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Oh, about that flawed FDA Covid-19 test . . . it may have been contaminated with the virus

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Here’s the report:

As the new coronavirus took root across America, the US Centers for Disease Control and Prevention sent states tainted test kits in early February that were themselves seeded with the virus, federal officials have confirmed.

The contamination made the tests uninterpretable, and—because testing is crucial for containment efforts—it lost the country invaluable time to get ahead of the advancing pandemic.

The CDC had been vague about what went wrong with the tests, initially only saying that “a problem in the manufacturing of one of the reagents” had led to the failure. Subsequent reporting suggested that the problem was with a negative control—that is, a part of the test meant to be free of any trace of the coronavirus as a critical reference for confirming that the test was working properly overall.

Now, according to investigation results reported by The New York Times, federal officials confirm that sloppy laboratory practices at two of three CDC labs involved in the tests’ creation led to contamination of the tests and their uninterpretable results.

That’s a real oopsie if so.

NYT adds:

Sloppy laboratory practices at the Centers for Disease Control and Prevention caused contamination that rendered the nation’s first coronavirus tests ineffective, federal officials confirmed on Saturday.

Two of the three C.D.C. laboratories in Atlanta that created the coronavirus test kits violated their own manufacturing standards, resulting in the agency sending tests that did not work to nearly all of the 100 state and local public health labs, according to the Food and Drug Administration.

Poor lab practices seem to be a concern surrounding this epidemic.

And, a failed test was indeed a big part of stumbling, multiplied by red tape hurdles to get other tests going. Time to connect dots. END

54 Replies to “Oh, about that flawed FDA Covid-19 test . . . it may have been contaminated with the virus

  1. 1
    kairosfocus says:

    Oh, about that flawed FDA Covid-19 test . . . it may have been contaminated with the virus

  2. 2
    daveS says:

    I hate it when that happens.

  3. 3
    kairosfocus says:

    Yup, and there is an as yet unfinished bill to pay for it. KF

  4. 4
  5. 5
    AaronS1978 says:

    KF thank you

  6. 6
    Ed George says:

    This is the danger with rushing a test, or a treatment, into broad use without following the ‘gold standard’ protocol for validation and verification.

  7. 7
    Ed George says:

    AaronS1977@4, but this is the same way that we classify flu deaths. The flu itself kills very few people. It is almost always underlying conditions that the flu makes worse that kills people. If we are going to compare COVID to the flu, we have to classify it in a similar fashion.

  8. 8
    AaronS1978 says:

    I wouldn’t say the flu kills very few people, Maybe in comparison to number of infected but it still killing people in the hundreds of thousands

    But I will say that the over classification of death in response to this disease has greatly diminished the amount of deaths caused by flu, pneumonia, and heart disease

    That’s on worldometer and the CDC
    The problem that I have with it is we are not testing those that have passed away for whether they had Covid or not. We NEED to confirm this, we can’t and should not assume

    This actually distorts the numbers and we make judgements off these distortions
    We need to be accurate right now, and not over overcompensate and knee jerk, which I feel this is.

    Overcompensating with the wrong information can be entirely ineffective and very harmful

    And with the way others have been arguing on this site about testing being inaccurate, this is something I take some issue with

  9. 9
    kairosfocus says:

    EG, testing kits were developed and were developed by a top flight agency. They also imposed reguloations that locked up alternatives, then managed to blow this deal. At minimum, a comparative test with other by then in-use tests would have showed up whether it was up to the mark, i.e. benchmarking. That actually underscores the point I have been making and highlights a second one, that over-regulation can be counter productive. As was noted as it happened, this also goes a long way to account for delays in getting testing moving in the US. KF

  10. 10
    AaronS1978 says:

    https://www.oann.com/coronavirus-outbreak-in-u-s-on-track-to-be-less-severe-than-this-years-seasonal-flu/?fbclid=IwAR0dpFbWuR5DWOoK7kChGFbKzh_3oYe9PH8pVz4ejTxBnTcwt30w8bkfi5o

    So even I am skeptical of this but one of my friends was just posting this I just wanted to get your take on this.

  11. 11
    orthomyxo says:

    The epidemic has already killed more people than a typical flu season, after the lockdowns and having only infected a few percent of the population. Deaths may well double within this peak, and could spike if the easing of suppression efforts is not carefully.

    The reported numbers are probably considerable underestimates of the true mortality. In most places, deaths in homes or nursing homes are not included. In the UK (the only country that I know produces this data quickly) there is a huge excess in mortality in recent weeks, much more than can be explained my registered covid deaths only: https://www.gov.uk/government/statistics/weekly-all-cause-mortality-surveillance-2019-to-2020

    We are now past the end of the typical northern flu season, so I think we can exclude that as a major contributor.

    Oh, very few flu deaths include a positive test for influenza virus, applying similar rules to both will still show an incredible burden for covid-19

  12. 12
    AaronS1978 says:

    @11 I actually disagree with you considerably when it comes to underestimating the mortality rate, for various reasons that I’ve already posted on before

    The rest of what you posted was kind of what I was thinking as well, which is why I questioned this report

  13. 13
    Barry Arrington says:

    The reported numbers are probably considerable underestimates of the true mortality.

    Except we know for a certain fact they are overstated as well, if the Italy’s Minister of Health, for one, is to be believed.

  14. 14
    orthomyxo says:

    The all cause mortality data makes it clear excess deaths outpace official covid deaths in the UK. No such data exists in the USA, but the prevalence of the disease is just to low for the “died with covid19″story to hold any weight.

    Just like the flu, the final estimates will come from excess mortality models, but I wouldn’t be surprised if we were only counting 2 of 3 covid19 deaths.

  15. 15
    orthomyxo says:

    I think you got that factoid wrong Barry, unless you have a link?

    Early on some advisor to the Italian government made a statement about comorbidities, but it was never linked to any actual data. The conclusion flies in the face of the actual mortality data too

  16. 16
    kairosfocus says:

    BA,

    we have proxies so far, really good numbers are going to require a lot of testing on antibodies and going back through statistical records then calibrating demographically. What we have is tracking the basic dynamics of sigmoids and related models well enough to guide decisions. We are seeing global peaking of wave 1, with China seeing minor onward waves, true Wave 2 is likely, come the next flu season.

    Damaging economic and social impacts of the lockdown are leading to early signs, pointing to a need for a managed exit from n-BAU.

    With the Raoult-Zelenko protocols allowing early targetted treatment of vulnerable groups on outpatient basis with 90 – 95% reduction in mortality relative to the n-BAU Flu with Complications & ventilators etc baseline, we have a reasonably plausible ALT1 and ALT2 to feed our scenario based planning exercise. The big weaknesses pivot on the polarisation of esp the US and its one-party media, which may cripple and delay moving to ALT-1 until a large wave of needless deaths shifts balance of power.

    The use of decision theory and sustainability thinking to counter the threat and compensate for the weakness may help shift balance of power. In particular, the gold standard fallacy must be exposed and corrected. That is, decision theory and BAU vs ALT using the n-BAU protocol as baseline shows an inductively cogent, epistemologiically relevant, ethically responsible answer to required evidence to move forward in the face of polarisation and mischaracterisation.

    Selective hyperskepticism has civilisation-level consequences and costs measured in blood and tears through pandemic and needless economic dislocation.

    We need to shift back to prudence based responsible rationality.

    KF

  17. 17
    AaronS1978 says:

    @ KF
    Exactly

  18. 18
    Barry Arrington says:

    Orthomyxo

    I think you got that factoid wrong Barry, unless you have a link?

    From a March 23 article in The Telegraph:

    According to Prof Walter Ricciardi, scientific adviser to Italy’s minister of health, the country’s mortality rate is far higher due to demographics – the nation has the second oldest population worldwide – and the manner in which hospitals record deaths. . . .
    Prof Ricciardi added that Italy’s death rate may also appear high because of how doctors record fatalities. “The way in which we code deaths in our country is very generous in the sense that all the people who die in hospitals with the coronavirus are deemed to be dying of the coronavirus.
    On re-evaluation by the National Institute of Health, only 12 per cent of death certificates have shown a direct causality from coronavirus, while 88 per cent of patients who have died have at least one pre-morbidity – many had two or three,” he says.

    That crashing sound you hear is your confirmation bias tumbling down around you. You have been caught out just making it up as you go in this instance. It colors everything you’ve said and will ever say in these pages.

  19. 19
    Barry Arrington says:

    KF

    What we have is tracking the basic dynamics of sigmoids and related models well enough to guide decisions.

    Well, we have that, and we also have the Jim Thibodeau’s and Orthomyxo’s who clinch their confirmation bias with all their might, refuse to face the obvious, and who by all appearances are content to watch the world’s economy burn to the ground. I wonder which will prevail.

  20. 20
    orthomyxo says:

    So, a month ago, not the minister but an advisor and no data just this lone statement?

    Sounds a bit like

    Early on some advisor to the Italian government made a statement about comorbidities, but it was never linked to any actual data. The conclusion flies in the face of the actual mortality data too

  21. 21
    kairosfocus says:

    BA, decision theory will prevail over the gold standard evidence threshold fallacy. We will recognise that nBAU gives a baseline comparison with Flu and its treatment so there is no need to give people facing a disease that can kill in 10 days, doing organ damage along the way, sugar pills in order to construct an artificial baseline. We will see evidence being belittled, dismissed and suppressed that points to 90 – 95% reduction in mortality among vulnerable groups for two credible ALTs. We will see that a US$20, outpatient oriented treatment can take pressure off the system, allowing better care for serious cases. We will see that this then allows responsible re-opening of community life and economic activity, leading to a surge in investor and consumer confidence. The lockstep globalist progessivist elites and their media mouthpieces and amplifiers will take a deserved, decisive blow to their credibility and dominance of opinion. As a result, civilisation-level trends are going to shift dramatically, starting with digitalisation of work and education. That’s a Kondratiev, long wave level shift. This pandemic marks a break in history. KF

  22. 22
    kairosfocus says:

    Ortho,

    “On re-evaluation by the National Institute of Health, only 12 per cent of death certificates have shown a direct causality from coronavirus, while 88 per cent of patients who have died have at least one pre-morbidity – many had two or three,”

    . . . does not constitute “no data.”

    It highlights the difference between dying from CV19 and dying with it.

    Yes, this is summary percentages issued by the technical advisor who would be behind a ministerial statement. Those percentages would not be put up by such a person without what my native land calls “backative.”

    In short, you are manifesting the gold standard fallacy.

    And besides, what was said is consistent with a given of decision theory: dirty, noisy, quick proxy data or summaries from reasonable source are enough for astute decision making when time is of the essence.

    Napoleon on the Austrians: they are always late, first with their payments and at length with their armies.

    KF

  23. 23
    orthomyxo says:

    To me that really amounts to no data: 88 premorbidity is a statistic, to assess its importance we have to know how serious those other ailments are. Hypertension and obesity are both comorbidities found in covid19 deaths, but they are also very common in the general population and many people live quite happily with them.

    So the statement alone is pretty much worthless.

    The idea that people are “dying with” covid19 is also very hard to marry with the spikes in mortality across the globe.

  24. 24
    Bob O'H says:

    Of relevance to the discussion – The Economist has data on excess mortalities across several countries. There’s a clear pattern of excess, even over deaths not attributed to covid-19.

  25. 25
    AaronS1978 says:

    https://www.weforum.org/agenda/2020/04/we-could-be-vastly-overestimating-the-death-rate-for-covid-19-heres-why/

    https://www.google.com/amp/s/www.nytimes.com/2020/04/17/us/coronavirus-death-rate.amp.html

    https://www.google.com/amp/s/www.washingtonpost.com/health/2020/04/06/americas-most-influential-coronavirus-model-just-revised-its-estimates-downward-not-every-model-agrees/%3foutputType=amp

    https://www.google.com/amp/s/www.newsweek.com/why-covid-19-death-forecasts-are-wrong-1499243%3famp=1

    All of these were in a quick Google search the same with yours bob oh

    Accompanied with bad testing, corrupted tests that were made by the cdc, And it is a fact that the populace is showing antibodies for it now, I really don’t think we can say one way or the other that something is over estimated or under estimated

    It’s hard for me to believe that it was underestimated though

    We’ve had to dial multiple models back, poor testing and lack of confirmation

    Honestly I’m not trying to be a skeptic to the disease but I think the alarmists are just as has guilty as the Hyper skeptics

    This is a personal Opinion of mine I am not a fan of economist, long story

    The one thing that I do watch constantly is worldometer and the cdc, And mostly I’ve been making my judgments off of those numbers

  26. 26
    kairosfocus says:

    Ortho, that insisted on overstatement is disappointing, as precision and accuracy are habits. Yes, we would like to see detailed data, but the summary data provided are just that, data. Given the source, it is likely details are there. KF

  27. 27
    kairosfocus says:

    BO’H: Lessee, we have a pandemic, check. Several countries are overwhelmed with Covid19 cases, check. The areas being highlighted in at least several cases come from such zoooones, e.g. Lombardy, Italy, NY City, check. Medical personnel and facilities are finite so if devoted to an overwhelming challenge they will not be available for more typical cases, check. So, it seems plausible that a good slice of excess deaths beyond normal expectations will be losses of people whose care is not up to the usual standard. Also, some may well be deaths with or accelerated by CV19, as opposed to primarily due to same. In short, we will need to sort out more detailed data to resolve various questions. There is plenty of room for what “Prof Walter Ricciardi, scientific adviser to Italy’s minister of health” said in summary of findings by presumably Italy’s “National Institute of Health” to be true. Especially if there is enough physician discretion that “The way in which we code deaths in our country is very generous in the sense that all the people who die in hospitals with the coronavirus are deemed to be dying of the coronavirus.” KF

  28. 28
    orthomyxo says:

    as I said, the summary data is worthless without detail.

    I also not the very next line in the telegraph article makes it clear that “This does not mean that Covid-19 did not contribute to a patient’s death”

    https://www.telegraph.co.uk/global-health/science-and-disease/have-many-coronavirus-patients-died-italy/

  29. 29
    kairosfocus says:

    Ortho, you are simply doubling down at this point. KF

    PS: I know, academics often want to dig into details, but this can make them dismissive of significant and crdible information relevant to the public and policy makers, where that a credible institution is source is enough. At minimum, this gives us a heads up that we are dealing with noisy proxies, not final results. Oddly, when the shoe is on the other foot, e.g. Climate debates, much the same circles are perfectly willing to give summaries and appeal to consensus.

  30. 30
    Barry Arrington says:

    Orthomyxo

    To me that really amounts to no data.

    And here we have the root cause of the problem on display. Ortho says there is no support for my statement that the Health Minister of Italy said COVID-19 deaths were overstated. I quote Prof Walter Ricciardi, scientific adviser to the minister, saying exactly that. Ortho’s response is two-fold:
    First he nit picks: He’s not the actual minister. Yeah, Ortho, you’ve got me there. He is the scientific advisor to the minister.
    Second: He does not agree with me; therefore he does not know what he is talking about when he makes statement’s about whether Italy’s mortality rate is overstated.
    Yet again, Ortho’s breathtaking arrogance asserts itself. He really is quite shameless.

  31. 31
    Barry Arrington says:

    Orthomyxo gets red in the face, stamps his feet, and petulantly insists the COVID-19 numbers are understated. There is strong evidence, however, that they are overstated. He asks for data to support that claim. I give him data. His response: “TO ME, that is not data.” Orthomyxo is so arrogant and consumed by confirmation bias, that he has arrogated unto himself the authority arbitrarily to expel from the category “data” anything that does not support his thesis.
    His antics are not unique of course. For example, many times a materialist has come into these pages and announced there is no “evidence” for the existence of God. He is then shown multiple strands of evidence for the existence of God. I can’t tell you how many times the response has been: “That is not evidence.”
    For Ortho, like the village atheist, evidence that does not persuade him is not “evidence that does not persuade me.” It is no evidence at all. It is really quite astonishing that a man who is by all appearances reasonably intelligent should have such a blinkered, almost adolescent, view of the world.

  32. 32
    daveS says:

    Does anyone else have a strange feeling of desensitization after watching these statistics for a few months? Maybe in part due to the numeral system we use.

    The “difference” between 4 and 40 is obviously quite large; the difference between 4000 and 40000 is perhaps less obvious. Keep adding zeros, and we tend to lose track of how quickly the sequence grows.

    Over 40000 Americans have died of Covid-19 in the last 3 weeks.

  33. 33
    asauber says:

    DaveS,

    “Over 40000 Americans have died of Covid-19 in the last 3 weeks.”

    Is this a scientifically rigorous figure?

    Andrew

  34. 34
    Truthfreedom says:

    @DaveS
    As if human life were objectively valuable.

  35. 35
    daveS says:

    asauber,

    I trust that it’s reasonably close to the true value.

  36. 36
    john_a_designer says:

    Have you ever noticed that the only people here who are trying to cram their beliefs down anyone else’s throat are anti-religious atheists? If I were an atheist I would leave other people alone because life from that perspective is meaningless and purposeless. What’s the purpose in convincing anyone else that it’s all pointless? Do they derive some meaning doing that? At best that is delusional; at worst it’s contemptuous and hypocritical.

    In the end all they succeed in proving is that atheistic naturalism/materialism is morally, spiritually and intellectually bankrupt.

  37. 37
    asauber says:

    DaveS,

    “I trust that it’s reasonably close to the true value.”

    You didn’t answer my question.

    So much for science.

    Andrew

  38. 38
    kairosfocus says:

    ASauber, is Statistics a science? A branch of Mathematics? A policy tool, too often poorly or even deceptively used? Or, what? KF

  39. 39
    asauber says:

    KF,

    s Statistics a science? Depends on who you ask.

    A branch of Mathematics? It incorporates math, yes.

    A policy tool, too often poorly or even deceptively used? Too Frequently.

    Or, what? Since this is open-ended I’ll use it to state that DaveS is just another troll. 🙂

    Andrew

  40. 40
    daveS says:

    I didn’t mean to disturb anyone here. I’m just asking if anyone else besides me is struggling to grasp these statistics and is feeling a bit disoriented. Another interesting point is that the number of deaths (in the US at least) is significantly lower than some predictions. Even though I expected even more deaths, I’m still shocked at what has actually happened.

  41. 41
    Truthfreedom says:

    ___
    @36 John_a_designer:

    What’s the purpose in convincing anyone else that it’s all pointless? Do they derive some meaning doing that?

    How Militant Atheists Stole Your Sense of Meaning to Enhance Theirs
    https://www.bernardokastrup.com/2016/02/atheism-historys-greatest-theft.html?m=1

  42. 42
    asauber says:

    “struggling to grasp these statistics and is feeling a bit disoriented”

    DaveS,

    I’d say you are more than a bit disoriented. 🙂

    Andrew

  43. 43
    kairosfocus says:

    DS, now you know why I love log-lin and log-log paper. OWID makes me feel like Christmas came extra early esp as I use rays to judge slopes. But then, the Bode Plot was an epiphany for me. KF

  44. 44
    daveS says:

    KF,

    Yes, I too find those other formats helpful sometimes. But it’s still a struggle for me.

  45. 45
    john_a_designer says:

    TF @ 41,

    Back in June 2018 I had this exchange with Seversky who I believe has been commenting on this site for at least 7 or 8 years. (Why? Who knows.)

    In a response to an OP entitled, “As Astrology Goes Mainstream, Will Big Science Start To Accommodate It?” I wrote @ #1:

    Atheistic naturalism/materialism provides no answers to mankind’s deepest spiritual and moral needs. It is a morally, spiritually and intellectually bankrupt world view, yet many people irrationally and absurdly cling to it. Why? They cannot give a rational explanation. They do not know but don’t even know they don’t know…

    https://uncommondescent.com/intelligent-design/as-astrology-goes-mainstream-will-big-science-start-to-accommodate-it/#comment-660948

    To which Seversky @ #2 replied, point by point:

    Me: Atheistic naturalism/materialism provides no answers to mankind’s deepest spiritual and moral needs.

    Seversky: “I agree. It can’t. But if you assume there is no God then we are forced to confront the reality that we are on our own, we are all we have so where do we go from here?”

    Me: It is a morally, spiritually and intellectually bankrupt world view, yet many people irrationally and absurdly cling to it.

    Seversky “If atheism, by definition, cannot provide moral and spiritual guidance then calling it bankrupt for not doing what it cannot do is unfair. That does not prevent us from constructing “worldviews” and moral codes that are atheist.”

    Me: Why? They cannot give a rational explanation. They do not know but don’t even know they don’t know…

    Seversky: “As I said, atheists can construct rational worldviews and moral codes. It’s just that they cannot appeal to the unquestionable authority of some deity to support them.”

    Notice, that Seversky basically concedes to each of my points.

    Of course that brings up a number of other questions like: who is obligated to follow a moral code constructed by atheists? Does it apply to just them or everyone else (society)? Do any human constructed moral codes carry any kind of real morally binding obligations?

    It’s because of irrational nonsense like this that I have said here many time before, “If I were an atheistic materialist, I would leave other people alone.” Why? Because atheistic materialism has nothing to offer as a world view.

  46. 46
    asauber says:

    “Because atheistic materialism has nothing to offer as a world view.”

    JAD,

    But they keep coming back to repeatedly, year after year, to offer the nothing they never had. 😉

    Andrew

  47. 47
    Truthfreedom says:

    ___
    John_a_designer:

    atheistic materialism has nothing to offer as a world view.

    Yes, it has. Despair and non-sense.

  48. 48
    Bob O'H says:

    ASauber, is Statistics a science? A branch of Mathematics? A policy tool, too often poorly or even deceptively used? Or, what? KF

    I feel I can speak with some authority on this matter, and say that it’s a Dark Art.

  49. 49
    asauber says:

    “I feel I can speak with some authority on this matter, and say that it’s a Dark Art.”

    Bob O’H,

    Not really. Any buffoon can do it. 🙂

    Andrew

  50. 50
    kairosfocus says:

    Asauber, doing it well is real high class voodoo. KF

  51. 51
    daveS says:

    Based on my observations, it takes considerable hardiness to succeed in statistics. There’s a reason some of us with a more delicate constitution call it “sadistics”.

  52. 52
    Seversky says:

    I’ve always thought Saruman was probably a statistician.

  53. 53
    kairosfocus says:

    Sev, you got me on that literary allusion. KF

    PS: My Dad was one of the last generation before computers. He could add three columns of digits to any length in his head and always cross checked calculators in his head. When he tried to teach me the algorithm, I boggled. But then, I was struggling to cram in stuff for O Level exams.

  54. 54
    Bob O'H says:

    Not really. Any buffoon can do it. ????

    Certainly, any fool of a Took can do it badly.

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