While I don't doubt the story, I would always take it with a grain of salt. I don't personally know the person they claim is running these "under the table" tests, but the tests are very simple, so it wouldn't surprise me if it was actually true. (Most first or second year biology/bioengineering students can easily run RT-PCR without an issue, especially if they already have the primers available.)
EDIT: I was just contacted by one of my friends who knows of a few students and their labs doing this. Apparently there is more than one.
- Spit in a 2 mL tube
- Purify the RNA from the saliva in that tube using qiagen's Viral RNA mini kit (https://www.qiagen.com/us/products/diagnostics-and-clinical-...)
- Get PCR primers against NCoV N by ordering IDT's CDC qPCR probe assay (https://www.idtdna.com/pages/landing/coronavirus-research-re...)
- Run one step RT-PCR using your choice of one-step reagent (CDC recommends https://www.thermofisher.com/order/catalog/product/A15300#/A...)
- Either do the reaction in a qPCR machine or run the PCR result on an agarose gel with positive control, if you see a band matching coronavirus positive control then the sample is positive, if not negative. Also helpful to have a human sample negative control to be sure as well.
There is no step here that requires critical thinking, it's just following instructions on the kits.
Also, this is not like a "bootleg" version of doing it, this is actually the official way the CDC does the test.
Edit: Please see official CDC instructions for how to run the test here: https://www.fda.gov/media/134922/download
Edit 2: In terms of test shortages, it seems to be due to shortages in RNA extraction kits and swabs, only the former of which is really necessary, since the official guidance for sample collection has switched from upper respitory swabs to collecting sputum (phlegm) from the lower respitory tract (by just spitting it out): https://www.ft.com/content/86efe246-692e-11ea-800d-da70cff6e...
Any environmental contamination will show up as a positive, particularly using the non-quantatative end-point method mentioned above. There's simple controls for that, but still....
Honestly we'd be better off having a widely available test that gives 50% false positives. Worst case, a bunch of people quarantine unnecessarily, but we at least catch all the infected. The alternative is what we have now: widespread community transmission with no end in sight.
Having more false positives than true positives only works if the people taking the test either don't understand statistics or don't know the test accuracy. I for one would probably ignore a positive result if I thought my chances of true positive were 0.001 and my chances of a false positive were 0.5.
How about we try this: when reporting "facts", how about we try noting that there is uncertainty involved? I know the average Joe and Jane public aren't intellectuals, and it is often how stupid people can be, but on the other hand I think it is also fair to say that we underestimate people.
I think we should at least consider trying this (noting uncertainty in reporting) - it's times like this where we need more ideas and more thinking, not less.
So, We lie to people and tell em they are infected. And then we are angry that FOX or the governor of WV are going to expose our scam?
What did I miss...
I'm assuming there's high false positive rate. If the test has even moderate false negative, then yes it's worse than useless.
(1) you are overwhelmingly unlikely to actually have the disease even if your test comes back positive but you don’t have obvious symptoms
(2) the pool of people testing positive is completely dominated by false positives. The fraction of people testing positive that will actually have the disease would be very small, so you lose the epidemiological benefit of the test (now you can’t actually track the disease well).
So — test is useless for people like you and me who don’t have symptoms or a strong prior probability of having covid BEFORE the test, because even a positive result is overwhelmingly more likely to be wrong, AND now the epidemiologists trying to actually track the disease are instead overwhelmed with false positives so the true signal disappears. It’s bad all around. You could imagine using this as a screening tool, but the false positive rate has to be small enough for that purpose as well (like, less than one percent).
In the context of a bona fide pandemic with a massive shortage of desperately needed testing, however, this would be a palatable improvement upon the status quo.
Let’s say there’s 100,000 people in the US with covid right now (like 10x the measured number)
TPR = 1
Disease rate = 1e5/3.3e8 = 3e-4
P(you have covid| test is positive) = 3e-4/(0.5(1-3e-4) + 3e-4) = 0.06%!!
This is less than useless. Now instead of tracking the disease you are completely overwhelmed with false positives and the result is exactly the same — everyone stay home.
A test needs to be materially more accurate than the odds of having the disease to be worth anything.
Classic thought experiment: if 0.0001% of the population has a disease and a test is 99% effective and you test positive, what are the odds you have the disease? Answer: 1%.
Complimentary thought experiment: if an expensive preventive drug was available in limited supply (for 0.1% of the population only) and the earlier you took it the more preventive it was should you give it blindly to as many positives as you can? Probably not because 99% of that would be going to waste. And you would run out of drugs to cover the actual sick. Only 10% of the sick would end up actually getting the drugs.
I make that mistake myself all the time, What helps me avoid it is this: you want a number that is a property of the test method alone, independent of case distributions. A ratio between misidentified positives and identified positives (or true positives) would depend on sample distribution.
I also have a hard time keeping these all straight: https://en.wikipedia.org/wiki/Sensitivity_and_specificity#Ap...
But the parent said 50% false positive, presumably with close to a 0% false negative would be VERY useful and save potentially millions of lives. We need enough tests yesterday or so to avoid a repeat of Italy and a 50% false positive rate (with a very low false negative rate) could help do that.
False positive rate is a confusing term; it means the % of tests that should be negative that report a false positive.
I think the term for what you're probably thinking of (% of positive results that are false positives) is the false discovery rate.
And yeah obviously we desperately need a decent test like three months ago.
That would mean that while you catch most cases of the virus, you’d also get a bunch of false positives. Flipping a coin as a hypothetical test would give false positives and negatives, or low specificity and low sensitivity.
A test with high sensitivity will have a low false positive rate.
A test with high specificity will have a low false negative.
So having a test with high sensitivity but low specificity will result in trust in the positives, but not trust in the negatives?
A sensitive test will catch many positive cases. It may or may not have false positives though, eg a test that’s always gives the right answer vs a test that always returns positive no matter what.
A specific test will give you few positive results when the true answer is negative. You could use it to rule something out. One test might say “patient has A or B condition”, and a second test with high specificity may then rule out A or B, leaving B or A, respectively, as the probable condition.
False negatives miss infected people and you fail to quarantine. False positives just mean you quarantine too many.
Shouldn't it just need to be better than 50/50?
>Classic thought experiment: if 0.0001% of the population has a disease and a test is 99% effective and you test positive, what are the odds you have the disease? Answer: 1%.
My odds still changed dramatically and the cost of a false positive is just me hanging out at home and not visiting my parents. I'm not getting a biopsy or taking expensive medicene.
Is it possible that some of the positive cases of Corona are actually positive cases of Influenza?
Each bar is one week.
Flu has totally different speed of increase and the amount of people needing treatment and dying.
We know what is the cause of the increase, the scenario repeats in many countries across the world, it's not one isolated setup.
Source: Christian Drosten (he created the test) on the NDR Coronavirus Podcast
> Regarding your question about if we might accidentally test for flu or other, already existing corona virii:
> This was a topic of discussion in yesterday's talk  with Dr. Drosten, a virologist who played an important part in the development of the currently used PCR test. He said that there were extensive studies done with hundreds of samples from both flu patients and patients infected with other corona virii and none returned a positive result. The only other positive results were from corona virii that are special to certain animals (bats, some cows IIRC), but none of those are present in humans. So the accuracy of our current PCR test for SARS-CoV-2 seems to be extremely high.
Edit: realize now that it's the same person (Dr. Drosten) so same source, but different format (podcast vs transcript)
What if I have flu and that corona virus which do not affect humans. People will think I have COVID.
The test developed was done against 75 people with various other diseases as listed below to find out the false positive rate. With the 75 samples (having listed diseases), the false positive rate was 0.
Clinical samples with known viruses Number of
Total clinical samples 75
By definition, you can't have the virus which doesn't affect humans. The virus that causes Covid-19 is called SARS-CoV-2:
2 means it's only a second ever recognized such. The first caused the original SARS in 2002-2003.
"mkagenius" sadly simply reiterates false claim dressed up as a restatement of the question after completely ignoring the answer to which he responds.
SARS-CoV-2 is in the same family as SARSv1, MERS, a number of viruses that cause the common cold (229E, OC43, NL63), plus a number of bat viruses. But not influenza!
The test would cause a false positive for the most related ones, specifically SARSv1 and some bat viruses.
While this has been addressed by the CDC, how is bootleg version different to not cause the same issues?
In practice everything from software versioning to knowing what might go wrong in NN training is gonna be a roadblock for someone who hasn't been shown.
In general, if you find yourself using the phrase "you just need (to)..." Then you should probably take a step back and consider the actual work that goes into "just" doing the work.
Or, in the case you've outlined, not even doing the work, but just ordering the PCR equipment, since apparently the kit will just run itself? (I'm also assuming here that you realize that this isn't PCR + gel electrophoresis, but qPCR.)
This would include gathering saliva samples and bringing them to the PCR machine in a safe way.
edit: sequences are apparently here https://www.cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-p...
You won't be doing all this [PCR] from scratch at home McGyver-style (okay, maaaaaybe with a biochemical education) - but if you've got access to a biochemical lab that's doing RT-PCR anyway, has all the machines and all necessary chemicals (expect the COVID-specific markers) it's much more straightforward.
Running these kits out of your garage is like running a tweaked, existing file system for a home network. Not completely trivial, but it's not Dropbox, guys.
And you don't think this test needs to scale, with the millions of people needing to be tested?
Is the band matching the specific SARS-CoV-2 or it's just recognizing any coronavirus in circulation? AFAIK coronaviruses aren't that rare and are present in humans every year.
I've heard a podcast (in German)  with Christian Drosten who is one of the co-authors of the pt-pcr paper . The relevant excerpt from the transcript (deepl translated):
> A very, very large validation study has been conducted. I would have to open it on my computer to go back to the numbers. But we have large numbers of real patient samples - with known positive evidence of other corona viruses and all the other cold viruses that we know of, and a whole number of these for each individual virus - and a whole number of patient samples, that is hundreds of samples with other corona viruses and other cold viruses, have been tested in this test. And not once has there been a false positive reaction. So this test does not react against any other human coronavirus or any other human cold virus.
> It is true, but this is of course completely misleading information, in theory this test would react against the old SARS corona virus. But that has not been present in humans for 16 years. And in theory, this test would also react against a whole range of bat coronaviruses, but they do not exist in humans either.
I'm currently working on adding the gene for bioilluminescence to p. cubensis fungi. If I can successfully breed offspring with the desire genotype, I hope to sell the novel spores and use those funds to invest in a variety of altruistic research like individualized DNA-based cancer treatment.
If you just want to use molecular biology to make things glow see: https://www.minipcr.com/products/p51-molecular-glow-lab/
EDIT: You can't just put this on a gel. Something that comes up at 35 cycles (likely negative - needs re-running) looks exactly the same as something that comes up at 15 cycles (likely positive). The quantitative part is important.
2nd EDIT: it uses dual-labelled probe - end point PCR is absolutely not good enough.
Anyway, an end-point PCR is not quantitative. You could do semi-quantitative on a gel, but it's a rubbish technique that was rightfully forgotten years ago, as it requires a lot of optimisation and has very little reproducibility.
The larger point is that there are many ways the test could have been designed around any possible combination of supply roadblocks (no DNA extraction reagent, choose phenol/chloroform; no cotton swabs, use paper; I could go on and on), so there are no excuses as to the massive and unwarranted and fatal delay in rolling out comprehensive testing in the U.S. Sure some work arounds are less desirable, but the alternative we have chosen is to fail a number (~>5,000) of people who didn't have to die by letting this thing spread without adequate testing.
Edit: A gel gives you the ability to select for size as well, which a qpcr machine does not. Not sure why I have to reply in the form of edits.
with the rtpcr machine readout which only gives you the signal corresponding to how much was amplified over time you need tricks like the dual labelling.
You need processes in place that ensure that these types of contamination are prevented, and constantly checked for. You need a very robust pipeline from sample collection to result dissemination that ensure no mix ups.
All these things are possible, but PCR is ultrasensitive and processes are hard; you could have a huge amount of false results if not very very careful.
The real problem seems to be the kit-cowboys who have no idea how to do anything unless it comes out of a kit.
- What bits of equipment would I need? (Generally speaking, not specific to what's in this auction lot)
- What reagents are needed? Where can I get them (both as a general rule, and also specifically given likely huge shortages)?
- How do I actually test for this?
- What do I watch out for to try and mitigate false positives and negatives?
I ask as someone
- completely naive - in the sense of "oh this sounds interesting and easy to do!" :)
- objectively absolutely underqualified to even think about doing this
- incapable of affording any of the equipment
so by all means feed me answers describing how impossibly hard and stupid this is to do, and pretend I'm not serious.
Also, as an aside, it'll be fun to watch the bid price on this. I wonder how statistically above average it'll be. Heh.
Curious what your thoughts are on the value - what markdown from market price can one typically expect?
Seems like there's a good opportunity for a nefarious get rich quick scheme here: setup a website, have hypochondriac rich people send in a swab, charge them lots, wait a couple of days and inform them of a random outcome with a warning about false positives. If this is going on, they should at least give people a positive so they quarantine them self.
The UK like many other countries the UK is advising self isolation for those with symptoms, and I imagine those who ignore this would not isolate even if they did test positive. There’s no specific treatment. Those admitted requiring ventilatory support have that decision made on other grounds, and a CT can show a consistent viral pneumonia and help rule out other causes, which is good enough diagnostically when the pre-test probability is likely to be so high. I believe when PCR testing was not readily available in China they were using ct based diagnostic criteria.
Unless there’s something I’m missing, the main benefits of a readily available test would be getting potentially symptomatic but actually negative key workers back from self isolation and perhaps catching the asymptotic if it could be rolled out widely enough.
Directly being the key word and kind of a weasel word. The real question should be if it is indirectly impacting mortality. For example by making cases look less numerous than they are which may result in a change in individual behavior and making it harder to track who has it so the people who might be able to go into far stricter isolation currently don't because their cost benefit analysis is saying it isn't yet at the threshold to do so.
For example, I have a brother living with our parents who is still having to go to his job. Because of the current reported spread in our state, his job hasn't closed and it he doesn't think it reasonable to take quarantined leave. Further testing would give him better information to make the choice to skip out on his job for the sake of protecting our parents or may otherwise lead to his job temporarily closing.
There is also the factor of if someone tests positive and is going to work they will be facing far more symptoms than if they can write it off as just being a cold or allergies. If someone shows up to work and has a positive test, the other workers are at a much better position to just walk on of the job until the manager sends the sick worker home than if the initial worker shows up with and claims it is a cold.
None of these are direct, but all of these are indirect ways of reducing spread and mortality.
Let's stop trying to rationalize the lack of testing though. It's embarrassing and shameful that we can't test people. Our infrastructure and our leadership weren't up to the task, even when other countries' was. That's a really difficult idea to confront. Saying "oh but we didn't really need that" won't change that.
Sorry, poor wording on my part.
I'm not sure what laws could/would apply.
I’m almost certain I’ve had Corona, but it’s almost impossible to get the medical system to test for that where I live (for good reasons).
Will it be possible to get a test kit like this https://www.biomedomics.com/products/infectious-disease/covi... as private individual (in the EU)? Will that test show if I have been infected previously? The graph on this PDF suggest it https://www.biomedomics.com/?fldl=3001
1) Unsure of the amount of blood required for this test. If it's just a pin prick you're fine, but if it requires a whole vial of blood, you will end up with some pretty nasty cuts trying to withdraw enough blood for the test.
2) Antibody tests such as these are inherently limited in their reliability. Not as reliable as the PCR tests, and that goes doubly so for these field litmus style tests. All it's really telling you is you how your body has reacted to potential exposures. A near-miss infection would show a false positive. It also takes time, so recent infections can give you a false negative.
3) If everyone on HN buys one of these because of this post, we will be depleting the available stock of these tests that could otherwise be used to save lives. Anything medical is going to be very scarce for the next several months, and we all need to do our part to help assuage the problem.
and if I found out through some kind of antibody test that I have NOT had it, and the thing is worse than the 'non-flu' I had some weeks ago, then dang, that thing is really bad and I'm going to try to stock up on other things that are not readily available.
If I can confirm that I’ve had it I would start going back to the office (better ergonomics) and start going out on lunches/dates, go to the gym, shop for clothes, meet older relatives etc with (almost) no fear of spreading it to other people.
I suppose some of those restrictions will be relaxed to include research labs when it's necessary to increase capacity.
The test itself could be reliably run by any phd student or lab analyst.
Doing all those things by hand also takes some time. Thinking back to my days in a lab at MIT, sample to PCR probably took a full day (rough approximation). Big labs can probably increase the parallelism a lot.
Getting demand is harder than scaling.
In this case the demand already exist and the money to scale as well.
In short, the question remains. If there is a will to scale, what is the holdup? People with experience?
I’m more interested in the parent question at the moment. I know almost nothing about the subject matter. What are the blockers for deploying a simple virus test at the scale we need?
Yes, we can produce the primers, develop the tests, ramp up the supply of RNA extraction kits, swabs, tips, etc. Individually easy, but together more challenging, especially when the entire world is also trying to acquire the same products.
Yes, large, fast and high-scale instruments exist. But, they need to be set up and calibrated. They need adequate power, cooling, water, space, etc. The technicians need training. They need network interfaces, etc.
Yes, it's a simple test. But there are still SO MANY steps needed to generate a result from a sample, and those take people. Just looking at the laboratory workflow:
1) Sample received in shipment -- unbox, scan manifest (if provided)
2) Unbag sample + requisition
3) Check sample label (usually handwritten) and verify accuracy to requisition (possibly handwritten). In an ideal case, orders are coming in as "interfaced orders" (meaning electronically) but many smaller clinics/hospitals will not have this.
4) Enter all demographics of the patient into laboratory system
5) Have second person verify the information
6) Re-bag and send sample to location in lab with test instrumentation
7) Technicians unbag, verify label + order accuracy
8) Decant sample from non-standardized tube sent to lab to standard tube used in lab
9) Scan into liquid handling robot...
...et cetera, et cetera
As I will probably find out in the replies there are "solutions" to all of these problems, and many labs utilize them. However, to scale such a complex system so quickly means that there is no room for a "test environment", and all changes have to be made "in production". Even simple changes to the workflow require days of prep to communicate to all of the staff across three daily shifts-- you get the idea.
source: i'm a laboratory medicine resident at the UW lab. We scaled from 0 to 3000 tests in 2 weeks and it's been an incredible all-hands effort.
Why keep such detailed records? Barcode it on the way in, run the test, and report the result - forget demographic data and any other paperwork, whoever ordered the test can deal with that.
The supplies for RNA extraction are common and readily available (I think all the raw components are mass produced?), but only specific kits are FDA approved.
Only specific swabs are FDA approved. (https://khn.org/news/as-coronavirus-testing-gears-up-special...)
> the government is considering expanding its recommended testing material options to allow for more general nasal swabs to keep up with the increased testing demand
Standard qPCR machines are incredibly common in both academia and industry and have 96 wells at minimum. The protocol published by the CDC has an 80 minute runtime. That's 1000 tests per day for a _single_ low-end machine.
The US response has been an absolute shitshow of bureaucratic dysfunction as far as I'm concerned, and people will likely end up dead as a direct result.
Detailed records and redundancies ensure you don't mix up any of the tens of thousands of samples coming in. These systems are crucial for being able to scale up as they have without complete chaos breaking out in the lab.
You are right that barcodes are far more efficient, after implementation. But implementation takes months, and requires diverting resources that would otherwise be used to run more samples. The lab would face significant downtime putting a barcode setup in place and retraining. (See nkrumm's comment about labs not having a "test" environment.)
> Standard qPCR machines are incredibly common in both academia and industry and have 96 wells at minimum. The protocol published by the CDC has an 80 minute runtime. That's 1000 tests per day for a _single_ low-end machine.
That's only if we ignore the sample preparation time (orders of magnitude longer than analysis time), and the many control wells necessary to ensure the technique was successful. While I suspect these will also be dismissed as bureaucratic inefficiency, they're needed to make sure your newly-installed instrument running 24/7 hasn't broken down, and that the high throughput sample prep wasn't botched for a given prep batch.
The stakes for these tests are high enough that cutting corners on QA/QC isn't acceptable, because it means more lives lost. Doing a mediocre job for testing at this scale will have a very real impact on our population.
The point I was trying to make with those numbers was just how readily accessible the necessary instrumentation is.
Regarding sample preparation, I'm well aware that it's a time sink (I've done DNA and RNA extractions before). But it's fairly trivial and can be done fully in parallel by multiple people; the primary bottleneck is likely to be available bench space. (Unless the sample prep has been fully mechanized, in which case I'm really not seeing the issue.)
My point being that multiple, parallel sample prep pipelines can feed a single qPCR machine to keep it running just about 24/7.
Regarding barcodes, I didn't mean it had to be fully automated. Just drop the excess data entry and switch to a serial number scheme with built-in redundancy (or at least error detection). Many academic labs employ such schemes by hand.
Given just how dire the circumstances are, I'm afraid I'd have to strenuously disagree that cutting corners on QA/QC (as compared to standard medical diagnostic testing) would be unacceptable. None of what I described is at all out of place for handling research samples, and in my experience those are quite reliable.
I used the combat medic analogy in my previous post for a reason - a significant number of people are likely to end up dead due to our having blindly stuck to the rules. A bit of pragmatism could have saved them, and I view that as a tragic systemic failure on the part of the US government.
> I'm afraid I'd have to strenuously disagree that cutting corners on QA/QC [...] would be unacceptable.
> I would _never_ dismiss controls as an inefficiency
So, the QC in QA/QC stands for Quality Controls. So, you're strenuously insisting they're unnecessary, yet vehement that you would never dismiss the thing you just said wasn't necessary? Which one is it?
> But [RNA extraction is] fairly trivial and can be done fully in parallel by multiple people
It takes longer than the instrument analysis was my point. That's the typical bottleneck in running samples, not your instrument sample throughput like you claim. So even if you can run 1000 samples on the instrument, if it takes longer to prepare them (which it always does), then that's your rate limiting step.
Unless, of course, you're working in this magic lab of yours where new, fully-trained techs suddenly materialize any time there's a spike in sample volume (whereas new benchspace doesn't? Might wanna take that up with your deity lab manager).
> Regarding barcodes, I didn't mean it had to be fully automated. Just drop the excess data entry and switch to a serial number scheme with built-in redundancy (or at least error detection)
With all hands on deck who do you think will have time to do this? Barcode migrations are a lot of work. Adding the word "just" to what I've described doesn't make something trivially easy.
Though apparently this whole process is trivial, from the sample check-in to the RNA extraction to the instrument analysis. Why not just fire the UW resident and all the staff, so that you can swoop in save the world, since it's all so terribly easy for you? I look forward to touring this fully-automated magic lab of yours.
First though, it seems a misunderstanding has developed. I was not calling the competence of the UW lab into question! They are bound by various state and federal regulations and I'm certain are doing the absolute best that they can under the circumstances. The examples I provided were to illustrate just how absurd the current state of affairs is, and to make it clear that bureaucratic ineptitude is to blame.
We obviously both agree that QA/QC is necessary; note that my back-of-the-envelope calculations included controls. I don't pretend to know precisely what requirements FDA regulations place on various diagnostic tests. What I do know, and attempted to illustrate in concrete terms, is that it is physically possible to scale testing in a sufficiently reliable manner using common instrumentation and bulk reagents. Any genuine attempt to explain US testing shortages _must_ account for this fact.
Yes, parallelizing sample prep requires a sufficient number of properly trained technicians. Presumably the US government is capable of locating and making use of qualified personnel in an emergency situation such as this? (To start with, literally any graduate student whose research includes running molecular biology protocols is likely over qualified for sample prep.)
Regarding serial numbers and labeling, it is indeed trivial. You can literally keep a list on paper and label tubes by hand (I did this for years in an academic lab). This step is fast compared to overall sample prep time.
I have no idea where you got the idea of a barcode migration from. Remember, I'm not describing a clinical lab operating according to FDA regulations; I'm describing a sufficiently reliable setup that closely resembles an academic research lab and would maximize throughput in an emergency situation. The only goal is to receive a package, label a corresponding tube, run a test, and report the result.
(BTW, I claimed that bench space for sample prep, not instrument throughput, was likely to be the bottleneck. In fact, instrument throughput not being the bottleneck was one of my primary points.)
I'm also confused by your apparent assumption that bench space is a universal constant that cannot be changed, even under a global pandemic, while lab personnel can be scaled up effortlessly.
> Regarding serial numbers and labeling, it is indeed trivial. You can literally keep a list on paper and label tubes by hand (I did this for years in an academic lab). This step is fast compared to overall sample prep time.
Scientists don't keep records on scraps paper for a reason, and I'm shocked your PI didn't read you the Riot Act for shoddy record-keeping.
With thousands of samples coming in, this is how you end up completely losing track of your samples. Once again: it's not trivial, particularly at this scale.
> I have no idea where you got the idea of a barcode migration from.
> Why keep such detailed records? Barcode it on the way in, run the test, and report the result - forget demographic data and any other paperwork
I never claimed that bench space was a universal constant, nor that hiring personnel is effortless. Rather, I attempted to make it clear that from both scientific and logistical perspectives the barrier to effective testing is quite low.
The point of the instrument throughput calculation was to make it clear that instrument availability can't possibly be the limiting factor because a single low-end one that many academic labs already have on hand can facilitate an incredible number of tests each day. That's important because you can't depend on being able to procure new instrumentation in a timely manner during a crisis so any estimates ought to assume that you're stuck with whatever you already have.
We see reagent shortages reported in the news, but that can't possibly be the limiting factor either because (as far as I know) only common chemicals (plus primers and probes) are required. (Actually you could probably dispense with the probes if you were willing to run an awful lot of gels, but that would further complicate the pipeline and require more labor so better not.)
So then we might suppose that personnel and training is the bottleneck, but that can't be it either because the government has deep pockets and just about any practicing molecular biologist is over qualified to perform such a trivial procedure.
Looked at this way, it should be abundantly clear that US policy is entirely to blame.
I also never said to use scraps of paper in lieu of proper record keeping. The obvious interpretation of what I wrote is to go line by line in a lab notebook, which is something I have in fact done before (obviously not on the scale described though). It works quite well in the long term provided that your serial numbers incorporate either a day or a page number and are strictly sequential. It's hardly the only way to go about it; I only mentioned it because the original post that I responded to explicitly called out record keeping as a necessarily time consuming and complicated part of the process. I was illustrating that once again, that is only true when complying with existing US regulations.
The bureaucratic aspects are to ensure you don't mix up the large volume of samples, and the quantitative QA/QC metrics are needed to objectively esablish what level of error is considered acceptable. Good record-keeping and QA/QC are all necessary when you're dealing with healthcare, particularly largescale healthcare.
That doesn't mean US policy or the administration's handling of this crisis was anything close to acceptable, but the issues there are pretty far removed from routine laboratory sample check-in and record-keeping.
Eg. Not enough cotton swabs: https://www.politico.com/news/2020/03/16/coronavirus-testing...
With all that said, there's still a lot of specialized skills required to competently run these tests. You'd still need significant training if starting from nothing. But there are enough un/underemployed lab techs out there that finding more techs won't be the bottleneck.
For something like snot you probably don’t need any extraction process beyond heating to 100C in buffer.
I'm skeptical of the value add when weighed against the risk of introducing unregulated / unverified medical tests with unknown false positive/negative rates during a crisis situation, but obviously folks disagree, and I'm sure I could be missing something.
This sort of thing is relatively easy to do for someone with the right background, but hard to do well. Aside from wasting reagents that could be potentially used by an actual diagnostic lab, some student running PCRs is going to get nowhere near acceptable test reliability. Those they falsely reassure will run around spreading it, and those they falsely diagnose will inappropriately self isolate. The more they test, the more accuracy matters.
Put another way (and apologies in advance for the example): if the guy was into watersports and noticed somebody's urine tastes sweet, is it a crime to tell them it might be diabetes? What if somebody asks him to taste theirs?
For anyone already feeling sick... stay home and self-quarantine.
If we could _just_ test everybody regardless of symptoms then we could quickly isolate people spreading it in ignorance. That is the main benefit I could reason out. Probably early detection and better planning as someone with it progresses, too.
The official statistics have a lag in them due to only showing confirmed cases.
Also depends on whether you're testing suspected cases or merely hypochondriacs.
In reality, even if no one got tested, Doctors would still be doing pretty much the same things they are doing now. The same numbers of people would live or die. Hypoxemia and pneumonia are easy to diagnose. The treatment is standard. Any medicines are likely to work the same without regard to the exact RNA makeup of the virus.
Quarantine is still a good idea. Remember, if it mutates all these tests are going to be useless anyway. So a negative result has to be treated as dangerous anyway.
Also this probably doesnt scale well to the thousands per day states need now.
I would not trust this organization. They're tainted.
I remember coming to the bay area and it wasn't long before someone that felt they had a cultural affinity with me invited me to a GroupMe group. Man that was years ago. Surprised to see people still use GroupMe, still seems to be for cliques exclusively.
Not sure what that adds to the conversation, just my experience with forms and layers of people paid to do nothing but sign them.
In bureaucracies, many positions/people only have the power to slow down or stop the process. People need to feel important and powerful, and they cannot contribute to moving a process forward because they are, for example, a cybersecurity analyst or a lawyer.
So they say "well this process doesn't check box #134 on the list, we need to circle back and solution this" and they hang up and go back to reading reddit until the next meeting on their calendar.
It's awful to be a "doer" in a bureaucracy.
The sad thing is the USA and Europe were fully capable of handling this just like South Korea. That's why this is really about a failure of leadership.
I would like to think that this crisis will force Americans and Europeans to demand accountability, but I don't think that's going to happen. A token scapegoat will be found, "the people" will be congratulated for taking action in a time of emergency (and failure of government) and the leadership that were out-to-lunch when this stuff started going down will be accountable to nothing.
South Korea wasn't a democracy for most of its history and it shows as soon as drastic measures need to be taken. The first reaction among the populous in the West is resistance against any form of government mandated measures due to a deep mistrust. Add to that federal structures versus centralised government and you get to the results we see today.
Calls for strong leadership end in dictatorships because measures taken in times of crisis tend not tobe taken back once the crisis is over. This is nothing new - this is how the Roman Empire got its emperors after all.
Sure, experience from SARS plays a role, too. But ignoring the emphasis of individual freedom and federal government structures and blaming leadership is a huge oversight.
Adult citizens should be mature and responsible in light of a crisis. The opposite is the case and the irrational hoarding of irrelevant goods (see the TP crisis) is a symptom of that.
The fact of the matter is that many European countries simply don't have the political means to react the same way a central government with compliant citizens can.
Just look at the Spring Breakers in Florida - they don't care about social distancing. Neither did the ski tourists in Ischgl and South Tirol where apre ski parties continued until the bodies started dropping (first metaphorically,later literally).
That's a cultural difference that's hard to deny.
South Korea holds regular country wide simulations for pandemics because of SARS and bird flu.
Their last one was 18 months ago and ironically focused on simulating a large scale coronavirus outbreak.
You might be overestimating the cultural differences here compared to plain old preparedness.
This is something that isn't technically possible in Europe and simply doesn't fly with the vast majority of the population. Their strategy is based on policies that just don't work in Europe.
EDIT: also not to forget that South Korea is technically an island with its only land border being the most fortified one in the world...
Another point I forget to mention is mask wearing which certainly is cultural. In Australia and much of the West it's considered not normal whereas no one thinks twice in Asia.
I've seen Australians say they wouldn't wear one even if sick and we've had incidents of people abusing perfectly healthy mask wearers in Sydney demanding they self quarantine.
These attitudes within a society have pretty clear outcomes for anything contagious.