Coronavirus

New CRISPR Coronavirus Test Could Be a Pandemic 'Game-Changer'

Cheap accurate testing would enable the safe reopening of the U.S. economy.

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The safe reopening of the U.S. economy depends on establishing a robust system of testing, tracing, and self-isolation to quickly contain new outbreaks. Yesterday, researchers at the McGovern Institute for Brain Research at MIT, the Broad Institute of MIT and Harvard, the Ragon Institute, and the Howard Hughes Medical Institute announced what promises to be a big step toward deploying millions of accurate, rapid, and cheap coronavirus tests using CRISPR technology.

The researchers have created molecular tags that latch onto sections of viral genes and emit a signal when their presence is detected. The new STOPCovid test enables the detection of as few as 100 copies of the coronavirus in a sample. "As a result, the STOPCovid test allows for rapid, accurate, and highly sensitive detection of Covid-19 that can be conducted outside clinical laboratory settings," note the researchers. The test initially used standard nasal swab samples, but preliminary data suggest that it will work using much more easily collected saliva samples.

The research team is talking with manufacturers to further simplify and produce the test. The New York Times reports that they estimate that the materials for one test would cost about six dollars now and would fall even further when mass-produced. "The ability to test for Covid-19 at home, or even in pharmacies or places of employment, could be a game-changer for getting people safely back to work and into their communities," said team member Feng Zhang in the press release.

President Trump and his circle of close aides are protected from COVID-19 infection by a moat of rapid coronavirus testing through their access to the Abbott ID NOW COVID-19 assay that can report results in as little as five minutes. The Abbott test is an automated real-time polymerase chain reaction (PCR) technology that detects the presence of specific nucleic aides that make up the virus' genome. Currently, samples must be collected and processed by trained health care workers. The company has already shipped 1.4 million tests and is ramping production to 2 million tests per month by June. The wide-scale deployment of much more easily administered  STOPCovid tests would provide moats of protection for the rest of us.

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  1. Wonder if the CDC or FDA will claim credit.

    1. Remember when you told everyone that you want to eat your own shit?

  2. The safe reopening of the U.S. economy depends on establishing a robust system of testing, tracing, and self-isolation to quickly contain new outbreaks.

    Why is this more true for coronavirus than for any other disease that kills tens of thousand of Americans every year? It’s very difficult to implement your own side’s agenda when you’re simply assuming the validity of the other side’s underlying assumptions.

  3. The death rate is .1% it’s already safe.

  4. The New York Times reports

    So, an anonymous source? Have Facebook, Twitter, Google and President Xi given permission for this “news” to be published or are you risking getting the social media ban hammer for spreading disinformation? I’d be careful if I were you, thinking you can just go around repeating stuff you’ve read or heard without checking first to see if these people are on the approved list of experts you’re allowed to listen to or talk about. I know you’re already on thin ice with these folks for being a climate denier because you’ve expressed some skepticism about the exact size and scope and timing of the looming incendiary apocalypse, I’d hate to see you Yezhov’ed right off the intertubes.

    1. You’re calling Bailey a climate apocalypse denier?

      LOL

      1. I caught what Jesse meant, but that is an awfully funny interpretation of Bailey. Though maybe he has an idea why CO2 levels are up this year vs last, despite nobody driving, and fossil fuel demand down so much that delivery contracts went negative for the first time ever?

        Irony indeed, if CRISPR ends up being used to help mitigate the effects of something that may very well have been created using that method.

        1. “Irony indeed, if CRISPR ends up being used to help mitigate the effects of something that may very well have been created using that method.”

          Yea, that sounds fun…

          And Bailey’s climate apocalypse “denial” consists of wholly embracing the bad science and pushing the narrative, but allowing that it would be better if “private” corporations, rather than governments, were in charge of artificially lowering the earth’s average temperature.

          1. Jezzus in a handbucket, you sure don’t do gray, do you? Bailey does not embrace the whole climate alarmist crap. I think he’s wrong, but not as wrong as the alarmists, and not as wrong as your judgment of his opinion. There are gradations.

            1. Point to me where he disagrees with the climate apocalypse cult in theory

            2. He’s as wrong as wrong can be when it came to the creation of carbon markets. Which I remember him being very much in favor of.

  5. Fuck you Bailey, you shit your pants over a cold and now you’ll spend the rest of your days trying to justify your irrational hysteria.

    Fuck you and your testing and contact tracing before you stop violating people’s rights you sad bitch prog.

    1. Talk about T value! You GOT some PROBLEMS!

      1. Rememeber when you told us you eat your own shit?

        But I’m glad pointing that out again this morning got your panties all bunched up.

      2. Talk about T value!

        Ya he was talking about Ron Bailey. And you too apparently, judging by how upset it made you.

        1. He’s upset that I point out he’s a sockpuppet and that he told us he eats his own shit. It’s why he takes soy-powered potshots at me every time I remind people.

      3. And those are?

        Bailey has shit on treatments because (Trump thought they sounded promising) a really shitty “study” got the predictably negative results they were looking for, and threw in the sparky “no, hydrochloroquine isn’t a magic bullet” line to mislead readers about others’ positions on it.
        Bailey has said that testing is the only solution to Covid19 (anybody got a magic bullet to spare?) and called for widespread testing to be mandated prior to (unconstitutional) restrictions on businesses and individuals be lifted.
        Bailey’s “conservative” (that means: low portion of predicted range) estimate was that 70% (230 million) of the US population would be infected and 300,000+ would die in the first wave.

        So what exactly are the problems with the comment you objected to?

        1. *snarky, not sparky

        2. “So what exactly are the problems with the comment you objected to”

          That it’s me and that I’ve repeatedly and continuously made him look extremely stupid.

          I.e. he’s lashing out like a little bitch

      4. He’s got problems because he doesn’t buy the slaver’s argument that we need all that unnecessary garbage to exercise our rights?

        Fuck off slaver.

      5. It’s fascinating how I’m such a threat that it takes half a dozen of you dogpiling the insults to entertain yourselves. You guys are wondrous.

        1. You’re not a threat.

        2. Thats an odd and unresponsive take

        3. Cry more slaver!

  6. Code Review of Ferguson’s Model
    https://lockdownsceptics.org/code-review-of-fergusons-model/
    The code. It isn’t the code Ferguson ran to produce his famous Report 9. What’s been released on GitHub is a heavily modified derivative of it, after having been upgraded for over a month by a team from Microsoft and others. This codebase for instance is split into multiple files for legibility and written in C++, whereas the original program was “a single 15,000 line file that had been worked on for a decade” (this is considered extremely poor practice). A request for the original code has been made 8 days ago but ignored, it will probably take some kind of legal compulsion to make them release it. Clearly Imperial are too embarrassed by the state of it to ever release it of their own free will, which is unacceptable given it was paid for by the taxpayer and belongs to them.

    I’ll illustrate with a few bugs. In issue 116 a UK “red team” at Edinburgh University reports that they tried to use a mode that stores data tables in a more efficient format for faster loading, and discovered to their surprise that the resulting predictions varied by around 80,000 deaths after 80 days:

    That mode doesn’t change anything about the world being simulated so this was obviously a bug.

    The Imperial team’s response is that it doesn’t matter: that they are “aware of some small non-determinisms” but “this has historically been considered acceptable because of the general stochastic nature of the model“. Note the phrasing here – Imperial know their code has such bugs but act as if it’s some inherent randomness of the universe, rather than a result of amateur coding. Apparently in epidemiology a difference of 80,000 deaths is “a small non-determinism”.

    Imperial advised Edinburgh that the problem goes away if you run in single threaded mode like they do, which means they suggest to use only a single CPU core rather than the many cores any video game would successfully use. For a simulation of a country using only a single CPU core is obviously a dire problem – that’s as far from supercomputing as you can get. Nonetheless that’s how Imperial use the code: they know it breaks when they try to run it faster. It’s clear from reading the code that in 2014 Imperial tried to make the code use multiple CPUs to speed it up but never made it work reliably. This sort of programming is known to be difficult and usually requires senior, experienced engineers to get good results. Results that randomly change from run to run is a common consequence of thread safety bugs or more colloquially, Heisenbugs.

    But Edinburgh come back and report that even in single threaded mode they still see the problem, so Imperial’s understanding of the issue is wrong. Finally Imperial admit there’s a bug by referencing a code change they’ve made that fixes it. The explanation given is “It looks like historically the second pair of seeds had been used at this point, to make the runs identical regardless of how the network was made, but that this had been changed when seed-resetting was implemented“. In other words in the process of changing the model they made it non-replicable and never noticed.

    Why didn’t they notice? Because their code is so deeply riddled with similar bugs and they struggled so much to fix them, that they got into the habit of simply averaging the results of multiple runs to cover it up … and eventually this behaviour became normalised within the team.

    1. Too bad this guy is not in Italy, they would have put him on trial for this.

    2. “the original program was “a single 15,000 line file that had been worked on for a decade” (this is considered extremely poor practice).”

      Jesus that’s the sort of shit you expect on a “I need this impossible thing done next week” so you just kinda flail through it without planning organization, and no concerns for the future.

      Not something you’ve been working on for a decade, with no immediate need date.

      1. My fav part is the fact we can’t see the original code, because we are all too stupid to judge the work of a “credentialed expert”. Peer review now means lack of accountability, not accountability. A small community of peers are accountable to each other and the rest of us can go fuck ourselves.

        The expert is to be submitted to, obeyed, and kept safe. We can all lose our jobs, but the expert (unless he becomes embarrassing for reasons other than being an idiot) never will.

    3. What. The. Fuck. That is worse than I could gave ever guessed. I would be in jail for fraud if my customers recieved that as their end product. I could never tell them any predictions with those problems. The fact they dismiss errors as fixing itself through averaging multiple runs is mind boggling. How do they do even simple sensitivity analysis?

      1. The credentialed expert is human. The rest of are just inputs to a mathematical model. If that model needs adjusting when the experts see the impact of their decisions, then they will adjust it based on what happens to us lab rats.

        We will suffer, they will get a better model with which to control us later.

  7. “The safe reopening of the U.S. economy depends on establishing a robust system of testing, tracing, and self-isolation to quickly contain new outbreaks.”

    Uh, no.
    The opening of the US economy depends on the government getting out of the way and allowing individuals to act as free citizens.

  8. Did ronnie ever put an update or correction on his last article about the 200k dying?

    1. Ahahahahahahahahaaj

      1. It gets worse and worse for ronnie on that story too.

        https://www.washingtonexaminer.com/news/author-of-report-predicting-3-000-daily-coronavirus-deaths-says-it-wasnt-intended-to-be-a-forecast

        This is why failed science majors shouldnt be science journalists.

        1. Bailey is a philosophy and “economics” major.

          How the fuck this clown ever got a job writing about science is beyond my understanding.

          1. Ouch. No wonder.

            Even a competent person with a science or engineering background smelled the bullshit from that projection at the outset.

  9. We are already open for business, or getting there at least. Didn’t need all that testing, didn’t need apps that track us, didn’t really have the full hospitals predicted, didn’t really have that many deaths. People just went about their daily business and life went on as normal.

    The only reason we’re not at full capacity is our state government, but there are plenty of ways around them.

  10. Sounds like Elizabeth Holmes at Theranos put this test together .

  11. Who the hell knows how contagious this is or how many get it without symptoms and can pass it on? In my county, 1,600 have tested positive and, so far, 9.3% of them with it have died. Maybe those deaths extrapolate to .1% or 2% or 5% of the population that will eventually get it but who knows?
    Do we need to test 330 million people, with those not having it tested every subsequent day until a 100% effective vaccine is discovered?
    Maybe those scared and/or with serious underlying conditions can quarantine themselves without taking away the liberties of those who will never catch it or don’t mind taking their chances,

  12. This is great news IMHO. To protect the workers at a business, I don’t see anything better than quick and cheap tests to identify infectious people, isolate them until well, and trace their contacts. Kudos to Bailey for reporting it first that I’ve seen.

  13. Meanwhile More Covid-19 related deaths.
    https://www.zerohedge.com/geopolitical/nearly-15-million-more-tuberculosis-deaths-expected-due-coronavirus-lockdowns

    Up to 6.3 million more people are predicted to develop TB between now and 2025 and 1.4 million more people are expected to die as cases go undiagnosed and untreated during lockdown. This will set back global efforts to end TB by five to eight years.

    “The fact that we’ve rolled back to 2013 figures and we have so many people dying, this for me is sickening,” said Lucica Ditiu, executive director of the Stop TB Partnership. “I am outraged that just by not being able to control what we do…and forgetting about programmes that exist we lose so much, starting with the loss of the lives of people.”
    “I have to say we look from the TB community in a sort of puzzled way because TB has been around for thousands of years,” Ditiu said. “For 100 years we have had a vaccine and we have two or three potential vaccines in the pipeline. We need around half a billion [people] to get the vaccine by 2027 and we look in amazement on a disease that … is 120 days old and it has 100 vaccine candidates in the pipeline. So I think this world, sorry for my French, is really fucked up,” she said.

    “The fear we have in the community is that researchers are heading towards just developing a vaccine for Covid. That’s on the agenda of everyone now and very few remain focused on the others [diseases]. We don’t have a vaccine for TB, we don’t have a vaccine for HIV, we don’t have a vaccine for malaria and out of all this, TB is the oldest. So why this reaction? I think because we are a world of idiots. What can I say?”

  14. And in West Odessa TX a SWAT team protects the community from dangerous scofflaws.
    https://www.zerohedge.com/political/texas-bar-owner-quarantine-protesters-arrested-after-swat-team-swoops

    1. Leading to an outpouring of support for these heroes.
      https://www.zerohedge.com/s3/files/inline-images/ector%20sheriffs%20treadmill.jpg?itok=ZmBgpZcm

      “We gotta get these boys in shape.”

  15. Trump will never allow this test to succeed.

    Why not?

    Because the inventor, Feng Zhang, works at the Broad Institute, and his boss, the Director of the institute, is Eric Lander, who was co-chair of the President’s Council of Advisors on Science and Technology, when the President was… [drum roll, please],,, OBAMA. Trump’s people will tell him this, and he will think of the CRISPR test as “the Obama Test” and shoot it down no matter how good it turns out to be.

    That’s why not.

    1. Sad to see that TDS is still rampant in the Reason comments section. Please self-isolate.

  16. Mr. Bailey….Thanks for bringing this out = new CRISPR test.

    To me, the development of this test represents what is best about America. A group of American scientists saw a problem, and worked to address it. It is an amazing feat of ingenuity.

  17. Are there enough CRISPR machines to do the needed testing, though?

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