6 ms·

New Technique Can Efficiently Detect All Known Human Viruses in a Blood Sample

126 points by agarden 11y ago

ed 11y ago
What's preventing something like this from wide-spread use? I'm always amazed (read: disappointed) humans are still involved in so much of the diagnosis process.
- anon4 11y ago
  1. People don't trust machines 2. No software company wants to deal with the liability issues An example of a place where technology takes over a large part of the diagnostic process is prescription glasses. Even then, after measuring your absolute dioptres, a human asks you to try a few combinations to find the most comfortable variant.
  - hellofunk 11y ago
    People have plenty of trust for machines, it's all around us. Unless you refuse to use an ATM, for example, the most wide-spread robot in the world, you probably trust machines too. Or automatic transmissions or anti-lock brakes. Nearly all of us trust the emergency telephone line when we need it.
- Asbostos 11y ago
  They needed to do 17 samples at a time to be financially viable. I suspect it's even worse than that and it's just cheaper if you already know what you're looking for and do it the normal way.
  - pavel_lishin 11y ago
    > * They needed to do 17 samples at a time to be financially viable.* Is this an actual fact, or a comedic exaggeration?
    - ghshephard 11y ago
      Underestimate - from the article, "The team can also analyze many patients at once. To do that, they fuse a unique barcode sequence to the viral DNA from each individual sample, before mixing them together and running them through VirCapSeq-VERT. After the system does its thing, the team can check the barcodes to work out which sample each virus came from. “We can do up to 21 at a time, which makes it financially viable,” says Lipkin." So, this is the sort of thing that you would do in bulk with a bunch of samples, not on a retail one-at-a-time basis.
    - sehugg 11y ago
      DNA sequencing is currently done in batches, dozens of samples to a plate. It's cheaper that way.
  - tkinom 11y ago
    The DNA Sequencing related techs seem to advancing even faster than Semiconductor techs. I used to work for Applied-biosystem to work on their 2nd gen DNA sequencer ~1996. At that time, sequence the human genome cost ~$1 billion. Today it is < $1000. At that speed, in 10-20 years. They might be able to sequence all the virus in your blood and provide real time info about them with the latest Apple Watch. :-) Still have doubt? Take a look at what high school kid (lady) did to detect ebola.... http://www.techinsider.io/olivia-hallisey-won-the-google-science-fair-with-a-fast-test-for-ebola-2015-9 http://www.techinsider.io/olivia-hallisey-won-the-google-sci...
- transfire 11y ago
  Three letters: F D A.
  - smanuel 11y ago
    Well actually for 2015 FDA has approved 96% of the new drugs [1] so it's not the same old tough regulator it's been before. Or maybe it's just tough for things that work and allows things that shouldn't be allowed [2]. [1] http://www.vox.com/2015/8/20/9182663/fda-rate-drug-approvals http://www.vox.com/2015/8/20/9182663/fda-rate-drug-approvals [2] http://www.vox.com/2015/9/18/9333639/female-pink-viagra-fda-approved http://www.vox.com/2015/9/18/9333639/female-pink-viagra-fda-...
- joezydeco 11y ago
  Do you mean: "Why won't this eventually be available on a drugstore counter so I can diagnose myself?" The FDA's response for decades is this: you don't have a lab to perform a more detailed confirmation (because false positives sometimes do happen), and you have no doctor or counselor to be there with you when you get the results. I worked for a biotech firm that had an instant HIV test available a long long time ago. It was deemed too irresponsible to let people to check themselves at home because the company (and the FDA, and everyone's lawyers) were afraid of people doing rash things after a positive result. If a false-positive HIV patient killed themselves and the family sues, that would be...bad. Even today, the home-HIV test that's on the market involves you sending in the sample and then getting a phone call with the results.
  - ada1981 11y ago
    This is no longer true. When I went I get tested for HIV in SF at the free clinic, they wouldn't do it because they said I wasn't really at risk(!) despite having multiple female partners since my last test, including a Standford doctor who was in the ER all the time.. Anyway, I went to a pharmacy and paid $50 for an at home test kit that did indeed tell me yes/no in about 15 minutes. My brother has taken the same kind of test in NYC.
  - maxxxxx 11y ago
    It's ironic that people need to be protected from the shock of a diagnosis but it's OK to shock them with a six figure hospital bill...
- ada1981 11y ago
  It's a research tool now, just needs an entrepreneur to make one that can be commercialized. Certainly that is the next step..
- ChuckMcM 11y ago
  Allow me a flippant response, "nothing." Looking at some of the papers that W. Ian Lipkin has published he's been working on this for a while. So as a researcher he provides data which the FDA will use to assess accuracy and viability, meanwhile Columbia will probably lease out the patents (https://patentimages.storage.googleapis.com/pdfs/US20060003352.pdf https://patentimages.storage.googleapis.com/pdfs/US200600033...) when it issues to a diagnostics company, perhaps to Elizabeth Holmes company (http://www.wired.com/2014/02/elizabeth-holmes-theranos/ http://www.wired.com/2014/02/elizabeth-holmes-theranos/) who will then create a cost effective way to put this into drug stores everywhere, and when you're feeling bad you go in, prick your thumb, and get a text message of everything you might be sick with.
vinaybn 11y ago
Where can I get one done?
- mhb 11y ago
  "Ian Lipkin, a virus hunter from Columbia University"
bhouston 11y ago
When I visited this page Chrome on Android asked to download a new certificate. Weird.
mkj 11y ago
Might be useful for increasing the number of people eligible to donate blood.
- hanklazard 11y ago
  This also might be a problem--we may begin finding out that more people carry benign viral infections than we previously thought (ie, subclinical carriers). The more fishing expeditions that we conduct, as opposed to specific viral tests, the more questions we may have about the definition of "clean" blood.
  - Kenji 11y ago
    How is that a problem? Questions are good. Defining "clean" blood better is a good thing, preferred to plain ignorance about certain things because they look scary. I am all for more information and questions.
    - hanklazard 11y ago
      I'm definitely not recommending ignorance, generally speaking. Just pointing out that if you go looking for viral DNA in blood, you'll likely find it in a lot of samples that would otherwise be considered acceptable for transfusions. The latest techniques are finding trace viral DNA in plenty of human samples previously deemed "negative." (1) Now what do you do? Technically, you've found contamination that might or might not lead to disease. Is the blood usable or not? The point is that we know which pathogens that we need to look out for in transfused blood. Better to continue with targeted tests for the pathogens that actually cause important human disease rather than just fish for everything you can find. And don't get me wrong, this technology could be really useful for better understanding epidemiology or understanding the common viral contents of human blood--I'm excited about the possibilities. I just wouldn't use it in the context of blood banking as I don't think it adds anything helpful (unless we are faced with a novel virus in the future that is being transmitted through blood and needs to be identified). 1. http://www.researchgate.net/publication/274394532_Small_circular_single_stranded_DNA_viral_genomes_in_unexplained_cases_of_human_encephalitis_diarrhea_and_in_untreated_sewage http://www.researchgate.net/publication/274394532_Small_circ...
ph0rque 11y ago
This sounds incredible. Can a modification of this system be used for detecting all known bacteria that infect humans?
codyb 11y ago
As someone who had HPV, I'd really be interested in something like this since the current system fails me as a male and refuses to test or tell me anything about it. It'd be a positive for my partners if I could tell them that I have HPV but the current vaccine prevents the strains I have, however, at the moment, I just have no idea. In the end I think American Males should be vaccinated as well. (Well males everywhere but currently I'm American so that's where my train of thought is).
- hanklazard 11y ago
  Physician-scientist here. Current recs from the American Academy of Pediatrics is for both males and females to be immunized for HPV prior to initiation of sexual activity (1). Initially I do believe that the recommendation was only for girls but that has changed for two major reasons: increase herd immunity in the overall population and because men can also get malignancies and lesions from HPV. Of note, the vaccine does not prevent all HPV infections. The 4-valent vaccine covers the two most common cancer-causing HPV strains as well as two others that commonly cause warts. As for whether a test like this would be useful in clinical practice, it would definitely depend on the situation. HPV is extremely prevalent ... by the time a person has been sexually active for a few years, it is almost guaranteed that they carry at least one strain of HPV (there are about 40-50 strains last I checked). However, most people never have any problems related to HPV, either because their immune system effectively suppresses the virus or because they have a strain that does not cause symptoms. Is it useful for one to know that they carry a non-malignancy forming, non-lesion causing strain of HPV? Is it useful for 50% of the population to believe that they have an STI although it will likely never cause any clinical symptoms in themselves or any sexual partners? I would say probably not. Is it useful to type the HPV strains of all infected patients? Maybe. Currently it would not be useful as we do not have effective antiviral therapies for HPV. However, understanding the epidemiology more clearly could certainly help as we decide which viruses to attempt to target therapeutically in the future. I will say this: the test described in this article would generally be described as a "fishing expedition" in the lab where I did my graduate studies. These types of studies can be very useful in certain cases but I predict they may also cause a lot of confusion as we begin to find subclinical viral processes occurring in plenty of healthy people. As a society, we will have to change our perception of what it means to be "infected" with a virus and as a clinician, it may become more challenging to reassure patients that they are healthy (gut and skin microbiome data will likely create a similar predicament with regard to bacteria). In any case, I'm sorry to hear about your difficulties with HPV. I see patients dealing with it on a fairly regular basis and it can be a frustrating situation. I do hope that there are effective therapies on the horizon. 1. https://www2.aap.org/immunization/illnesses/hpv/hpv.html https://www2.aap.org/immunization/illnesses/hpv/hpv.html
tomkinstinch 11y ago
For comparison, Illumina sequencing with normal viral enrichment might use software like Kraken to perform taxonomic identification of resulting reads. Physical isolation as is described in the article[2] can be a decent way to improve SNR. 1. https://ccb.jhu.edu/software/kraken/ https://ccb.jhu.edu/software/kraken/ 2. http://mbio.asm.org/content/6/5/e01491-15 http://mbio.asm.org/content/6/5/e01491-15
deleted 11y ago
[deleted]
ck2 11y ago
and it costs $750 per scan? seriously though, $1 or $1000, is it priced for insurance or people without insurance
- thephyber 11y ago
  It's a research paper at this point. Pricing comes after FDA approval and the ability to scale. The article says it is financially viable if there are 21 patient scans done per batch. If an additional breakthrough allows more than 21 patients per batch, then end-user pricing can fall.
davidw 11y ago
It'd be cool if they could get this cheap enough to tell the difference between a cold and a bacterial sinus infection. I'm plagued by the latter, but feel guilty about taking antibiotics. It really sucks to feel like crap for 2+ weeks only to realize you could have been back on your feet in a few days by popping some pills.
- hanklazard 11y ago
  Agreed. Same with cold virus vs. atypical pneumonia. I've actually been trying to figure out how this could be done for quite a while because it could save a TON of healthcare dollars, sick days, etc.
- thephyber 11y ago
  The paper only talks about virus detection, not bacteria. It does seem to benefit from being able to tell you exactly which genome you have.
  - davidw 11y ago
    If you're sick, and it detects a lot of a cold/flu virus, presumably you could hold off on the antibiotics.
hvidgaard 11y ago
I really like this. It takes the human element of guesswork out of the equation. Need to do bloodwork? Perform this test and if anything comes back positive, do a different and more thorough confirmation test.

126 points by agarden 11y ago

ed 11y ago

What's preventing something like this from wide-spread use? I'm always amazed (read: disappointed) humans are still involved in so much of the diagnosis process.

anon4 11y ago
1. People don't trust machines 2. No software company wants to deal with the liability issues An example of a place where technology takes over a large part of the diagnostic process is prescription glasses. Even then, after measuring your absolute dioptres, a human asks you to try a few combinations to find the most comfortable variant.
- hellofunk 11y ago
  People have plenty of trust for machines, it's all around us. Unless you refuse to use an ATM, for example, the most wide-spread robot in the world, you probably trust machines too. Or automatic transmissions or anti-lock brakes. Nearly all of us trust the emergency telephone line when we need it.
Asbostos 11y ago
They needed to do 17 samples at a time to be financially viable. I suspect it's even worse than that and it's just cheaper if you already know what you're looking for and do it the normal way.
- pavel_lishin 11y ago
  > * They needed to do 17 samples at a time to be financially viable.* Is this an actual fact, or a comedic exaggeration?
  - ghshephard 11y ago
    Underestimate - from the article, "The team can also analyze many patients at once. To do that, they fuse a unique barcode sequence to the viral DNA from each individual sample, before mixing them together and running them through VirCapSeq-VERT. After the system does its thing, the team can check the barcodes to work out which sample each virus came from. “We can do up to 21 at a time, which makes it financially viable,” says Lipkin." So, this is the sort of thing that you would do in bulk with a bunch of samples, not on a retail one-at-a-time basis.
  - sehugg 11y ago
    DNA sequencing is currently done in batches, dozens of samples to a plate. It's cheaper that way.
- tkinom 11y ago
  The DNA Sequencing related techs seem to advancing even faster than Semiconductor techs. I used to work for Applied-biosystem to work on their 2nd gen DNA sequencer ~1996. At that time, sequence the human genome cost ~$1 billion. Today it is < $1000. At that speed, in 10-20 years. They might be able to sequence all the virus in your blood and provide real time info about them with the latest Apple Watch. :-) Still have doubt? Take a look at what high school kid (lady) did to detect ebola.... http://www.techinsider.io/olivia-hallisey-won-the-google-science-fair-with-a-fast-test-for-ebola-2015-9 http://www.techinsider.io/olivia-hallisey-won-the-google-sci...
transfire 11y ago
Three letters: F D A.
- smanuel 11y ago
  Well actually for 2015 FDA has approved 96% of the new drugs [1] so it's not the same old tough regulator it's been before. Or maybe it's just tough for things that work and allows things that shouldn't be allowed [2]. [1] http://www.vox.com/2015/8/20/9182663/fda-rate-drug-approvals http://www.vox.com/2015/8/20/9182663/fda-rate-drug-approvals [2] http://www.vox.com/2015/9/18/9333639/female-pink-viagra-fda-approved http://www.vox.com/2015/9/18/9333639/female-pink-viagra-fda-...
joezydeco 11y ago
Do you mean: "Why won't this eventually be available on a drugstore counter so I can diagnose myself?" The FDA's response for decades is this: you don't have a lab to perform a more detailed confirmation (because false positives sometimes do happen), and you have no doctor or counselor to be there with you when you get the results. I worked for a biotech firm that had an instant HIV test available a long long time ago. It was deemed too irresponsible to let people to check themselves at home because the company (and the FDA, and everyone's lawyers) were afraid of people doing rash things after a positive result. If a false-positive HIV patient killed themselves and the family sues, that would be...bad. Even today, the home-HIV test that's on the market involves you sending in the sample and then getting a phone call with the results.
- ada1981 11y ago
  This is no longer true. When I went I get tested for HIV in SF at the free clinic, they wouldn't do it because they said I wasn't really at risk(!) despite having multiple female partners since my last test, including a Standford doctor who was in the ER all the time.. Anyway, I went to a pharmacy and paid $50 for an at home test kit that did indeed tell me yes/no in about 15 minutes. My brother has taken the same kind of test in NYC.
- maxxxxx 11y ago
  It's ironic that people need to be protected from the shock of a diagnosis but it's OK to shock them with a six figure hospital bill...
ada1981 11y ago
It's a research tool now, just needs an entrepreneur to make one that can be commercialized. Certainly that is the next step..
ChuckMcM 11y ago
Allow me a flippant response, "nothing." Looking at some of the papers that W. Ian Lipkin has published he's been working on this for a while. So as a researcher he provides data which the FDA will use to assess accuracy and viability, meanwhile Columbia will probably lease out the patents (https://patentimages.storage.googleapis.com/pdfs/US20060003352.pdf https://patentimages.storage.googleapis.com/pdfs/US200600033...) when it issues to a diagnostics company, perhaps to Elizabeth Holmes company (http://www.wired.com/2014/02/elizabeth-holmes-theranos/ http://www.wired.com/2014/02/elizabeth-holmes-theranos/) who will then create a cost effective way to put this into drug stores everywhere, and when you're feeling bad you go in, prick your thumb, and get a text message of everything you might be sick with.

vinaybn 11y ago

Where can I get one done?

mhb 11y ago
"Ian Lipkin, a virus hunter from Columbia University"

bhouston 11y ago

When I visited this page Chrome on Android asked to download a new certificate. Weird.

mkj 11y ago

Might be useful for increasing the number of people eligible to donate blood.

hanklazard 11y ago
This also might be a problem--we may begin finding out that more people carry benign viral infections than we previously thought (ie, subclinical carriers). The more fishing expeditions that we conduct, as opposed to specific viral tests, the more questions we may have about the definition of "clean" blood.
- Kenji 11y ago
  How is that a problem? Questions are good. Defining "clean" blood better is a good thing, preferred to plain ignorance about certain things because they look scary. I am all for more information and questions.
  - hanklazard 11y ago
    I'm definitely not recommending ignorance, generally speaking. Just pointing out that if you go looking for viral DNA in blood, you'll likely find it in a lot of samples that would otherwise be considered acceptable for transfusions. The latest techniques are finding trace viral DNA in plenty of human samples previously deemed "negative." (1) Now what do you do? Technically, you've found contamination that might or might not lead to disease. Is the blood usable or not? The point is that we know which pathogens that we need to look out for in transfused blood. Better to continue with targeted tests for the pathogens that actually cause important human disease rather than just fish for everything you can find. And don't get me wrong, this technology could be really useful for better understanding epidemiology or understanding the common viral contents of human blood--I'm excited about the possibilities. I just wouldn't use it in the context of blood banking as I don't think it adds anything helpful (unless we are faced with a novel virus in the future that is being transmitted through blood and needs to be identified). 1. http://www.researchgate.net/publication/274394532_Small_circular_single_stranded_DNA_viral_genomes_in_unexplained_cases_of_human_encephalitis_diarrhea_and_in_untreated_sewage http://www.researchgate.net/publication/274394532_Small_circ...

ph0rque 11y ago

This sounds incredible. Can a modification of this system be used for detecting all known bacteria that infect humans?

codyb 11y ago

As someone who had HPV, I'd really be interested in something like this since the current system fails me as a male and refuses to test or tell me anything about it. It'd be a positive for my partners if I could tell them that I have HPV but the current vaccine prevents the strains I have, however, at the moment, I just have no idea. In the end I think American Males should be vaccinated as well. (Well males everywhere but currently I'm American so that's where my train of thought is).

hanklazard 11y ago
Physician-scientist here. Current recs from the American Academy of Pediatrics is for both males and females to be immunized for HPV prior to initiation of sexual activity (1). Initially I do believe that the recommendation was only for girls but that has changed for two major reasons: increase herd immunity in the overall population and because men can also get malignancies and lesions from HPV. Of note, the vaccine does not prevent all HPV infections. The 4-valent vaccine covers the two most common cancer-causing HPV strains as well as two others that commonly cause warts. As for whether a test like this would be useful in clinical practice, it would definitely depend on the situation. HPV is extremely prevalent ... by the time a person has been sexually active for a few years, it is almost guaranteed that they carry at least one strain of HPV (there are about 40-50 strains last I checked). However, most people never have any problems related to HPV, either because their immune system effectively suppresses the virus or because they have a strain that does not cause symptoms. Is it useful for one to know that they carry a non-malignancy forming, non-lesion causing strain of HPV? Is it useful for 50% of the population to believe that they have an STI although it will likely never cause any clinical symptoms in themselves or any sexual partners? I would say probably not. Is it useful to type the HPV strains of all infected patients? Maybe. Currently it would not be useful as we do not have effective antiviral therapies for HPV. However, understanding the epidemiology more clearly could certainly help as we decide which viruses to attempt to target therapeutically in the future. I will say this: the test described in this article would generally be described as a "fishing expedition" in the lab where I did my graduate studies. These types of studies can be very useful in certain cases but I predict they may also cause a lot of confusion as we begin to find subclinical viral processes occurring in plenty of healthy people. As a society, we will have to change our perception of what it means to be "infected" with a virus and as a clinician, it may become more challenging to reassure patients that they are healthy (gut and skin microbiome data will likely create a similar predicament with regard to bacteria). In any case, I'm sorry to hear about your difficulties with HPV. I see patients dealing with it on a fairly regular basis and it can be a frustrating situation. I do hope that there are effective therapies on the horizon. 1. https://www2.aap.org/immunization/illnesses/hpv/hpv.html https://www2.aap.org/immunization/illnesses/hpv/hpv.html

tomkinstinch 11y ago

For comparison, Illumina sequencing with normal viral enrichment might use software like Kraken to perform taxonomic identification of resulting reads. Physical isolation as is described in the article[2] can be a decent way to improve SNR. 1. https://ccb.jhu.edu/software/kraken/ https://ccb.jhu.edu/software/kraken/ 2. http://mbio.asm.org/content/6/5/e01491-15 http://mbio.asm.org/content/6/5/e01491-15

deleted 11y ago

[deleted]

ck2 11y ago

and it costs $750 per scan? seriously though, $1 or $1000, is it priced for insurance or people without insurance

thephyber 11y ago
It's a research paper at this point. Pricing comes after FDA approval and the ability to scale. The article says it is financially viable if there are 21 patient scans done per batch. If an additional breakthrough allows more than 21 patients per batch, then end-user pricing can fall.

davidw 11y ago

It'd be cool if they could get this cheap enough to tell the difference between a cold and a bacterial sinus infection. I'm plagued by the latter, but feel guilty about taking antibiotics. It really sucks to feel like crap for 2+ weeks only to realize you could have been back on your feet in a few days by popping some pills.

hanklazard 11y ago
Agreed. Same with cold virus vs. atypical pneumonia. I've actually been trying to figure out how this could be done for quite a while because it could save a TON of healthcare dollars, sick days, etc.
thephyber 11y ago
The paper only talks about virus detection, not bacteria. It does seem to benefit from being able to tell you exactly which genome you have.
- davidw 11y ago
  If you're sick, and it detects a lot of a cold/flu virus, presumably you could hold off on the antibiotics.

hvidgaard 11y ago

I really like this. It takes the human element of guesswork out of the equation. Need to do bloodwork? Perform this test and if anything comes back positive, do a different and more thorough confirmation test.