already it's routine in research settings to amplify and sequence a full viral genome sequence from an infected individual - with essentially 100% accuracy.

      In another decade or so, such sequencing will also be routine in clinical settings. And this will allow viral transmission to be tracked between individuals (that is, match the specific viral strain that you're infected with to the strain of the individual who infected you). We'll basically have epidemiological transmission data at a resolution of individual transmission events within a community.

      And, from the perspective of basic biology, even viruses that insert into the host genome during (new) infection typically only infect a narrow range of cell type. As a consequence, it's rare for a new viral infection to result in insertion into the genome of germ line cells (egg and sperm cells). So DNA sequencing might have trouble distinguishing between someone who had a previous infection with, say, chicken pox, and someone who has an active recent infection. But DNA sequencing could fairly easily identify someone who had never had a chicken pox infection in their life.

    6. Re:Doctor what's wrong with me? by Anonymous Coward · · Score: 0

      Except the people that refuse to be checked, because with the vaccines gone, it will be these scans that cause autism

      In most cases, it will be possible to detect infection from saliva or urine. In rare case, blood may be needed. So, unless someone wants to claim that spitting and peeing cause autism, then that's going to be a tough claim to sell.

      Then there will be people who have never been exposed to a vast array of illnesses and because of that have underdeveloped immune systems.

      There's a lot we still don't know about the immune system. But, generally speaking, the infection one gets from being infected by a particular pathogen only results in immunity to that particular pathogen. Getting sick with one strain of the flu typically doesn't even provide immunity against other strains of the flu, for example. So, there's little evidence that getting sick a lot makes the immune system stronger in some general sense. There even specific pathogens where a previous infection makes one more vulnerable to future infections (e.g. Dengue).

      They'll take a trip someone (an undeveloped country) and die a few hours after getting off the plane.

      Of course, you'd want to get vaccinated against whatever happened to be circulating in the developing country that you intended to visit. But it's not like you'd have a generally weak immune system and drop dead the minute you stepped off the plane.

    7. Re: Doctor what's wrong with me? by BronsCon · · Score: 2

      spitting and peeing cause autism

      I think it's actually the other way around.

      --
      APK quotes people (including myself) without context and should not be trusted. Just thought you should know.
    8. Re:Doctor what's wrong with me? by ColdWetDog · · Score: 4, Informative

      In intact blood (well treated, processed correctly) the genomic DNA will be in cells which can be spun out quickly to create plasma. In fact, most lab tests are done on cell free fractions because the proteins and assorted other molecules bugger up the process.

      You should also be able to determine in flanking sequences (if any). If you have a lot of extraneous DNA, it probably doesn't come from a free floating viral particle.

      And finally, since the vast majority of viruses have some sort of protein capsid and are of a fairly constrained size, you can always fractionate the blood to include only those sized structures.

      So, it is a potential issue but one that can be overcome in a fairly straightforward fashion.

      --
      Faster! Faster! Faster would be better!
    9. Re:Doctor what's wrong with me? by amRadioHed · · Score: 1

      We don't know what most viruses do yet. Detect them is the first step towards understanding what they do.

      --
      We hope your rules and wisdom choke you / Now we are one in everlasting peace
    10. Re:Doctor what's wrong with me? by Immerman · · Score: 4, Informative

      I think resistance tends to be considerably more resilient than that in many/most cases. Influenza is actually one of the more volatile viruses we encounter on a regular basis - its actual mutation rate is much slower than something like HIV, but thanks to its incredibly widespread "host base" across the animal kingdom, and the facility with which it can "interbreed" with distant relatives, we are getting constantly barraged by radically new variants on a regular basis, a few of which manage to thrive. There's a reason the flu makes epidemiologists nervous - highly infectious, genetically unstable, and with a proven track record of occasionally spawning extremely lethal variants.

      And of course, just for completeness sake, most of the things people commonly label as "the flu" are completely unrelated to influenza in the first place. Just part of the microbial medley passing through us on a regular basis.

      --
      --- Most topics have many sides worth arguing, allow me to take one opposite you.
    11. Re:Doctor what's wrong with me? by Anonymous Coward · · Score: 2, Insightful

      So GATACA but without the benefits of improved DNA, Got a virus? You're fired, no reason to risk everyone else at the company. We don't want your type here. No public transportation too, so all the poor get to starve to death in their homes. As since we're checking your blood, we might as well compare it with all the unsolved crime cases and keep it on file just in case you do something later. Oh, is that a drug in your blood stream? Off to jail with you. Hmm, did you know 80% of people with that sequence are gay?

    12. Re:Doctor what's wrong with me? by Anonymous Coward · · Score: 0

      I've always been amazed that so-called "winter flu's" have never been properly "cured" when (it seems) we know that ONE thing (time of year) seems to be a MAJOR factor in transmission and contagion.
      If you KNEW that measles was only ever contracted when oranges were in season, I would think that THAT information would allow a much quicker path to eradication of measles, enabling a huge reduction to contributing "variables".
      The same SHOULD be the case with seemingly "weather related" illnesses, where you can just continue to isolate the variables that contribute to the illness. Perhaps it's just that it's much more PROFITABLE to sell cold "remedies".

    13. Re:Doctor what's wrong with me? by F.Ultra · · Score: 1

      That is because the flu is not the same virus, each new outbreak is from a new strain.

    14. Re:Doctor what's wrong with me? by AmiMoJo · · Score: 2

      molecules bugger up the process.

      The jargon in these medical articles always goes way over my head.

      --
      const int one = 65536; (Silvermoon, Texture.cs)
      SJW, n: "Someone I don't like, and by the way I'm a fuckwit" - AC
    15. Re:Doctor what's wrong with me? by jbmartin6 · · Score: 1

      Those genes are not expressed, and we don't have copies of those viruses floating around our bloodstream.

      --
      This posting is provided 'AS IS' without warranty of any kind, implied or otherwise.
    16. Re:Doctor what's wrong with me? by dcw3 · · Score: 1

      molecules bugger up the process.

      The jargon in these medical articles always goes way over my head.

      Pull the foreskin back next time.

      --
      Just another day in Paradise
    17. Re:Doctor what's wrong with me? by Bruce+Perens · · Score: 1

      Those genes are not expressed, and we don't have copies of those viruses floating around our bloodstream.

      Probably, and for the most part. But we used to think the genome was mostly "junk DNA" before we understood that much of it was homeotic in function. It seems to me that virus copies would not be conserved over time unless they were serving some function.

      --
      Bruce Perens.
    18. Re:Doctor what's wrong with me? by bigpat · · Score: 1

      Of course, this is important for individual diagnosis. But it's the longer term implications on the epidemiology side that are absolutely huge.

      This seems to me to be the real benefit of these types of tests. I would hope that CDC, NIH in conjunction with other agencies would begin funding these types of tests on a randomized basis so they could see how viruses are spreading through the population and finding out how viral infections are interacting with other diseases and treatments. The data collection effort would be well worth it.

      The other test that has a similar implication was the one announced back in June This blood test can tell you every virus you’ve ever had

      Come up with a statistically meaningful sampling. Say 10,000 kits per 100,000 patients and just start collecting data.

    19. Re:Doctor what's wrong with me? by jbmartin6 · · Score: 1

      Well, the only function they would need is the ability to get themselves replicated. There isn't a need for them to have any function in the larger picture of the body. But I read the same thing, many of the genes are turning out to be not as quiet as we thought.

      --
      This posting is provided 'AS IS' without warranty of any kind, implied or otherwise.
    20. Re:Doctor what's wrong with me? by Bruce+Perens · · Score: 1

      If I had to guess, I'd say heritable immunity.

      --
      Bruce Perens.
  4. application of "whole proteome tiling microarrays" by iggymanz · · Score: 2

    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

  5. Slightly more technical by Fwipp · · Score: 5, Informative

    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.

    1. Re:Slightly more technical by Iamthecheese · · Score: 4, Insightful

      If you're testing for that many viruses any false positive is unacceptable. So what's the false positive rate?

      --
      If video games influenced behavior the Pac Man generation would be eating pills and running away from their problems.
    2. Re:Slightly more technical by Anonymous Coward · · Score: 1

      Does it matter? Test for them all, get your positives, then run a specific test on the ones that could cause the symptoms. Or am I missing something?

      captcha: nonsense

    3. Re:Slightly more technical by MobyDisk · · Score: 2

      Suppose the false positive rate is 2%. The article says it detects 700 vriuses. 2% of 700 viruses is 14 viruses. 14 tests could require 14 samples: so 5 blood draws + 6 urine samples + 3 stool samples. Ugh! (And no - you can't usually run 2 arbitrary tests from one sample.) So to make this work, the doctors would have to look through the results to see which viruses match the symptoms, so they only run the specific tests for those. That is probably what happened in this example. They probably saw a dozen viruses, and said "Hey, this one might actually fit."

      Of course, this example makes one wonder why didn't they consider dengue in the first place. Perhaps it just goes to show that the test still is useful since it compensates for human fallibility.

    4. Re:Slightly more technical by Anonymous Coward · · Score: 0

      If you're testing for that many viruses any false positive is unacceptable. So what's the false positive rate?

      The initial results are going to depend a lot on the quality of the bioinformatics analysis - which is actually pretty hard. But once you know what to look for you can go back and do a specific test to verify the initial results.

      To use a computer analogy, imagine that someone develops a technique that guesses a person's password with a 1% false positive rate (1% of the time the technique suggests the wrong password). Well, all you have to do double check that the password is correct (for example, try logging in with their password). And the 1% false positive rate doesn't matter.

    5. Re:Slightly more technical by wwalker · · Score: 2

      What?! False *negatives* would be unacceptable. If the broad test is less sensitive than the specific tests and often misses a lot of viruses, then what's the point of having a broad test? False positives are perfectly fine on the other hand. You can always run a specific test to confirm the results of a broad test. In fact that's how it works for a lot of conditions. You run a highly sensitive cheaper or less invasive test that's known to be imprecise and only then you confirm the result with a more comprehensive test, if you get a positive reaction.

    6. Re:Slightly more technical by Immerman · · Score: 3, Informative

      You're ignoring the second half of their suggestion - test for the "detected" viruses that could cause the symptoms. If you had a 2% false positive rate, and 10% of the "viral library" your checking against could cause the symptoms, then you're averaging 2%*10%*700 = 1.4 false positives per patient.

      Of course RTFAing tells me that they're expecting no false positives at all thanks to the fact that this technique provides the complete genome of everything detected, as it occurs in the patient. It's not a "yes/no" like most current tests, or even a "70% certainty", it tells you that "this *exact* genome was in the sample", even if it's something that you've never seen before that was just similar enough to stick to one of the "hooks". You then look up the freshly-sequenced genome in your library to figure out what it is. False positives would imply that the replication system somehow managed to spontaneously create recognizable genomes from scratch.

      As I read it the methodology is:
      1) catch a wide range of "suspicious" viral DNA
      2) replicate it so that you can...
      3) sequence it all
      4) compare sequenced DNA to database to identify pathogens and unknown viruses.

      (1) will likely generate a fair amount of false positives, but unlike traditional tests at that point it's just bringing in "suspicious characters" for questioning. (2) and (3) should be pretty much immune to false positives, and (4) will give you a fully "fingerprinted" list of "confirmed-present" viruses, along with a confidence-rated identification of anything with a match in the database.

      --
      --- Most topics have many sides worth arguing, allow me to take one opposite you.
    7. Re:Slightly more technical by AmiMoJo · · Score: 4, Informative

      A few false positives would be fine, you can just run other more traditional tests to rule them out. This sort of diagnostic is for people who have problems that cannot be readily diagnosed. The choice is either do many expensive tests for different and very unlikely viruses, or use this technique to narrow it down to a small field.

      You wouldn't start treatment on the results of this test alone, you would confirm them first.

      --
      const int one = 65536; (Silvermoon, Texture.cs)
      SJW, n: "Someone I don't like, and by the way I'm a fuckwit" - AC
    8. Re:Slightly more technical by omnichad · · Score: 2

      False positives would imply that the replication system somehow managed to spontaneously create recognizable genomes from scratch.

      A "false" positive could also mean that the virus is present, but not replicating at any real level of infection.

    9. Re:Slightly more technical by MobyDisk · · Score: 1

      To set the record straight, I skimmed the article and missed the "no false positives" claim. Doh! But I am skepitcal of that claim. The article says:

      And since the technique offers up the full genomes of whatever virus it detects, it shouldn't throw up any false positives

      That's like me saying "because I showed my work, my answer cannot be wrong." Just because it gives the sequence of what it thinks it found, doesn't mean that it was actually present, and that the sequence is correct. I've worked on PCR systems, but never sequencing systems. Are they really 100% perfect? If so, then... wow... that's amazing.

    10. Re:Slightly more technical by Anonymous Coward · · Score: 0

      That's not a false positive... You are trying to hard to be contrary.

    11. Re:Slightly more technical by Fwipp · · Score: 1

      They're not 100% perfect, but they're much much much more accurate than they need to be for this sort of analysis.

      For example; I picked out a sample mostly at random from an internal dataset. In this shallow sample of 4 million reads, over 90% of reads have all 36 bases with quality > 30. (Quality is in Phred score: q30 = the sequencer estimates a 99.9% chance that this base is read correctly). Even if 3-4 bases are incorrect, it's still usually possible to map the read to the genome with high confidence (even if the aligner discards the base-quality information!). This combines with the fact that you'll have multiple reads mapping to each target, so even if several reads are mapped to the wrong target, the right calls will be made. Finally, I'm sure there's some heuristic for "we found 98% of the expected targets for E. xamplis, and trace amounts of T. atoeba, we're pretty sure it's the former."

      The false positive rate is obviously not zero - it's irresponsible of the article to claim that. But it's much lower than other competing methods, and I wouldn't be at all surprised if in their testing they found 0 false positives.

    12. Re:Slightly more technical by Immerman · · Score: 1

      I'll admit I'm not even remotely well versed in the details of DNA replication and sequencing techniques, but I imagine a certain degree of error is inevitable - even properly functioning living cells are incapable of 100% accurate DNA replication (quite possibly by "design", but still.)

      It seems likely though that the nature of those errors would result in "bad reads"/"noise" in sections of the sequenced genomes, not the wholesale creation of genomes that weren't in the original sample to begin with. That might interfere with the detection of a pathogen (false negatives), but it seems extremely unlikely that the "corrupted" genome would look similar enough to some other pathogen in the screening database to cause it to be mistakenly identified as something else, which is what would be required to generate a false positive.

      --
      --- Most topics have many sides worth arguing, allow me to take one opposite you.
  6. Labs out of business by Jumunquo · · Score: 1

    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?

    1. Re:Labs out of business by Anonymous Coward · · Score: 0

      Since this technique currently requires electron microscopy it likely won't be available on the cheap anytime soon. It does however open the door for enterprising inventors to develop analogous techniques which could potentially drive some cost out of the process in the name of competition. In the meantime much grant money will likely be spent studying the specificity and sensitivity of the current technique.

    2. Re: Labs out of business by Anonymous Coward · · Score: 0

      Yes, but now they can charge 100x the normal rate for the ubertest!

    3. Re:Labs out of business by Michael+Woodhams · · Score: 1

      Only if all the tests were for viruses.

      --
      Quattuor res in hoc mundo sanctae sunt: libri, liberi, libertas et liberalitas.
    4. Re:Labs out of business by skids · · Score: 3, Informative

      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.
    5. Re:Labs out of business by Anonymous Coward · · Score: 1

      Since this technique currently requires electron microscopy it likely won't be available on the cheap anytime soon.

      No, they only put an electron micrograph at the head of the article to provide a bit of pizzazz and give the sense that viruses are small.

      It's actually based on next-gen DNA sequencing which is dirt cheap - $1,000 for your entire (human) genome from a few drops of saliva at current rates.

    6. Re:Labs out of business by labnet · · Score: 1

      Interesting you mention lymes disease. A friends wife recently acquired this, and had to go to Germany for treatment, as Australian doctors still deny its existence in our country. Yet you start talking to people about it, and it seems everyone knows someone who has had lymes.

      --
      46137
    7. Re:Labs out of business by Michael+Woodhams · · Score: 1

      There are many people who will give bogus Lyme disease diagnoses. This might be what happened with your friend's wife. I haven't the knowledge or expertise to say more than 'it is a possibility'.

      --
      Quattuor res in hoc mundo sanctae sunt: libri, liberi, libertas et liberalitas.
    8. Re:Labs out of business by Michael+Woodhams · · Score: 1

      Lyme disease is bacterial, not viral. (Although maybe one day the methods used here will be able to be extended to the much larger genomes of bacteria.)

      --
      Quattuor res in hoc mundo sanctae sunt: libri, liberi, libertas et liberalitas.
  7. Something seems kinda stupid. by Nutria · · Score: 1

    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
    1. Re:Something seems kinda stupid. by iggymanz · · Score: 1

      A couple of my relatives with AIDS visit the rest of the family in southeast asia without incident. That's common. Maybe you have some misconceptions.

    2. Re:Something seems kinda stupid. by jedidiah · · Score: 1

      Yes. Quite. There are some things you can't avoid in that condition and others that should be easily avoidable.

      Although we still have to pick up the pieces after someone inflicts stupid upon themselves.

      --
      A Pirate and a Puritan look the same on a balance sheet.
    3. Re:Something seems kinda stupid. by Anonymous Coward · · Score: 0

      "What am I missing here?"

      A 10 year old prostitute and a few hundred American $$

    4. Re:Something seems kinda stupid. by Nutria · · Score: 1

      What's always puzzled me about CP is the practicality of the matter. ISTM that that Tab A just wouldn't fit into Slot B (and creeps me out just thinking about it).

      --
      "I don't know, therefore Aliens" Wafflebox1
    5. Re:Something seems kinda stupid. by skids · · Score: 3, Insightful

      Availability of $13 generics for drugs that cost $750 here?

      --
      Someone had to do it.
    6. Re:Something seems kinda stupid. by Dog-Cow · · Score: 1

      If you're talking about an adult penis into a 10 year old's vagina, why wouldn't it fit? A baby's head can fit through a 12 year old's vagina, after all. If you're talking about the anus, that's not a big deal either -- you just stretch it. There's no physical barrier.

    7. Re:Something seems kinda stupid. by Nutria · · Score: 1

      But the damage, the pain. And the two year olds!

      --
      "I don't know, therefore Aliens" Wafflebox1
  8. To much information not necessary a good thing. by lewildbeast · · Score: 1

    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.

    1. Re:To much information not necessary a good thing. by ColdWetDog · · Score: 3, Informative

      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!
    2. Re:To much information not necessary a good thing. by KGIII · · Score: 1

      Do you mean "incidentaloma," perhaps? I was unable to find your word at The Free Dictionary or at the OED site. What does this have to do with finding a tumor without having exhibited signs or, basically, by accident? I'm assuming they'd not just be doing this sort of testing at random or anything but will be limiting its use to just those who appear to be suffering from viral infections. (Is it considered an infection if it is viral and not bacterial?)

      After the 'review' button, well, this reply looks as if I'm attempting to be snarky. I'm not, really. I simply don't get it. Also, using a reasonable approximation of good grammar while having the option to show the domain name enabled is rather confusing. Oh well, hopefully you can parse it. I don't think it's that confusing. This subject is, however, confusing to me, at least. Woohoo! I'll just shotgun those commas. No, no I haven't slept.

      --
      "So long and thanks for all the fish."
    3. Re:To much information not necessary a good thing. by Anonymous Coward · · Score: 0

      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

      So instead of getting shotgun-approach treatment for things the person doesn't have, they will get treatments for things they do have... and this is .... WRONG in your eyes?

      Do you take Mercury supplements?

    4. Re:To much information not necessary a good thing. by Ungrounded+Lightning · · Score: 1

      Since we have very few antivirals, it isn't much of a problem.

      If I understand it correctly: When you have a sequence you can CONSTRUCT a specific antiviral for it.

      Better yet: You can also construct (or select off-the-shelf) antibodies to it, for antiseura treatment. That's very effective and blazingly fast for any infection that is accessible from the bloodstream.

      --
      Bantam Dominique roosters crow a four-note song. Once you've heard it as "Happy BIRTHday" you can't NOT hear it that way
  9. Re:application of "whole proteome tiling microarra by Michael+Woodhams · · Score: 5, Informative

    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.
  10. Re:Expect the Republicans to... by Anonymous Coward · · Score: 0

    They won't outlaw it, that would be insane! They'll sell it to Martin Shkreli so he can charge $700,000 per test.

  11. Count me out! by GoodNewsJimDotCom · · Score: 4, Funny

    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
    1. Re:Count me out! by Anonymous Coward · · Score: 0

      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?

      Obligatory Simpsons: They draw blood from C. Montgomery Burns: https://www.youtube.com/watch?...

    2. Re:Count me out! by Anonymous Coward · · Score: 0

      LOL @ was thinking about that one.

  12. Re: Expect the Republicans to... by Anonymous Coward · · Score: 0

    I have six figures of uninsured motorist medical coverage and well into seven figures of health insurance, but that still wasn't enough to get care at Overlake Hospital in Beelevue, WA. They wouldn't even see me until the cops came and confirmed the accident wasn't my fault. I was rear ended on my motorcycle at a red light. The other driver had USAA, and thirty months later I'm still fighting to get them to pay. If they make it 36 months I this state without me filing a lawsuit then they don't have to pay a penny.

  13. Re: Expect the Republicans to... by Anonymous Coward · · Score: 0

    Strange. I didn't have a problem there since they assumed I worked for Micosoft since I was hit in a parking garage in a Microsoft building. I was in the 450 108th building. Two surgeries later, I'm fine. I'm still trying to collect from the guy that hit me insurance company which is USAA.

  14. Trolls, lmao - please... apk by Anonymous Coward · · Score: 0

    There's no need for a cure when you're winning (me) & you? Losing - @ all possible turns too no less! Quit projecting it's you, & those LIKE you, that need a "cure"... lol!

    * :)

    (Let me tell you what - it's not easy being "world-class", like me... & what would "the trolling off-topic likes of 'you'" know about it? Zero - I'm trying to make a blind man in yourself understand the color Blue... lol!)

    APK

    P.S.=> Face facts: You *wish* you were ME, & you know it... I don't blame you! Quit trolling - that'd be a start in the right direction for you... apk

    1. Re:Trolls, lmao - please... apk by Anonymous Coward · · Score: 0

      Nobody wishes they were you, but everyone wishes you'd quit spamming your bullshit everywhere.

    2. Re:Trolls, lmao - please... apk by Anonymous Coward · · Score: 0

      That dull response indicates that you do.

    3. Re:Trolls, lmao - please... apk by Anonymous Coward · · Score: 0

      Yes, I do wish you'd quit spamming your bullshit everywhere!

    4. Re:Trolls, lmao - please... apk by Anonymous Coward · · Score: 0

      If if your spamminess weren't bad enough, you're a smilie-face making lol-tard too.

      How low can you go?

      cat /etc/hosts
      127.0.0.1 apk

    5. Re:Trolls, lmao - please... apk by Anonymous Coward · · Score: 0

      No. You projected you wish you were him troll.

    6. Re:Trolls, lmao - please... apk by Anonymous Coward · · Score: 0

      You're an off topic troll and you project you wish you were apk.

    7. Re:Trolls, lmao - please... apk by Anonymous Coward · · Score: 0

      You refer to yourself in the third person because nobody else will support you.

  15. Re: Expect the Republicans to... by Anonymous Coward · · Score: 0

    > WA...had USAA, and thirty months later

    File the law suit! If you're even a day late, this state will not not make them pay a penny. I got screwed when one of their drivers turned left in front of me. He admitted to being at fault and was given a ticket at the scene. USAA paid nothing on my claim. My uninsured motorist coverage paid nothing since he was insured. I would have been much better off if he had not had insurance versus USAA which refused to pay the for the damage and hospital bill. The insurance adjuster for USAA was Eric Lassiter. His boss, Kathy Smith, was even more vile. James Hensley(x40724) finally offered me ten cents on the dollar for my claim. I should have taken that.

  16. Re: Expect the Republicans to... by Anonymous Coward · · Score: 0

    I hope the USAA employees die of stomach cancer. I hear that is painful. One of their customers ran a red light and hit me. He got a ticket, but USAA still wouldn't pay the claim. I ended up having to declare bankruptcy and ruined my credit. Johnathon Barnes was the adjustor, and he is simply heartless.

  17. Brave New World by Anonymous Coward · · Score: 0

    How long until your viral load gets turned into yet another biometric for the FBI to stash away in their NGI database?

  18. Re:Expect the Republicans to... by Nutria · · Score: 1

    Exactly. OP is confusing money grubbing tools with the scientifically illiterate.

    --
    "I don't know, therefore Aliens" Wafflebox1
  19. Re: Expect the Republicans to... by Anonymous Coward · · Score: 1

    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.

  20. Re: Expect the Republicans to... by Anonymous Coward · · Score: 0

    He couldn't have been worse than Tom Johnston at x40141. He threatened to sue me for trying to collect on a claim.

  21. Re: Expect the Republicans to... by Anonymous Coward · · Score: 0

    Thank you Google alerts for letting me know another web page mentioned that jerk.

    He refused to pay a claim after one of their members was drunk and hit my trunk that was parked in my driveway. I ended up getting screwed in the claim but I made Eric's life hell for the three years I called him nearly daily until the statute of limitations ran out and I could no longer collect.

  22. Re: Expect the Republicans to... by Anonymous Coward · · Score: 0

    He screwed my family over after a USAA member who was drunk rear ended my wife. They even hired a private investigator to talk to our neighbors that inferred to them that my wife had done something wrong. She was stopped at a stop sign when the USAA member rear ended her.

  23. Re: Expect the Republicans to... by Anonymous Coward · · Score: 0

    Fuck USAA.

  24. Re: Expect the Republicans to... by Anonymous Coward · · Score: 0

    To bring that back to the GP's topic, USAA is a very Republican organization. They hire a lot of veterans and market to veterans so they're typically untouchable in court even when they refuse to pay claims that they obviously owe.

  25. It's actually good news by waynemcdougall · · Score: 1

    It makes you indestrucible

    https://vimeo.com/96581518

    --
    Recycle PCs and build a wireless community network www.hillsborough.org.nz
  26. Re: Expect the Republicans to... by Anonymous Coward · · Score: 0

    Bunch of crooks is right. When my neighbor's car rolled downhill into my house, they refused to pay a penny. My neighbor had to pay out of his own pocket for the damage.

  27. Re: Expect the Republicans to... by Anonymous Coward · · Score: 0

    This!

  28. Re: Expect the Republicans to... by Anonymous Coward · · Score: 0

    Not just very Republican, but extremely Republican. Premiums are only a small profit, but refusing to pay a valid claim is all profit.

  29. Re: Expect the Republicans to... by Anonymous Coward · · Score: 0

    Agreed. They destroyed my family by refusing to pay for my daughter's hospital bills.

  30. Re: Expect the Republicans to... by Anonymous Coward · · Score: 0

    > They could have saved over $30k

    You're attacking the wrong problem. USAA shouldn't have to pay for someone's medical bills. The US should have a single payer healthcare system.

  31. Re: Expect the Republicans to... by Anonymous Coward · · Score: 0

    I know I'm late to the party, but screw USAA. They wouldn't pay my hospital bill after their driver was drunk and hit me.

  32. Incredible. by badpool · · Score: 1

    One step closer to a medical tricorder that tells you exactly what's wrong with your patient. Amazing.

  33. Yep by Anonymous Coward · · Score: 0

    Checked the paper. I'm sure people who know how to analyze data in a way that detects a previously unknown virus would use excel to make their plots. Moreso that they display their results using an x axis of equally spaced 10,30,100,300,1000,5000 (fig 4). Good luck all, slashdot has added more crap for me to allow before posting so this is the last one.

  34. Now also add more data. by Z00L00K · · Score: 1

    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.
    1. Re:Now also add more data. by Anonymous Coward · · Score: 0

      How else would they get to Madagascar before they close the ports?

  35. Thanks by Anonymous Coward · · Score: 0

    Thanks (Score:?)
    by Anonymous Coward on Thursday September 24, 2015 @02:11AM
    he New Technique That Finds All Known Human Viruses In Your Blood is nice topics. thanks

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  36. In MY blood? by wonkey_monkey · · Score: 1

    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.
  37. Re:application of "whole proteome tiling microarra by gringer · · Score: 2

    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
  38. All Known Viruses? by Cro+Magnon · · Score: 1

    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.
  39. I don't spam... apk by Anonymous Coward · · Score: 0

    I post where inferior browser addons (ghostery/adblock/ublock/privacybadger) are noted. I show others how hosts are better.

    You haven't ever prove my points validly technically wrong either.

    * You've nothing valid to stand on in your accusation - not a thing & you know it, troll...

    APK

    P.S.=> Face facts: You ac trolls started this here, as you do all your other juvenile games directed my way - doesn't mean much other than you're showing others I've gotten the best of you SO many times, you're reduced to the games of a little schoolgirl, nothing more - & you certainly haven't produced a better more useful program than I have... lol, FACT!

    ... apk

    1. Re:I don't spam... apk by Anonymous Coward · · Score: 0

      Yes you do spam, you're posting mass unsolicited advertisements. Before you counter saying that your software is free so it can't be spam, that's complete bullshit. Lots of things are free like LinkedIn, Facebook, etc. but if they spew out unsolicited advertising it's still spam. You don't see the authors of MalwareBytes making dozens of shady advertising comments on Slashdot every day do you? Reputable software and reputable developers don't do that shit. Hell the other day you were in a MAC OSX discussion making post after post pimping your Windows software. So not only do you spam, you're not even good at it!

  40. Why do your offtopic trolling post then? by Anonymous Coward · · Score: 0

    Take a read of truth you can't handle -> http://science.slashdot.org/co...

    APK

    P.S.=> By the way - grow up! apk

  41. Even if the hardware becomes cheap... by omnichad · · Score: 1

    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.

  42. one = 65536 by Bruce+Perens · · Score: 1

    const int one = 65536;

    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.
    1. Re:one = 65536 by AmiMoJo · · Score: 1

      Sure, that's exactly what it is. I can't remember why it was needed as the .NET stuff it exists in handles floats just fine, and performance wouldn't be an issue... Anyway, I just thought it was indicative of the general quality of the code. Slightly nonsensical, but you can see what they were trying to do and of course they picked a really terrible variable name.

      I wasted many hours of my life fixing bugs in that thing, including a tricky memory leak. I remind myself of it to make sure I'm never tempted to just crap out some terrible code to get the job done, because technical debt and all that.

      --
      const int one = 65536; (Silvermoon, Texture.cs)
      SJW, n: "Someone I don't like, and by the way I'm a fuckwit" - AC
  43. Re:application of "whole proteome tiling microarra by Rutulian · · Score: 1

    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.