14 ms·

We’re Testing the Wrong People

137 points by elorant 7y ago

vikramkr 7y ago
The article mentioned using bar-coding to run pooled tests - that sounds really interesting. Anyone know if there's a link to a paper on that? The article doesn't link to anything on that unfortunately but that sounds really interesting. I'm trying to visualize how that works with qpcr, where the barcode is attached and where the primers bind (and presuambly after amplification you sanger them to read the barcode?).
- jamessb 7y ago
  Here's one preprint: https://docs.google.com/document/d/1kP2w_uTMSep2UxTCOnUhh1TMCjWvHEY0sUUpkJHPYV4/edit https://docs.google.com/document/d/1kP2w_uTMSep2UxTCOnUhh1TM... ("A Massively Parallel COVID-19 Diagnostic Assay for Simultaneous Testing of 19200 Patient Samples") I think Figure 1b is the diagram you want.
  - vikramkr 7y ago
    Awesome! Thanks for finding that. So they do give up the extra specificity from the reverse primer by having it be a constant region in the barcode, I guess having a sanger step makes up for that a bit though since you can read what it ligated to past the barcode and see if it's a SARS-COV-2 fragment, but that does slow down getting the results. Like a truck of hard drives barreling down a street versus sending data over fiber. Get a lot of reads in giant batches or get less reads but with less latency.
- ziga 7y ago
  Here’s a paper from the Broad Institute: https://www.biorxiv.org/content/10.1101/2020.04.06.025635v1 https://www.biorxiv.org/content/10.1101/2020.04.06.025635v1
alex_young 7y ago
The only data that is somewhat reliable in this pandemic is COVID deaths. Testing the population that is very sick / dying is crucial to understanding the baseline for the worst part of the problem. Once you have that under control, and we are not nearly there yet, you have to get every first responder tested regularly so you can prevent them from spreading the disease and give them some assurance that coming to work isn’t a death sentence. Next we have to focus on getting a baseline of the population regularly tested to estimate the spread of the disease. This should be randomized and geographically distributed so we can start to obtain reliable data about the spread of the disease and deploy resources proactively.
- rantwasp 7y ago
  it sounds like you’re advocating for the use of logic. with the current administration this is a strong no-go.
- Trasmatta 7y ago
  I would say the number of hospitalizations is reliable as well. Those are the only two numbers I've really been paying attention to, because the number of total cases is really just a factor of testing, and doesn't yet give us an accurate picture of the situation.
  - explorigin 7y ago
    I disagree. In order for a hospitalization to count, they have to have a positive test. First, we have to factor in test inaccuracy and then the fact that doctors are still triaging tests even if a patient has symptoms. These numbers can't be considered accurate until we have enough tests to test everyone in the waiting room indiscriminately.
    - Retric 7y ago
      We have enough tests to cover people who are candidates for ventilators or have similarly severe symptoms. That’s still a lagging indicator, but not nearly as delayed as deaths.
lokar 7y ago
This seems to ignore the importance of testing symptomatic people to rule out COVID (the most common outcome) so care givers can stop wasting PPE (which is is short supply).
- raldi 7y ago
  Non-covid diseases still require the use of PPE. Also, PPE is much easier to produce than tests.
  - dragonwriter 7y ago
    > Non-covid diseases still require the use of PPE. The PPE required for some COVID-19 symptoms in the absence of clear indication of a droplet/airborne transmissible condition are different than for COVID-19. You don't usually use droplet, much less airborne, protections for every patient presenting with a fever, or GI symptoms, or several of the other ways COVID-19 can present, but you must with the prevalence of COVID-19 until you can rule it out. And it's even more critical to identify COVID-19 or it's absence in sick patients when part of your containment strategy involves segregating ftreatment facilities (part of the capacity surge has been in establishing either new COVID-19 specific facilities or new facilities to handle non-COVID-19 cases while existing capacity is dedicated to COVID-19.)
- greendave 7y ago
  That works up to a point, but test accuracy makes it risky to be too definitive in interpreting the results. For example the Abbott test appears to have a 15% false negative rate[1]. That's potentially a lot of infectious people who would incorrectly be ruled out. [1] https://www.npr.org/sections/health-shots/2020/04/21/838794281/study-raises-questions-about-false-negatives-from-quick-covid-19-test https://www.npr.org/sections/health-shots/2020/04/21/8387942...
- empath75 7y ago
  During a pandemic, it's more likely than not that any negative test on a symptomatic person is false. It's also quite likely that a positive test on an asymptomatic person is also false -- depending on how prevalent it is in the general population.
PeterStuer 7y ago
"This type of voluntary contact tracing is labor-intensive and requires some training, but it does not require highly specialized skills. Technology can speed it up without risking a permanent erosion of privacy or the further intrusion of for-profit firms into our personal lives." This requires a huge leap of faith, which frankly, under surveillance capitalism you would be a fool to accept at face value. Austria developed such an app, but only 3% of people could be convinced to install it which makes it completely useless even if it would have worked (which I believe it would not for technical reasons).
ryanobjc 7y ago
Since many states cannot deficit spend, the strategy of 'leaving it to the states' is a deliberate strategy of abdicating responsibility at the federal executive level. With a federal unitary executive disinterested in expanding testing, and no other backstop, we are left without a country-wide strategy. I'm thinking that we won't get out from under this shroud until we get a new president.
- votepaunchy 7y ago
  The only thing stopping states from deficit spending (selling bonds to pay for general obligations) are the states’ own rules. As we have seen, constitutional requirements are not an impediment in a pandemic.
  - SlowRobotAhead 7y ago
    > As we have seen, constitutional requirements are not an impediment in a pandemic Agreed. It’ll be interesting to see the 1A cases that come out of this though. There is only so much tolerance to freedom of religion, right to peaceful assembly, and right to petition the government that people will accept. Of course, if there was even a single issue with freedom of press there would be nonstop coverage from the very same. I’m pro-self-quarantine but I can recognize the issue with ticketing people who went to a drive in church service, or walking alone, or playing outside with their kids. I haven’t see “THE” case that could go to Supreme Court, but I wonder if it’s out there.
    - chasd00 7y ago
      i'm both impressed and worried over the level of compliance from the American people. It's good that everyone is working together to "flatten the curve" however it's also worrisome how willing citizens are to do throw their rights out the window. I'm sure many politicians are rubbing their chins right now wondering if the rights of the people even matter anymore.
      - edmundsauto 7y ago
bo1024 7y ago
But the tests aren't perfect, so how to get actionable data from them isn't clear. We saw this with the flawed west coast studies. If a test has false positive or false negative rates even as high as 1%, and we run hundreds of thousands to millions of tests per day...that's thousands or tens of thousands wrongly quarantined for 14 days, and the same number who are contagious but told it's okay to go out.
- sesuximo 7y ago
  Isn't that better than quarantining everyone?
- munificent 7y ago
  We are currently quarantining about 300 million here in the US, so tens of thousands would be a massive improvement. The way to think about this is: who do we need to test so we can start un-quarantining people. The goal is not to find out who has it because right now, we are essentially behaving as if the entire US population is infected. The goal is to efficiently determine who is very unlikely to have it so that those people can start incrementally returning to normal life. It's not worth testing symptomatic people: they've already "failed" one test in that we at least know they have symptoms. Simply continue to treat them as infected.
  - beamatronic 7y ago
    It's all about putting people into risk categories. Then each group's members can act in the optimal way for their group. Then retest/rebalance periodically.
  - kd0amg 7y ago
    I'm pretty sure GP means actual quarantine. We are not quarantining hundreds of millions. We are advising hundreds of millions to practice social distancing.
    - Marsymars 7y ago
      Depends on the circumstances. I live alone and work from home, so there's very little difference for me between the current situation and an indefinite quarantine.
RandallBrown 7y ago
I've been saying this since the beginning of this whole thing. I don't understand why we haven't focused all of our testing on people that aren't sick so we can catch the asymptomatic cases that are out in the world spreading it to everyone.
- exhilaration 7y ago
  Because we don't have enough tests. We could reopen the country if we could test enough people, but we're stuck. Even in New York and New Jersey, tests are still limited to symptomatic people because there isn't enough testing capacity.
  - blueplanet200 7y ago
    It's a problem of limited resource allocation. The _point_ is that we have limited tests, so given limited supply why are we wasting the tests on those we think are sick. The limited supply could still be directed towards asymptomatic carriers. Wouldn't be testing everyone we want, but it's still more valuable than the allocation of tests right now.
    - scott00 7y ago
      It's far too widespread right now to successfully control via contact tracing and isolation, even if we had infinite testing capacity. The optimal use of testing right now is whatever produces the largest number of positive results, so that large case counts stay in the headlines, helping to ensure political support for stay at home orders. And that's more or less how the tests are being allocated.
  - RandallBrown 7y ago
    But what's the point of testing people that are already sick? We don't treat Covid patients any differently than any other patients that develop pneumonia
    - uxp100 7y ago
munificent 7y ago
> Another promising pathway is to pool many tests and run them together. If a pooled sample tests negative, everyone in the pool is negative. If it is positive, the members of the pool can be tested individually. Well, it took a global pandemic, but we finally found a use for bloom filters!
- joshuamorton 7y ago
  This is not a new thing in medical testing. They do it for donated blood already.
- LolWolf 7y ago
  This idea is called group testing [0] and has been used by the army for quite a while. It is also a well-studied problem in information theory as a (useful) basic model and we know optimal solutions to it. What is surprising is that group testing tells us that we can actually do better: the specific construction you pinpoint the people who come up positive, without needing to have a test for each person [1] and this result is optimal in the expected number of tests. I'm surprised that most labs haven't already been doing this (but I would suspect some have). Wootters has wonderful notes on the mathematical background for this—I really recommend them. [2] ----- [0] https://en.wikipedia.org/wiki/Group_testing https://en.wikipedia.org/wiki/Group_testing [1] Of course, we require an upper bound on the total prevalence, but even a weak upper bound yields fairly good savings in testing. [2] Page 3 on of http://web.stanford.edu/~marykw/classes/CS250_W18/lectureNotes/Lecture8-compressed.pdf http://web.stanford.edu/~marykw/classes/CS250_W18/lectureNot...
  - yshvrdhn 7y ago
    germany has been doing this for a while now
  - enchiridion 7y ago
    So you might together the samples before testing?
  - LolWolf 7y ago
    Gah, I've passed the editing window. If it's confusing to read, it is supposed to say: > the specific construction lets you pinpoint the people who come up positive
awinter-py 7y ago
sampling bias debate reminds me of this stats legend from ww2: the USAF wanted to armor planes where the bullet holes were. statistician abe wald recommended armoring where the bullet holes weren't on the theory that those were the non-survivable hits can't interpret a statistic until you think about what's excluded from the sample
- jldugger 7y ago
  We don't really know that 'the USAF' wanted anything; that bit has the 'citation needed' flag set in wikipedia. The paper itself makes no comment on the presumed answer to the question, focusing mostly on mathematical models. It certainly makes for a good drama though.
- pirocks 7y ago
  When I first heard this story it was the RAF not the USAF. I somewhat doubt how true it was.
  - awinter-py 7y ago
    yup, 'stats legend', not history there's an american math society article about this -- it evaluates the fun version of the story in the context of wald's actual paper and a journal entry by another scientist named wallis
- opo 7y ago
  >sampling bias debate reminds me of this stats legend from ww2: the USAF wanted to armor planes where the bullet holes were. statistician abe wald recommended armoring where the bullet holes weren't on the theory that those were the non-survivable hits It wasn't quite that simple, but the story has a gem of truth. As this article quotes Stephen Stigler (son of George Stigler who worked with Abraham Wald): >..."The military was inclined to provide protection for those parts that on returning planes showed the most hits. Wald assumed, on good evidence, that hits in combat were uniformly distributed over the planes. It follows that hits on the more vulnerable parts were less likely to be found on returning planes than hits on the less vulnerable parts, since planes receiving hits on the more vulnerable parts were less likely to return to provide data. From these premises, he devised methods for estimating vulnerability of various parts." http://www.ams.org/publicoutreach/feature-column/fc-2016-06 http://www.ams.org/publicoutreach/feature-column/fc-2016-06 This paper goes into detail for those interested in statistics: https://people.ucsc.edu/~msmangel/Wald.pdf https://people.ucsc.edu/~msmangel/Wald.pdf
pmoriarty 7y ago
This was covered about a month ago in episode 595 of This Week in Virology[1], in answer to a listener question: Rich Condit: Garrett writes: The CDC guidelines are to test hospitalized patients and symptomatic health care workers first, and the symptomatic general public last. This seems backwards to me. Alan Dove: Yeah. I just had this conversation with my wife after she had some, I mentioned this before, she had some coughing and shortness of breath, got immediately sent to the ER in the hospital where she works, and they did a chest x-ray, it was clear, and they said, "Ok, you don't meet criteria for testing. Go back to work." And she's been fine since then, and she, we were talking about it and she said, "Well, isn't that exactly who they should test, because then I could go and infect patients?" and I said, "Well, if they had enough tests, yes. But if you expand the testing to the people who are less sick, you don't have enough tests. Whereas if you restrict the testing to the people who are sickest, you do have enough tests." So it's a.. it's not the right way to do it, but it's the way that you actually can do it. Vincent Racaniello: Yeah, we're in this position because we don't have enough tests. We didn't ramp up... Dove: Because we don't have enough tests. We didn't prepare fast enough. Racaniello: If we had, we could test a lot of people and get an idea of how many actual infections there were, which would be very useful. But... we can't. So we're stuck with this current policy. [1]- http://www.microbe.tv/twiv/twiv-595/ http://www.microbe.tv/twiv/twiv-595/ about 1 hour and 19 minutes in to the program
- jeremyjh 7y ago
  We will never have enough testing capacity if this is not the policy objective. Right now no government leadership is working towards a goal of millions of tests per day. That is what this article is trying to change.
- RandallBrown 7y ago
  But why test the people with the worst symptoms? People with bad symptoms aren't the one's going out into the world spreading the virus and the difference in treatment between a Covid and non-Covid patient (from what I've heard) is minimal.
  - rovolo 7y ago
ctoth 7y ago
Maybe someone here can explain to me how this is supposed to work. Let's assume we have enough tests in the US to test every single person in the country every 3 days, and are contact tracing everyone with a smartphone, and providing smartphones to everyone without. Now, with all this in place, isn't the best we can do to alert people after they have already been exposed to the virus? It feels a bit like the safe sex crusaders switching to say everybody can have unprotected sex now, we'll let you know if you catch something, hopefully before you infect your next partner. Which I suppose is more reasonable for the group, but ... as the individual who is expected to actually go out in the world to consume or whatever, this doesn't feel like a viable solution. What am I missing?
- dragonwriter 7y ago
  > Now, with all this in place, isn't the best we can do to alert people after they have already been exposed to the virus? No, the best we can do in that case is treat COVID-19 like a dangerous communicable disease that isn't too widespread for surveillance and do specific quarantines of the infected and exposed, which then vastly limits the possibility that anyone else gets exposed, while not requiring shelter-in-place restrictions for those not already infected/exposed. That's the whole point of disease surveillance with widespread testing and extensive contact tracing, and why it is key for a general reopening of the economy in the absence of an effective cure/vaccine.
  - toasterlovin 7y ago
    You and I are often in disagreement on here, but not on this!
- heraclius 7y ago
  The target is to ensure that each case infects no more than one additional person (‘R<1’). Each infected person will come into contact with some other people. Testing allows three things— - first, we can tell this person to stay at home and so stop them from infecting more people; - second, we can tell the people they have seen to stay at home with good contact-tracing, so that even if they get it they don’t spread it further; and - third, with enough tests and contact tracing, those who were exposed but not infected don’t have to stay at home. We are winning so long as R<1, even if there is some chance the infection spreads; we do not need R=0. The other way of reducing R requiring much less testing and contact tracing is a lockdown. This has obvious downsides. The point of a programme of testing and conyact tracing is that we can turn the cost of avoiding disaster from a lockdown to sticking some things up people’s noses. edit: typo in first para
dragonwriter 7y ago
No, we need to test everybody, so we can't be testing the wrong people (the reason we need to test sick people is different than the reasons we need to test other people, but they all need tested.) But we don't have nearly enough testing capacity (either tests or the organized infrastructure to administer them, though both problems are being worked on) to meaningfully test the general population, whether or not we focussed our entire effort on the most important subset for reopening, so it would be extraordinarily stupidly premature to shift our current testing priority in that direction. This also means that general reopening is, a fortiori, extraordinarily stupidly premature.
- jeremyjh 7y ago
  The article explained its reasoning. Maybe you could explain yours. Specifically what is the value of testing very sick people when it cannot affect the treatment plan ?
losvedir 7y ago
I appreciate the HN title ("We're Testing the Wrong People") in contrast to the article title ("Without More Tests, America Can't Reopen"), even though it's usually against policy to have them be different. But the HN title is actionable: if we can change our testing policy and deploy our tests more usefully, that's great to know and eminently achievable. But "not testing enough" isn't really actionable. There's a shortage of tests because there's a shortage of the raw materials that goes into making the tests. The U.S. already has tested far and away more people than anyone else, and is second only behind Italy in tests per capita, and has a "positive test to test" rate roughly in line with (as low of a rate as) any other country's rate. See [0] and related charts. "Just test more" isn't really useful at this point. [0] https://ourworldindata.org/grapher/full-list-total-tests-for-covid-19 https://ourworldindata.org/grapher/full-list-total-tests-for...
- theaeolist 7y ago
  In tests/capita US is 42nd. https://www.worldometers.info/coronavirus/#countries https://www.worldometers.info/coronavirus/#countries
  - adventured 7y ago
    > In tests/capita US is 42nd That requires that you compare the US to Iceland, Faeroe Islands, Falkland Islands, UAE, Malta, Gibraltar, Luxembourg, Bahrain, Estonia, San Marino, Cyprus, Isle of Man, Lithuania, Brunei, Qatar, Liechtenstein, Ireland, Latvia, Andorra, Channel Islands, Bermuda, Aruba. Nice try. Back on planet earth, here's the list of actual sane comparables that are in front of the US, in order: Italy, Germany, Spain, Australia, Russia, Canada And Russia is fake. They haven't tested much at all. The US has tested at a higher rate than South Korea (which is behind all of those tiny nations also). The US testing rate is just behind Belgium, a nation 1/29th the size of the US. And it's not very far behind Singapore at this point, either.
    - lostapathy 7y ago
      This shouldn't be getting downvoted. Many of the countries testing "more per capita" have a lower population than cities that many here on hacker news wouldn't even consider "real cities". Scaling testing in the Isle of Man above the US only takes a total of 1100 tests. Of course they are testing more per-capita than we are.
polygotdomain 7y ago
I think this article is getting things out of order. The question right now shouldn't be who to test, but rather how do we increase the volume of testing. The article states that we should be running 500k tests a day, as if we're not simply because we choose not too. Right now we don't have the capacity and so we can't scale up at all. Why don't we have the capacity? Well the complete lack of coordination and leadership at the federal level means that each individual entity, whether it be state level government or a private entity, is having to do everything from scratch. That means developing SOPs, procuring supplies, and validating both the processes and reagents. This is being done on emergency orders as well, so some of the standards are relaxed to quickly get things up and running. There's also a shortage of reagents and kits because we didn't have or need this testing just a few months ago. There's also international competition for these resources, and because the US has decided it doesn't want to actually work with or coordinate with other countries, it's a free for all. Because everyone's frantically working on the same thing, but looking out for themselves it also means that true high throughput solutions are slow to develop as well. I could go on and on, but it's a clusterfuck and no one at the federal level either A) seems to care or B) thinks that it's their responsibility. Source: wife is currently in charge of starting up Covid testing
- mjul 7y ago
  The Danish Serum Institute published an alternative workflow for testing without using the scarce reagent. Instead, they use an old method of heating the samples like boiling an egg. See Fomsgaard and Rosenstierne’s preprint on medrxiv here: https://www.medrxiv.org/content/10.1101/2020.03.27.20044495v1 https://www.medrxiv.org/content/10.1101/2020.03.27.20044495v...
- makomk 7y ago
  There's, frankly, probably not enough reagents and consumables on the planet for the US to achieve 500k tests a day. As far as I know no country anywhere has managed this level of testing. Germany - who've been doing the best at testing lately - have been stuck at about 50,000 tests a day for a few weeks now, maybe even decreasing slightly. If you take into account the difference in population, that's only the equivalent of the US doing 200,000 tests a day - and of course scaling up to a larger population is harder. That doesn't stop the American press making it sound like not achieving those 500,000 tests a day is the result of some uniquely American political failing though.
corny 7y ago
Everyone has an opinion. The only opinions I am taking seriously right now are from professional epidemiologists - not doctors, nurses, oncologists, bioethicists, or economists. This article is just noise to me.
rapjr9 7y ago
If the goal is to stop deaths and prevent economic damage, then what is the alternative to testing (both for antibodies and for active presence of the virus), assuming that testing everyone in the US multiple times in the near term is not possible? Without testing a lot of people will not willingly return to work, which is already hurting the economy. Without testing we don't know the new places where the virus is spreading until a week or two later, so reactionary measures like contact tracing don't work as well. Total lockdown reduces deaths, but destroys the economy and reduces the scope of life. Maybe we need to use the tools we already have, such as flu surveillance and data from hospitals, to detect excess non-flu infections. We seem to be able to do flu tests, are they more scalable so that at least flu can be ruled out in many cases? If widespread testing can not happen because we can't build factories to make reagents/swabs/tubes/PCR array machines/etc. fast enough, we need to start thinking of alternatives. We don't actually seem to understand yet how the virus spreads, too many clinicians trained in handling infectious disease are getting sick despite PPE. If the new small antibody test results are right, then the virus is spreading much faster than can be accounted for via droplet spread as the main mechanism; we may have to consider birds, mosquitoes, surfaces, skin touching, and other methods as possible common spreading mechanisms. If we understood transmission better then it might be possible to tell people how to truly protect themselves, and then they could go back to work. So understanding transmission better is something that could be used in addition to whatever testing is available in order to prevent deaths and economic damage. But people may not follow the new rules based on that understanding, so get the social scientists involved to get the message across. Get OSHA involved to set best practices for workplaces. It seems like there is probably a lot that can be done, even without testing, and at present we may have to assume testing will not be sufficient in the near term (3-6 months). But someone has to start thinking about these things and doing them, and I'm not seeing any evidence of this in the news. Given that contact tracing is not already ramping up (I've seen only Massachusetts as having a plan to scale it up but I tend to only see East Coast news) I have to wonder if anyone is even thinking about alternatives to testing if testing at scale is not possible.

137 points by elorant 7y ago

The article mentioned using bar-coding to run pooled tests - that sounds really interesting. Anyone know if there's a link to a paper on that? The article doesn't link to anything on that unfortunately but that sounds really interesting. I'm trying to visualize how that works with qpcr, where the barcode is attached and where the primers bind (and presuambly after amplification you sanger them to read the barcode?).

jamessb 7y ago
Here's one preprint: https://docs.google.com/document/d/1kP2w_uTMSep2UxTCOnUhh1TMCjWvHEY0sUUpkJHPYV4/edit https://docs.google.com/document/d/1kP2w_uTMSep2UxTCOnUhh1TM... ("A Massively Parallel COVID-19 Diagnostic Assay for Simultaneous Testing of 19200 Patient Samples") I think Figure 1b is the diagram you want.
- vikramkr 7y ago
  Awesome! Thanks for finding that. So they do give up the extra specificity from the reverse primer by having it be a constant region in the barcode, I guess having a sanger step makes up for that a bit though since you can read what it ligated to past the barcode and see if it's a SARS-COV-2 fragment, but that does slow down getting the results. Like a truck of hard drives barreling down a street versus sending data over fiber. Get a lot of reads in giant batches or get less reads but with less latency.
ziga 7y ago
Here’s a paper from the Broad Institute: https://www.biorxiv.org/content/10.1101/2020.04.06.025635v1 https://www.biorxiv.org/content/10.1101/2020.04.06.025635v1

alex_young 7y ago

The only data that is somewhat reliable in this pandemic is COVID deaths. Testing the population that is very sick / dying is crucial to understanding the baseline for the worst part of the problem. Once you have that under control, and we are not nearly there yet, you have to get every first responder tested regularly so you can prevent them from spreading the disease and give them some assurance that coming to work isn’t a death sentence. Next we have to focus on getting a baseline of the population regularly tested to estimate the spread of the disease. This should be randomized and geographically distributed so we can start to obtain reliable data about the spread of the disease and deploy resources proactively.

rantwasp 7y ago
it sounds like you’re advocating for the use of logic. with the current administration this is a strong no-go.
Trasmatta 7y ago
I would say the number of hospitalizations is reliable as well. Those are the only two numbers I've really been paying attention to, because the number of total cases is really just a factor of testing, and doesn't yet give us an accurate picture of the situation.
- explorigin 7y ago
  I disagree. In order for a hospitalization to count, they have to have a positive test. First, we have to factor in test inaccuracy and then the fact that doctors are still triaging tests even if a patient has symptoms. These numbers can't be considered accurate until we have enough tests to test everyone in the waiting room indiscriminately.
  - Retric 7y ago
    We have enough tests to cover people who are candidates for ventilators or have similarly severe symptoms. That’s still a lagging indicator, but not nearly as delayed as deaths.

lokar 7y ago

This seems to ignore the importance of testing symptomatic people to rule out COVID (the most common outcome) so care givers can stop wasting PPE (which is is short supply).

raldi 7y ago
Non-covid diseases still require the use of PPE. Also, PPE is much easier to produce than tests.
- dragonwriter 7y ago
  > Non-covid diseases still require the use of PPE. The PPE required for some COVID-19 symptoms in the absence of clear indication of a droplet/airborne transmissible condition are different than for COVID-19. You don't usually use droplet, much less airborne, protections for every patient presenting with a fever, or GI symptoms, or several of the other ways COVID-19 can present, but you must with the prevalence of COVID-19 until you can rule it out. And it's even more critical to identify COVID-19 or it's absence in sick patients when part of your containment strategy involves segregating ftreatment facilities (part of the capacity surge has been in establishing either new COVID-19 specific facilities or new facilities to handle non-COVID-19 cases while existing capacity is dedicated to COVID-19.)
greendave 7y ago
That works up to a point, but test accuracy makes it risky to be too definitive in interpreting the results. For example the Abbott test appears to have a 15% false negative rate[1]. That's potentially a lot of infectious people who would incorrectly be ruled out. [1] https://www.npr.org/sections/health-shots/2020/04/21/838794281/study-raises-questions-about-false-negatives-from-quick-covid-19-test https://www.npr.org/sections/health-shots/2020/04/21/8387942...
empath75 7y ago
During a pandemic, it's more likely than not that any negative test on a symptomatic person is false. It's also quite likely that a positive test on an asymptomatic person is also false -- depending on how prevalent it is in the general population.

PeterStuer 7y ago

"This type of voluntary contact tracing is labor-intensive and requires some training, but it does not require highly specialized skills. Technology can speed it up without risking a permanent erosion of privacy or the further intrusion of for-profit firms into our personal lives." This requires a huge leap of faith, which frankly, under surveillance capitalism you would be a fool to accept at face value. Austria developed such an app, but only 3% of people could be convinced to install it which makes it completely useless even if it would have worked (which I believe it would not for technical reasons).

ryanobjc 7y ago

Since many states cannot deficit spend, the strategy of 'leaving it to the states' is a deliberate strategy of abdicating responsibility at the federal executive level. With a federal unitary executive disinterested in expanding testing, and no other backstop, we are left without a country-wide strategy. I'm thinking that we won't get out from under this shroud until we get a new president.

votepaunchy 7y ago
The only thing stopping states from deficit spending (selling bonds to pay for general obligations) are the states’ own rules. As we have seen, constitutional requirements are not an impediment in a pandemic.
- SlowRobotAhead 7y ago
  > As we have seen, constitutional requirements are not an impediment in a pandemic Agreed. It’ll be interesting to see the 1A cases that come out of this though. There is only so much tolerance to freedom of religion, right to peaceful assembly, and right to petition the government that people will accept. Of course, if there was even a single issue with freedom of press there would be nonstop coverage from the very same. I’m pro-self-quarantine but I can recognize the issue with ticketing people who went to a drive in church service, or walking alone, or playing outside with their kids. I haven’t see “THE” case that could go to Supreme Court, but I wonder if it’s out there.
  - chasd00 7y ago
    i'm both impressed and worried over the level of compliance from the American people. It's good that everyone is working together to "flatten the curve" however it's also worrisome how willing citizens are to do throw their rights out the window. I'm sure many politicians are rubbing their chins right now wondering if the rights of the people even matter anymore.
    - edmundsauto 7y ago

bo1024 7y ago

But the tests aren't perfect, so how to get actionable data from them isn't clear. We saw this with the flawed west coast studies. If a test has false positive or false negative rates even as high as 1%, and we run hundreds of thousands to millions of tests per day...that's thousands or tens of thousands wrongly quarantined for 14 days, and the same number who are contagious but told it's okay to go out.

sesuximo 7y ago
Isn't that better than quarantining everyone?
munificent 7y ago
We are currently quarantining about 300 million here in the US, so tens of thousands would be a massive improvement. The way to think about this is: who do we need to test so we can start un-quarantining people. The goal is not to find out who has it because right now, we are essentially behaving as if the entire US population is infected. The goal is to efficiently determine who is very unlikely to have it so that those people can start incrementally returning to normal life. It's not worth testing symptomatic people: they've already "failed" one test in that we at least know they have symptoms. Simply continue to treat them as infected.
- beamatronic 7y ago
  It's all about putting people into risk categories. Then each group's members can act in the optimal way for their group. Then retest/rebalance periodically.
- kd0amg 7y ago
  I'm pretty sure GP means actual quarantine. We are not quarantining hundreds of millions. We are advising hundreds of millions to practice social distancing.
  - Marsymars 7y ago
    Depends on the circumstances. I live alone and work from home, so there's very little difference for me between the current situation and an indefinite quarantine.

RandallBrown 7y ago

I've been saying this since the beginning of this whole thing. I don't understand why we haven't focused all of our testing on people that aren't sick so we can catch the asymptomatic cases that are out in the world spreading it to everyone.

exhilaration 7y ago
Because we don't have enough tests. We could reopen the country if we could test enough people, but we're stuck. Even in New York and New Jersey, tests are still limited to symptomatic people because there isn't enough testing capacity.
- blueplanet200 7y ago
  It's a problem of limited resource allocation. The _point_ is that we have limited tests, so given limited supply why are we wasting the tests on those we think are sick. The limited supply could still be directed towards asymptomatic carriers. Wouldn't be testing everyone we want, but it's still more valuable than the allocation of tests right now.
  - scott00 7y ago
    It's far too widespread right now to successfully control via contact tracing and isolation, even if we had infinite testing capacity. The optimal use of testing right now is whatever produces the largest number of positive results, so that large case counts stay in the headlines, helping to ensure political support for stay at home orders. And that's more or less how the tests are being allocated.
- RandallBrown 7y ago
  But what's the point of testing people that are already sick? We don't treat Covid patients any differently than any other patients that develop pneumonia
  - uxp100 7y ago

munificent 7y ago

> Another promising pathway is to pool many tests and run them together. If a pooled sample tests negative, everyone in the pool is negative. If it is positive, the members of the pool can be tested individually. Well, it took a global pandemic, but we finally found a use for bloom filters!

joshuamorton 7y ago
This is not a new thing in medical testing. They do it for donated blood already.
LolWolf 7y ago
This idea is called group testing [0] and has been used by the army for quite a while. It is also a well-studied problem in information theory as a (useful) basic model and we know optimal solutions to it. What is surprising is that group testing tells us that we can actually do better: the specific construction you pinpoint the people who come up positive, without needing to have a test for each person [1] and this result is optimal in the expected number of tests. I'm surprised that most labs haven't already been doing this (but I would suspect some have). Wootters has wonderful notes on the mathematical background for this—I really recommend them. [2] ----- [0] https://en.wikipedia.org/wiki/Group_testing https://en.wikipedia.org/wiki/Group_testing [1] Of course, we require an upper bound on the total prevalence, but even a weak upper bound yields fairly good savings in testing. [2] Page 3 on of http://web.stanford.edu/~marykw/classes/CS250_W18/lectureNotes/Lecture8-compressed.pdf http://web.stanford.edu/~marykw/classes/CS250_W18/lectureNot...
- yshvrdhn 7y ago
  germany has been doing this for a while now
- enchiridion 7y ago
  So you might together the samples before testing?
- LolWolf 7y ago
  Gah, I've passed the editing window. If it's confusing to read, it is supposed to say: > the specific construction lets you pinpoint the people who come up positive

awinter-py 7y ago

sampling bias debate reminds me of this stats legend from ww2: the USAF wanted to armor planes where the bullet holes were. statistician abe wald recommended armoring where the bullet holes weren't on the theory that those were the non-survivable hits can't interpret a statistic until you think about what's excluded from the sample

jldugger 7y ago
We don't really know that 'the USAF' wanted anything; that bit has the 'citation needed' flag set in wikipedia. The paper itself makes no comment on the presumed answer to the question, focusing mostly on mathematical models. It certainly makes for a good drama though.
pirocks 7y ago
When I first heard this story it was the RAF not the USAF. I somewhat doubt how true it was.
- awinter-py 7y ago
  yup, 'stats legend', not history there's an american math society article about this -- it evaluates the fun version of the story in the context of wald's actual paper and a journal entry by another scientist named wallis
opo 7y ago
>sampling bias debate reminds me of this stats legend from ww2: the USAF wanted to armor planes where the bullet holes were. statistician abe wald recommended armoring where the bullet holes weren't on the theory that those were the non-survivable hits It wasn't quite that simple, but the story has a gem of truth. As this article quotes Stephen Stigler (son of George Stigler who worked with Abraham Wald): >..."The military was inclined to provide protection for those parts that on returning planes showed the most hits. Wald assumed, on good evidence, that hits in combat were uniformly distributed over the planes. It follows that hits on the more vulnerable parts were less likely to be found on returning planes than hits on the less vulnerable parts, since planes receiving hits on the more vulnerable parts were less likely to return to provide data. From these premises, he devised methods for estimating vulnerability of various parts." http://www.ams.org/publicoutreach/feature-column/fc-2016-06 http://www.ams.org/publicoutreach/feature-column/fc-2016-06 This paper goes into detail for those interested in statistics: https://people.ucsc.edu/~msmangel/Wald.pdf https://people.ucsc.edu/~msmangel/Wald.pdf

pmoriarty 7y ago

This was covered about a month ago in episode 595 of This Week in Virology[1], in answer to a listener question: Rich Condit: Garrett writes: The CDC guidelines are to test hospitalized patients and symptomatic health care workers first, and the symptomatic general public last. This seems backwards to me. Alan Dove: Yeah. I just had this conversation with my wife after she had some, I mentioned this before, she had some coughing and shortness of breath, got immediately sent to the ER in the hospital where she works, and they did a chest x-ray, it was clear, and they said, "Ok, you don't meet criteria for testing. Go back to work." And she's been fine since then, and she, we were talking about it and she said, "Well, isn't that exactly who they should test, because then I could go and infect patients?" and I said, "Well, if they had enough tests, yes. But if you expand the testing to the people who are less sick, you don't have enough tests. Whereas if you restrict the testing to the people who are sickest, you do have enough tests." So it's a.. it's not the right way to do it, but it's the way that you actually can do it. Vincent Racaniello: Yeah, we're in this position because we don't have enough tests. We didn't ramp up... Dove: Because we don't have enough tests. We didn't prepare fast enough. Racaniello: If we had, we could test a lot of people and get an idea of how many actual infections there were, which would be very useful. But... we can't. So we're stuck with this current policy. [1]- http://www.microbe.tv/twiv/twiv-595/ http://www.microbe.tv/twiv/twiv-595/ about 1 hour and 19 minutes in to the program

jeremyjh 7y ago
We will never have enough testing capacity if this is not the policy objective. Right now no government leadership is working towards a goal of millions of tests per day. That is what this article is trying to change.
RandallBrown 7y ago
But why test the people with the worst symptoms? People with bad symptoms aren't the one's going out into the world spreading the virus and the difference in treatment between a Covid and non-Covid patient (from what I've heard) is minimal.
- rovolo 7y ago

ctoth 7y ago

Maybe someone here can explain to me how this is supposed to work. Let's assume we have enough tests in the US to test every single person in the country every 3 days, and are contact tracing everyone with a smartphone, and providing smartphones to everyone without. Now, with all this in place, isn't the best we can do to alert people after they have already been exposed to the virus? It feels a bit like the safe sex crusaders switching to say everybody can have unprotected sex now, we'll let you know if you catch something, hopefully before you infect your next partner. Which I suppose is more reasonable for the group, but ... as the individual who is expected to actually go out in the world to consume or whatever, this doesn't feel like a viable solution. What am I missing?

dragonwriter 7y ago
> Now, with all this in place, isn't the best we can do to alert people after they have already been exposed to the virus? No, the best we can do in that case is treat COVID-19 like a dangerous communicable disease that isn't too widespread for surveillance and do specific quarantines of the infected and exposed, which then vastly limits the possibility that anyone else gets exposed, while not requiring shelter-in-place restrictions for those not already infected/exposed. That's the whole point of disease surveillance with widespread testing and extensive contact tracing, and why it is key for a general reopening of the economy in the absence of an effective cure/vaccine.
- toasterlovin 7y ago
  You and I are often in disagreement on here, but not on this!
heraclius 7y ago
The target is to ensure that each case infects no more than one additional person (‘R<1’). Each infected person will come into contact with some other people. Testing allows three things— - first, we can tell this person to stay at home and so stop them from infecting more people; - second, we can tell the people they have seen to stay at home with good contact-tracing, so that even if they get it they don’t spread it further; and - third, with enough tests and contact tracing, those who were exposed but not infected don’t have to stay at home. We are winning so long as R<1, even if there is some chance the infection spreads; we do not need R=0. The other way of reducing R requiring much less testing and contact tracing is a lockdown. This has obvious downsides. The point of a programme of testing and conyact tracing is that we can turn the cost of avoiding disaster from a lockdown to sticking some things up people’s noses. edit: typo in first para

dragonwriter 7y ago

No, we need to test everybody, so we can't be testing the wrong people (the reason we need to test sick people is different than the reasons we need to test other people, but they all need tested.) But we don't have nearly enough testing capacity (either tests or the organized infrastructure to administer them, though both problems are being worked on) to meaningfully test the general population, whether or not we focussed our entire effort on the most important subset for reopening, so it would be extraordinarily stupidly premature to shift our current testing priority in that direction. This also means that general reopening is, a fortiori, extraordinarily stupidly premature.

jeremyjh 7y ago
The article explained its reasoning. Maybe you could explain yours. Specifically what is the value of testing very sick people when it cannot affect the treatment plan ?

losvedir 7y ago

I appreciate the HN title ("We're Testing the Wrong People") in contrast to the article title ("Without More Tests, America Can't Reopen"), even though it's usually against policy to have them be different. But the HN title is actionable: if we can change our testing policy and deploy our tests more usefully, that's great to know and eminently achievable. But "not testing enough" isn't really actionable. There's a shortage of tests because there's a shortage of the raw materials that goes into making the tests. The U.S. already has tested far and away more people than anyone else, and is second only behind Italy in tests per capita, and has a "positive test to test" rate roughly in line with (as low of a rate as) any other country's rate. See [0] and related charts. "Just test more" isn't really useful at this point. [0] https://ourworldindata.org/grapher/full-list-total-tests-for-covid-19 https://ourworldindata.org/grapher/full-list-total-tests-for...

theaeolist 7y ago
In tests/capita US is 42nd. https://www.worldometers.info/coronavirus/#countries https://www.worldometers.info/coronavirus/#countries
- adventured 7y ago
  > In tests/capita US is 42nd That requires that you compare the US to Iceland, Faeroe Islands, Falkland Islands, UAE, Malta, Gibraltar, Luxembourg, Bahrain, Estonia, San Marino, Cyprus, Isle of Man, Lithuania, Brunei, Qatar, Liechtenstein, Ireland, Latvia, Andorra, Channel Islands, Bermuda, Aruba. Nice try. Back on planet earth, here's the list of actual sane comparables that are in front of the US, in order: Italy, Germany, Spain, Australia, Russia, Canada And Russia is fake. They haven't tested much at all. The US has tested at a higher rate than South Korea (which is behind all of those tiny nations also). The US testing rate is just behind Belgium, a nation 1/29th the size of the US. And it's not very far behind Singapore at this point, either.
  - lostapathy 7y ago
    This shouldn't be getting downvoted. Many of the countries testing "more per capita" have a lower population than cities that many here on hacker news wouldn't even consider "real cities". Scaling testing in the Isle of Man above the US only takes a total of 1100 tests. Of course they are testing more per-capita than we are.

polygotdomain 7y ago

I think this article is getting things out of order. The question right now shouldn't be who to test, but rather how do we increase the volume of testing. The article states that we should be running 500k tests a day, as if we're not simply because we choose not too. Right now we don't have the capacity and so we can't scale up at all. Why don't we have the capacity? Well the complete lack of coordination and leadership at the federal level means that each individual entity, whether it be state level government or a private entity, is having to do everything from scratch. That means developing SOPs, procuring supplies, and validating both the processes and reagents. This is being done on emergency orders as well, so some of the standards are relaxed to quickly get things up and running. There's also a shortage of reagents and kits because we didn't have or need this testing just a few months ago. There's also international competition for these resources, and because the US has decided it doesn't want to actually work with or coordinate with other countries, it's a free for all. Because everyone's frantically working on the same thing, but looking out for themselves it also means that true high throughput solutions are slow to develop as well. I could go on and on, but it's a clusterfuck and no one at the federal level either A) seems to care or B) thinks that it's their responsibility. Source: wife is currently in charge of starting up Covid testing

mjul 7y ago
The Danish Serum Institute published an alternative workflow for testing without using the scarce reagent. Instead, they use an old method of heating the samples like boiling an egg. See Fomsgaard and Rosenstierne’s preprint on medrxiv here: https://www.medrxiv.org/content/10.1101/2020.03.27.20044495v1 https://www.medrxiv.org/content/10.1101/2020.03.27.20044495v...
makomk 7y ago
There's, frankly, probably not enough reagents and consumables on the planet for the US to achieve 500k tests a day. As far as I know no country anywhere has managed this level of testing. Germany - who've been doing the best at testing lately - have been stuck at about 50,000 tests a day for a few weeks now, maybe even decreasing slightly. If you take into account the difference in population, that's only the equivalent of the US doing 200,000 tests a day - and of course scaling up to a larger population is harder. That doesn't stop the American press making it sound like not achieving those 500,000 tests a day is the result of some uniquely American political failing though.

corny 7y ago

Everyone has an opinion. The only opinions I am taking seriously right now are from professional epidemiologists - not doctors, nurses, oncologists, bioethicists, or economists. This article is just noise to me.

rapjr9 7y ago

If the goal is to stop deaths and prevent economic damage, then what is the alternative to testing (both for antibodies and for active presence of the virus), assuming that testing everyone in the US multiple times in the near term is not possible? Without testing a lot of people will not willingly return to work, which is already hurting the economy. Without testing we don't know the new places where the virus is spreading until a week or two later, so reactionary measures like contact tracing don't work as well. Total lockdown reduces deaths, but destroys the economy and reduces the scope of life. Maybe we need to use the tools we already have, such as flu surveillance and data from hospitals, to detect excess non-flu infections. We seem to be able to do flu tests, are they more scalable so that at least flu can be ruled out in many cases? If widespread testing can not happen because we can't build factories to make reagents/swabs/tubes/PCR array machines/etc. fast enough, we need to start thinking of alternatives. We don't actually seem to understand yet how the virus spreads, too many clinicians trained in handling infectious disease are getting sick despite PPE. If the new small antibody test results are right, then the virus is spreading much faster than can be accounted for via droplet spread as the main mechanism; we may have to consider birds, mosquitoes, surfaces, skin touching, and other methods as possible common spreading mechanisms. If we understood transmission better then it might be possible to tell people how to truly protect themselves, and then they could go back to work. So understanding transmission better is something that could be used in addition to whatever testing is available in order to prevent deaths and economic damage. But people may not follow the new rules based on that understanding, so get the social scientists involved to get the message across. Get OSHA involved to set best practices for workplaces. It seems like there is probably a lot that can be done, even without testing, and at present we may have to assume testing will not be sufficient in the near term (3-6 months). But someone has to start thinking about these things and doing them, and I'm not seeing any evidence of this in the news. Given that contact tracing is not already ramping up (I've seen only Massachusetts as having a plan to scale it up but I tend to only see East Coast news) I have to wonder if anyone is even thinking about alternatives to testing if testing at scale is not possible.