Machine Learning Used to Create an HIV Vaccine

hiv-vaccine-microspheres

When we think of machine learning it’s usually in the context of robotics—giving an algorithm a large set of input data in order to train it for a certain task like navigation or understanding your handwriting. But it turns out you can also train a nasty virus to go to sleep and never wake up again. That’s exactly what the Immunity Project has been doing. They believe that they have a viable HIV vaccine and are trying to raise about $25 million to begin human testing.

The vaccine hacks the Human Immunodeficiency Virus itself, forcing it to mutate into a dormant form that will not attack its human carrier. It sounds so simple, but a lot of existing knowledge and procedures, as well as new technology, went into getting this far. Last week we spoke with [Reid Rubsamen, M.D.] about the process, which began by collecting blood samples from a wide range of “Controllers“. Controllers are people who carry HIV but manage to suppress the virus’s progression to AIDS. How do you find these people? That’s another story which Scientific American covered (PDF); the short answer is that thanks to the work of [Bruce D. Walker, M.D.] there was already a database of Controllers available.

The information accumulated by [Walker] then underwent a data crunching exercise. The data set was so enormous that a novel approach was adopted. For the laymen this is described as a spam filter: using computers to look at large sets of email to develop a complex process for sifting real messages out of the noise. The task at hand is to look at the genotype of a Controller and compare it with the epitope— a short chain of proteins—in the virus they carry. The power of machine learning managed to whittle down all the data to a list of the  first six epitopes that have the desired dormant-mutation property. The vaccine consists of a cocktail of these epitopes. It does, however, require some clever delivery tactics to reach the parts of the world where it’s most needed. The vaccine must not require refrigeration nor any special skills to administer.

The vaccine’s production uses existing methods to synthesize the amino acid peptides, which are the epitopes themselves. The packaging, however, is a new concept. [Dr. Rubsamen's] company, Flow Parma, Inc., is using microspheres to encapsulate the vaccine, which render it shelf-stable and allow it to be administered through a nasal spray. Learn more about the technology behind the production of microspheres from this white paper (PDF).

If the vaccine (which will be produced without profit) passes clinical trials, it could see mass distribution as early as 2017.

The $25M we mentioned earlier is a tall hill to climb, but think of the reward if the vaccine is successful. You can donate directly to help reach this goal. If you’re planning on giving gift cards this year, you can purchase them for many different retailers through Gyft, who is donating 100% of December proceeds to the project.

Comments

  1. Augur says:

    This is I think the coolest thing I’ve seen about the HIV/AIDS research in a long time.

    • gabriel says:

      what’s cool? if i understood that… they would dump large quantities of the dormant type? and then what? you will have both HIVs in your body…

      • Elias says:

        Vaccine does not help if you already have the virus…

      • Luke says:

        That’s not how it works. The vaccine has no actual HIV virions. That being said, it’s really not clear how it works. Something to do with surface proteins, but it has nothing to do with antigens or antibodies, and they don’t elaborate on what it actually does apart from claiming it produces robust cell-mediated immune responses.

        Apparently machine learning was used to compare people with natural HIV immunity to those who developed AIDS, and discover what factors allow controllers to avoid developing AIDS for extended periods of time.

        There’s jargon associated with this project that doesn’t appear anywhere else, their animal studies haven’t been published in a scientific journal (nor are they available for the public to read), and the literature on their site is incredibly dumbed down. The scientists look legitimate and respected, but the same could be said for many quacks throughout history. Calling their vaccine “[sic] a completely, novel, disruptive, avant garde, off the beaten path approach” doesn’t engender confidence.

        Color me extremely skeptical, not just of this vaccine, but also of this organization. Let’s give them the benefit of the doubt and say it does indeed work as they claim, that it really is a revolutionary approach to treating viral diseases and will eradicate everything from ebola to hep C to influenza to the common cold. Even if that is the case (and I’m not convinced), you can bet they’re going to patent the shit out of this, viciously attack and potential competitors in court, and charge top dollar for this, squeezing every last penny they can out of it, minus a handful of PR-boosting charity cases in Africa.

        This is only going to be a non-profit effort until there’s a profit to be made.

  2. Duncan Gunn says:

    Sounds very interesting. I happen to be very wary of the many snake oil pushers out there so hope this isn’t one of them. As an unfortunate of said virus I will be studying this closely. Please be a success!

  3. truthspew says:

    I do hope they get the funding they seek. Because a nasal spray that effectively renders one of the biggest plagues of a century would be stopped in it’s tracks.

  4. kommune78 says:

    So why exactly doesn’t a big pharma player like Novartis or any Government give the $25M ? It’s peanuts anyway for them. The situation now would be private people funding this, and a big pharma player marketing it afterwards. Or does anyone exspect a small startup to bottle up a vaccine and hand it out to billions of people?

    • Mike Szczys says:

      When speaking with Dr. Rubsamen it sounded like there are plenty of sources for funding when it comes to manufacturing and distributing a proven vaccine. But the the money for taking this to clinical trials first is not as easy to come by.

  5. Concerned says:

    I hope it works. So that they will stop prescribing Reverse Transcriptase Inhibitors which not only block HIV from replicating but also the patients cells. Taking regular doses will kill the patient even if the HIV does not.

    • Dr. Z says:

      I’m sorry my friend, but you’re somewhat mis-informed. Although it is true that RTI’s inhibit replicating cells in general, the have a much much higher affinity for Reverse Transcriptase (which is an HIV protein) than for human DNA polymerase. Thus, very few cells are affected in comparison to the effect on HIV replication. The end result is that regular doses of RTI, although in some cases might make the patient feel worse for wear, *do not* kill the patient.

      -Dr. Z. , M.D.

      • Concerned says:

        The toxicity of azidothymidine (AZT) in the treatment of patients with AIDS and AIDS-related complex. A double-blind, placebo-controlled trial.

        http://www.ncbi.nlm.nih.gov/pubmed/3299090

        “Twenty-one percent of AZT recipients and 4 percent of placebo recipients required multiple red-cell transfusions”

        AIDSinfo Drug Database
        Zidovudine Other Names: azidothymidine, AZT, ZDV

        http://aidsinfo.nih.gov/drugs/4/zidovudine/0/patient

        “Zidovudine can cause serious, life-threatening side effects. These include lactic acidosis (buildup of acid in the blood), liver problems, and blood disorders, including severe anemia. Use of zidovudine for a long time can cause muscle weakness (myopathy).”

        Sounds like AZT a Reverse Transcriptase Inhibitor, A drug that causes anemia so severe the patient needs multiple transfusions to live, has the potential to kill a patient.

        • Greenaum says:

          Well, yeah, but so does getting AIDS. As long as the cure’s not as bad as the disease, it’s a net gain. Much cancer treatment is based on the same principle.

        • James says:

          Eating too many carrots also has the potential to kill a patient. Dosage and frequency matter a lot. The purpose of a lot of trials and studies is to study the current state of the art and develop the knowledge further, optimise dosages etc.

  6. N5DUX says:

    A friend of mine is featured in this post by Harvard for his research in similar research:

    http://www.seas.harvard.edu/news/2013/12/programming-smart-molecules

  7. Jan Molemans says:

    This looks like a scam, if you visit the site looking for the results they ve had until now, you just get a brief timeline. If they have had any results, they don’t make them public (other than “trials were succesfull”), which is weird because they re a non profit organisation, and they could use the help of others. flashy site, no content.

  8. Mark says:

    Someone forward this article to the Gates Foundation.

  9. Daniel says:

    Very interesting. I tried to contribute them but the form on the rally.org/immunityproject keeps responding: “Sorry, your transaction could not be processed at this time. Please try again later.”. Does anybody know if this is a temporary problem or an error?

  10. matt says:

    So over population is a problem in many areas and is only getting worse, their solution? Save the people who cant make responsible decisions.

    • gabriel says:

      lol. i can’t argue you do have a point. but there are also the rare cases of blood transfusion, doctors and accidents, childs…

    • Dr. Z says:

      More like: “Prevent people from getting sick and having to stop working. Thus improving (food and overall economic) productivity”

    • AKA the A says:

      Overpopulation? Where? Even in India one can’t speak of overpopulation, only bad decisions in planning…

    • Greenaum says:

      Hm, thing about AIDS as a control for overpopulation, is the massive amount of death it causes to living people. People just don’t *like* that, for some illogical reason.

      In the meantime you carry on feeling nice and safe, while irresponsible people have sex with each other. Death’s the least they deserve, really.

  11. Nitpicker Smartyass says:

    Sorry, I don’t buy this. Neither the site looks in ANY way scientificly (does this word exist yet?) serious enough nor the actual information given here in the article or via the videos I could watch.
    To me it looks like a scam to make money by playing around with biochemical equipment.

    I really wish it was true, but it takes a LOT more to make me believe into a vaccine that tells SPECIFIC cells to go asleep and is variable and flexible enough to do this with ALL versions of HIV that are already present (taking the high mutation rate that bummer can come up with into consideration).

  12. OmegaManM4 says:

    Perhaps this is the beginning of the extinction of mankind.

    Ever see the Will Smith movie, “I Am Legend” ? A “cure” for
    cancer turned out to be the instrument of destruction (and
    that movie was just a remake of the classic sci-fi movie with
    the late Charlton Heston, “The Omega Man”).

  13. zuul says:

    hmm they first start off that they want to make people like “controllers”
    then what they do is just described as making a vaccine in a similar way that you’d make other vaccines

    sounds more like they wanted to do gene therapy but instead worked on a vaccine

    i think it won’t work on some people because of the mutation rate of HIV

  14. Greenaum says:

    Everyone get ready to short-sell those shares in Durex. Yay!

  15. fm` says:

    So this dormant form mutation process is irreversible? Is the dormant form still transferable/contagious?

    This work sound more like a cure than a vaccine. It treats symptoms, but doesn’t prevent infection or transmission.

  16. KillerBug says:

    If it actually does that, just think of what could come of it. Much of what we are comes from viruses and bacteria that no longer attack us but still live in us. If HIV is a deadly enemy it might eventually make an excellent friend. Just imagine if it were mutated to destroy cancer cells instead of white blood cells…just an example of course.

  17. Luke says:

    If anyone’s curious, there’s an FAQ page. For some strange reason, it’s not linked on their main page. You’ll find it at, obviously enough: http://www.immunityproject.org/faq

  18. Jonathan Wilson says:

    No way will big pharma allow a “cure” for HIV (i.e. take this one easy course of drugs then its gone for good) when the current treatments (that you need to keep taking and taking and taking) are so profitable.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

Follow

Get every new post delivered to your Inbox.

Join 93,871 other followers