Stanford Student Claims to Run Bootleg Covid-19 Testing Lab | Hacker News Reader

Stanford Student Claims to Run Bootleg Covid-19 Testing Lab

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279 pointsrandycupertino227 comments

It's incredible seeing this on hn. For context, while the FoHo is sometimes good for very, very breaking and recent stories, it's a little hard to overdo the niche it fits in Stanford culture: it's pretty much the main and only tabloid for fast-paced news and (sometimes) absurd 'takes' on things happening around campus.

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.

If I heard someone in my lab was running PCR on saliva samples potentially infected with 2019-nCoV, I'd lose my shit.

At the moment, you shouldn't be going to a lower than a biosafety level 4 lab at all.

This is incorrect. The CDC recommends BSL-2 for routine diagnostics and BSL-3 for isolating the virus in cell culture. (https://www.cdc.gov/coronavirus/2019-nCoV/lab/lab-biosafety-...)

At the moment, most tests are certainly being done in less than BSL4, there aren't that many of them.

https://www.liquisearch.com/biosafety_level/list_of_bsl-4_fa...

You don't need live viruses for testing. You only need some viral RNA material so you can inactivate the virus by heating the samples to a certain temperature for example. Hazardous work for sure.

So your plan is to greatly reduce testing capacity?

Yea, the test itself is incredibly simple. The challenge to scale it up is regulations and bureaucracy, because they all fear the liability of a test that can sometimes produce false negatives.

It's not the liability here, it's the fact that cutting corners means you now have more people walking around that your lab said was fine, that aren't, and vice versa. If someone gets a false positive then, following recovery, they'll assume they don't need to take safety precautions like social distancing seriously, which can put them in real danger. And false negatives mean you've now infected the "non-corona" wing of the hospital when your patient with non-corona pneumonia is admitted.

The test is trivial. It's just RT-PCR.

- 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...

Agree it's trivially easy to do, but as anyone you does a lot of qPCR knows, they're rife with false positives.

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....

> Agree it's trivially easy to do, but as anyone you does a lot of qPCR knows, they're rife with false positives.

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.

With a 50% false positive rate, most of your positives are false positive. You might as well just tell everyone who asks for a test that they're infected.

Having 50% of all tests come back positive is way too high and makes the test basically useless. But having 50% or more of positive tests being false positives is probably the right tradeoff, though you probably want to re-test people who don't show symptoms.

From a public health perspective ... this could be a brilliant solution.

Until they all decide that they’re immune and don’t need to worry about it anymore.

Exactly. I think many people, upon learning they're positive by asymptomatic would (maybe) wait a week to make sure they don't feel ill, and then go out into the world, potentially spreading the virus with abandon because they're among the group that doesn't get ill from it.

You should account for ignorance in public health policy, but you shouldn't rely on it.

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.

That's a great way to lose any remaining confidence the population might have on the establishment. It is also probably unethical so I doubt any doctor would go with it.

It's a perfectly valid concern, but I don't think it needs to turn out the way your fear.

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.

Until Fox News or the governor of West Virginia blows the illusion away.

Huh, I'm lost in this thread.

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...

You could tell them the test came back positive. That's not really a lie.

50% is a bit of information. You can repeat the test - even if you consider that some contamination survives repeated tests, if you even get half a bit from subsequent tests you can easily get to eliminate quite a bit of population.

Yea but not nearly enough of the population for this to meaningfully change the response, and now you’ve made the testing results completely meaningless so that we can’t track the disease. Maybe it’s not intuitive to people but we are actually worse off with a test that’s this bad than just the extremely limited testing that’s being done now

I admit it's not intuitive. Tell me more?

I'm assuming there's high false positive rate. If the test has even moderate false negative, then yes it's worse than useless.

High false positive rate (I’m talking like more than 1%) means

(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).

There is a big system-level difference: with 50% false positive, half of the population goes back to living regular lives. False positives stay home, and go to a hospital only if they need a ventialtor (which very few will need since they are not actually sick)

There are 50% false positive, and there are some false negative. And some more not exactly false negative, but simply got sick after the test. And you tell them: we tested everyone, all negatives can just resume normal life. What could go wrong?

If you can't breath you go to the hospital regardless of it being COVID-19.

This is an interesting tradeoff to consider. Under many many circumstances I could see that rate of false positives being awful and intolerable.

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.

In the case of a generally mild disease, it's much less of a problem. Usually, the problem with false positives is unnessary, risky treatments and overwhelming the medical system. But in this case, you just need to know whether to self quarantine. You only need treatment if symptoms become severe.

Until the global economy unnecessarily collapses.

You also need to consider that when the false positives get over their flu or cold or whatever, they will assume they are immune to COVID.

Really? That test is meaningless. It screws up the numbers, and you might as well do a complete quarantine anyway, since you need to not just quarantine but isolate anyone who’s positive.

Let’s say there’s 100,000 people in the US with covid right now (like 10x the measured number)

FPR =0.5 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.

hmm, how many false negatives is it giving?

A 50% false positive rate means that, since most people don't have the virus, about 50% of all the tests will come back positive. You just about might as well flip a coin instead.

This is a classic statistical fallacy. A test that is 50% accurate serves 0 purpose. You might as well consider coin flipping a valid test. If you tested America with this test you’d end up thinking half the country is infected. And within the ones that tested positive only half would actually be and within the negatives half would be and you would have missed them.

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.

Isn't the false positive rate the percentage of positives that should have been negative? E.g. if I test 10000 people and 100 of them test positive, but really only 50 of those are sick (and almost none of the other 9900 people are), then I have a false positive rate of 50% and a very useful test. Obviously, this is very different from flipping a coin. And flipping a coin could also have a very high false negative rate.

It's the rate of actual negatives that are perceived as positives.

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.

The metric you're talking about is called the "false discovery rate": https://en.wikipedia.org/wiki/False_discovery_rate

I also have a hard time keeping these all straight: https://en.wikipedia.org/wiki/Sensitivity_and_specificity#Ap...

50% accurate I'd agree is useless.

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.

Even the properly-conducted version of this test has a fairly substantial false negative rate, somewhere around the 30% mark, and if it's done by students using samples that might not be taken correctly on a rigged-together testing setup that's going to get worse. Seriously, you might as well flip a coin.

A test with a 50% false positive rate, administered to 100 million people who aren't infected, would say 50 million people were infected.

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.

That’s fair, if the assumption is that false negatives are very low or 0 (in which case it’s a super high accuracy test at low contamination rates and super useful).

And yeah obviously we desperately need a decent test like three months ago.

A test might have a high false positive rate, ie “low specificity”, but can still have “high sensitivity”.

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.

Isn’t false negative specificity and false positive sensitivity?

https://en.wikipedia.org/wiki/Sensitivity_and_specificity

No, sensitivity is TPs / all positives (detected TP and FN). It’s the green half of the diagram in your link. The language is very easy to get tripped up by though. :)

I think I’m getting tripped by false positive, true positive.

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?

For me it’s easier to think of sensitivity as being “sensitive to the true positive” without saying much about false positive or negative.

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.

I think you need to learn the difference between false positives and false negatives. A 50% false positive rate with no false negatives is absolutely better than 50% false negative and positive.

False negatives miss infected people and you fail to quarantine. False positives just mean you quarantine too many.

You’re not differentiating between sensitivity and specificity - in this case the test is highly sensitive but not specific. That means that it could be effectively hard to rule out cases while failing to provide strong evidence of actual infection in individual cases.

You're applying conventional knowledge to an unusual situation where it doesn't apply. The current test in my country is something like "was sitting within 4 rows of a known patient on a plane". That's obviously got a massive false positive rate but we do it anyway. The action you take when officially tested positive is the same as you take when learning you had contact with a patient - isolate yourself at home. There's no wasted drugs because there's no treatment for it! At worst, you might do an official test, but if those are in short supply, they're not going to be given to anyone who just walks in with a home-made result.

>A test needs to be materially more accurate than the odds of having the disease to be worth anything.

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.

Given one of the best pieces of advice about managing COVID-19 is to "Act Like You Already Have it" [1], a less accurate test with more false positives isn't necessarily a bad thing.

[1] https://www.huffingtonpost.com.au/entry/act-like-you-have-co...

Aren’t the primers supposed to be pretty selective for the RNA sequences being targeted? Otherwise any other random RNA in the sample (like from some other viral infection) would result in a false positive, right?

Once you have a successful PCR, you have billions of copies of your target sequence that are easy to aerosolize and/or transfer by contact onto your pipettes, gloves, and other lab surfaces. When a few of these molecules find their way into a new PCR you just set up, you get a false positive. There are protocols clinical labs employ to avoid this (e.g. never open the cycled PCRs in same room where you set up new PCRs, etc.) but they require strict adherence. (Or you can just give up all your sensitivity and only detect the cases with a huge viral load.)

Looking at the assay - it uses a dual labelled probe. That gives the specificity in addition to the PCR primers. Primers themselves presumably aren't selective enough.

> they're rife with false positives.

Is it possible that some of the positive cases of Corona are actually positive cases of Influenza?

No, it is not, see the numbers compared by the Italian National Biotechnology Association:

https://en.wikipedia.org/wiki/File:Is_COVID-19_like_a_flu%3F...

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.

I was curious about the possible mix up of flu and covid by the testing kit since they are similar, I am not denying that covid exists, just that if the tests are mixing the two up.

No, the covid testing kit was tested with more than a thousand probes and there wasn't a single false positive.

Source: Christian Drosten (he created the test) on the NDR Coronavirus Podcast

There is another source (in German) claiming the same, HN comment here: https://news.ycombinator.com/item?id=22627958 and source here: https://www.ndr.de/nachrichten/info/16-Coronavirus-Update-Wi...

> 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 [1] 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)

> And theoretically, the test would give a positive result on some bat corona viruses, but they do not affect humans.

What if I have flu and that corona virus which do not affect humans. People will think I have COVID.

Edit:

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

samples tested in all three assays HCoV-HKU1 2 HCoV-OC43 5 HCoV-NL63 5 HCoV-229E 5 MERS-CoV 5 Influenza A (H1N1/09) 6 Influenza A (H3N2) 5 Influenza A(H5N1) 1 Influenza B 3 Rhinovirus/Enterovirus 3 Respiratory syncytial virus (A/B) 6 Parainfluenza 1 virus 3 Parainfluenza 2 virus 3 Parainfluenza 3 virus 3 Parainfluenza A or -B virus 5 Human metapneumovirus 3 Adenovirus 3 Human Bocavirus 3 Legionella spp. 3 Mycoplasma spp. 3

   Total clinical samples 75

I hope we didn't any other major common virus, and also is 75 a big enough number to say that the false positive rate is definitely 0?

> What if I have flu and that corona virus which do not affect humans.

By definition, you can't have the virus which doesn't affect humans. The virus that causes Covid-19 is called SARS-CoV-2:

https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndr...

2 means it's only a second ever recognized such. The first caused the original SARS in 2002-2003.

And that low chance of false positive can be easily derived (as in, just looking at the bars) from the Italian National Biotechnology Association graph, based on the known cases in Italy, which I've cited before. The numbers are orders of magnitude different, so the same can be concluded -- the can be no significant misrepresentation. There's the whole Italy and actual people dying or having to be connected to the machines to keep them alive -- a much bigger and more horrifying confirmation of low chance of false positives than just comparing thousand probes.

"mkagenius" sadly simply reiterates false claim dressed up as a restatement of the question after completely ignoring the answer to which he responds.

The viruses are not similar at all, the symptoms are to some degree.

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.

We really need a test for anti-bodies as well.

Antibody tests are also fairly unreliable in a number of circumstances as well.

The early CDC tests were not accurate, or the labs were not, correct? I am not qualified to speak to this, however, inaccurate results (positive and negative) could lead to overloading the healthcare system. https://www.technologyreview.com/s/615323/why-the-cdc-botche...

While this has been addressed by the CDC, how is bootleg version different to not cause the same issues?

It was only one of the tree parts of the CDC test that was giving false positives in most cases. Also, the experts on This Week In Virology thought that the CDC was being too clever in how it designed its test and that's why it got into trouble but I don't feel qualified to try to explain why exactly.

A false positive in the case of corona virus shouldn't be a problem since you shouldn't seek medical treatment unless the symptoms become severe.

As others have said, it's a huge problem if it leads people to think they're now immune to the coronavirus.

The steps are trivial to write out but executing this for someone inexperienced is not trivial. However, someone in the field, no doubt can do this, I'm sure.

My thoughts exactly. This is like saying it's trivial to do face recognition. All you have to do is load some libs, train the NN on them, and use the trained network on new data.

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.

As someone who had experience in both - PCR is similar, if not simpler to setting up NN. You just need equipment.

And setting up a NN is easy, you just need a laptop.

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.)

The hard part is to do 10K tests per day like the South Koreans did to successfully contain the spread of covid-19 (or 60K tests per day since the USA have 6 times the Korean population).

This would include gathering saliva samples and bringing them to the PCR machine in a safe way.

New York State is at that level of testing per-capita, although a bit belatedly: it tested 7500 people between the Wed 3/18 and Thu 3/19 updates. If all states were testing at that per-capita rate, there would be about 125k tests per day nationwide.

I wonder if primers are in short supply? CDC authorized only two kits. Are the sequences known? Can you custom order/synthesize your own?

edit: sequences are apparently here https://www.cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-p...

If you put in an order for the primers by noon, you can have enough of them in your lab by the morning to run a thousand tests, maybe 10,000.

This comments reads like the classic "dropbox is trivial, it's just rsync" except it's more like "dropbox is trivial, it's just rsync on kubernetes with a reactJS frontend and a backend written in Haskell"

It's more like "We already have implemented dropbox for .jpg-files, also doing it for .png-files is trivial".

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.

2d later, not that anyone still sees this. But: I know from a friend that their university lab is making plans to have their PCR-cabable equipment and staff on standby to run corona tests.

Maybe for someone with no bio background. But these are pretty standard techniques in molecular biology. The only tricky part is collecting the sample without exposing yourself to the virus.

Yeah, the Dropbox example doesn't make sense. Dropbox is hard to build because it needs to work at scale and for general enterprise purposes. Similarly, regional/state-sponsored testing is hard because it needs to work at scale and for a large population of people.

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.

> Dropbox is hard to build because it needs to work at scale

And you don't think this test needs to scale, with the millions of people needing to be tested?

As far as I can read, this is literally the next sentence in my comment.

Whoops, so used to the "it's so easy" comments on here that I missed that part.

These are techniques high school students learn and practice in AP Bio... at least I did, 25 years ago.

Yes, and middle school students learn to write "Hello World!" HTML pages. So, by that logic, any web developer is interchangeable with a middle schooler.

Really? PCR was pretty new at that point.

Reading through some archived curricula, it was in a 1993 practice exam, at least. [0] I'm pretty surprised as well.

[0] http://www.csun.edu/science/biology/AP_biology/text%20files/...

no it isn't . there are lot of research labs that can do the test. the problem is safety, not the test itself.

...and to dig one layer deeper, the actual problem is diffusing blame in cases where the test is wrong or someone wants to blame the lab for the fact that they caught the bug, not safety. That's what certifications are for (in this case), and that's the real reason why running without one is risky.

risk tolerance changes in times of crisis though

Statutes of limitation run past the crisis when the lawsuits phrased, "you should have known" come out.

Yeah, imagine the janitor gets exposed to the virus, they then expose their entire family, those people then expose more, etc. You could easily kill someone.

> a band matching coronavirus positive control

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.

> 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) [0] with Christian Drosten who is one of the co-authors of the pt-pcr paper [1]. 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.

[0]: https://www.ndr.de/nachrichten/info/16-Coronavirus-Update-Wi...

[1]: https://www.eurosurveillance.org/content/10.2807/1560-7917.E...

the biggest fear is the handling of the samples and the possibility to get infected. Is there a way to make this completely automated? I know institutes in many countries have asked to perform PRC but the part of submitting samples en masse is the most critical, and labs need safety level certification for dangerous viruses. Drive-in submission is a solution, but sample depositories are even better

Would this be easy to do yourself if you were able to find (or make) a PCR machine?

FYI, the same core equipment and supplies will also allow you to do dna-based lab work, such as crispr/cas and fingerprinting for phylogeny, at home. If you're clever, you can replicate the same cutting-edge work step-by-step from published research papers and then use that knowledge to run your own experiments.

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.

How hard is it to get started doing stuff like this? Do you need thousands of dollars of lab equipment or is the entry barrier relatively low? Making your own bioluminescent genetically modified organisms sounds really neat

You need a set of pipettes, a thermal cycler (i.e. https://www.ebay.com/b/PCR-Thermal-Cyclers/185231/bn_1153835... ), some consumables (i.e. pipette tips, vials, gels), reaction reagents (listed by the top level comment), a centrifuge, and probably some other things I'm forgetting. For some reactions you are much better off using a quantitative PCR machine but those are quite expensive.

If you just want to use molecular biology to make things glow see: https://www.minipcr.com/products/p51-molecular-glow-lab/

thanks so much, this will be a fun rabbit hole i think

Governments could open source all patents and design specifications for all relevant technology.

You can make your own pcr machine with thermometers, 3 pots of water on your stove, and a stop watch

You would also need a microcentrifuge and pipettes and stuff, but yes.

You need a quantitative real-time PCR machine, not just a PCR machine. Not cheap.

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.

Totally wrong. Take a sample out in 15 cycles. Take a sample in 30. Run a gel. Compare. Done. Most of the issues you think exist are because an RT pcr machine cannot distinguish between primer-dimer and pcr product. A gel can distinguish.

This argument is pointless as the assay relies on a dual-labelled probe. Look up how that works [1].

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.

[1] https://www.sigmaaldrich.com/technical-documents/articles/bi...

You seem to miss the point entirely. The point is that the assay doesn't NEED or REQUIRE dual labelled probes at all. The only need for quantification at all is to avoid mistaking signal for spurious noise (e.g., primer dimer). The gel provides both semi-quantification and provides amplicon size, which massively increases specificity of an end-point version of the assay. It is perfectly adequate.

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.

you really think anyone cares how much of the corona you got in the particular blob of snot you gave for testing?

You deserve a 1000 upvotes for your succinct and accurate comment.

You are totally wrong. Your comment is dangerous misinformation. NO coronavirus assay requires quantitation.

Or you could just run the PCR product on a gel for much cheaper...

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.

on a gel you see the size, something coming up with exactly the right size even at 35 cycles indicates that there was at least some of what you designed the primers on in the sample. if you want higher certainty, with three primers you can get two different sizes ruling out any doubt.

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.

Why is that? Is it really impossible to do the test on a simple PCR machine, or is it just too slow?

pPCR is quantitative - measures fluorescence. End point PCR just measures whether you have the sequence there or not. It's slower, more work, and prone to false positives (see edit above).

I saw a whole kit including laptop, software, and license for $3,500 buy-it-now on eBay last week.

Yes. You can buy a PCR machine for about $1,000 US. You can build your own agarose gel box for about $100. THe power supply might be tricky, but probably not. The CDC has published all of the primer and probe sequences. It is trivial to run the assay yourself if you buy the PCR machine and a few water baths for the RT and DNAse reactions.

If you aren't worried about safety then you can use e.g. a full bridge rectifier hooked up to 110 V AC to get a usable (but shitty) agarose gel power supply. I really don't recommend this but it does show how easy it can be.

For someone who has zero previous knowledge, what are some good online resource to learn this stuff? Is it realistic to do in, say, a couple of weeks?

it's a specialized swab shortage

You ruined the Clickbait \s

100+ disappointments

If anyone else wants to start a bootleg test lab, there's a disposition auction next week for a defunct biotech startup with most of what you'll need: https://svdisposition.com/auction-detail?id=281

I'd advise against this unless you really know what you're doing. Equipment is just one thing. You need a very well controlled environment that absolutely prevents cross-contamination and environmental contamination. My lab is a very clean molecular biology lab and it isn't good enough for that.

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.

It really isn’t that difficult to avoid cross-contamination. As someone who has done literally 10s of thousand of PCR reactions (probably 100s of thousands) you just need to do your extraction and set-up seperate from where you run the reactions.

The real problem seems to be the kit-cowboys who have no idea how to do anything unless it comes out of a kit.

I'm not sure what sort of answer is possible/in good faith/responsible, but this information immediately prompts some probably-predictable questions:

- 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.

I can't answer any of your questions except the last observation, there will be an uptick in the sale prices for sure.

i'm interested. nrp can i reach out to you via email? what is your email?

To be clear, I'm not affiliated in any way with them. I just like to keep track of asset disposition auctions to pick up equipment.

How do you keep track? Are there a standard list of sites you monitor?

Curious what your thoughts are on the value - what markdown from market price can one typically expect?

Given the number of rich celebrities that apparently manage to get a test just because they're rich, I wonder if there is more illicit testing going on. Meanwhile a colleague of a doctor I know remains untested due to lack of tests despite symptoms entirely consistent with covid. Lack of tests are likely behind the comparatively high UK death rate.

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.

I doubt the lack of test availability is directly increasing mortality.

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.

>I doubt the lack of test availability is directly increasing mortality.

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.

Directly? No. There's no cure. If you're in the ER and dangerously short of breath, they're going to treat you as best they can. Since there isn't a cure or a proven treatment approved by the FDA for Covid-19, you'll be treated for viral pneumonia and hope that you get better. We don't have a cure, so the test really only says if you're highly infectious, so they know which corner of the hospital to put you in, and what level of precautions nurses and doctors should take around you.

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.

That's not what I meant. It is affecting the published rates, i.e. the statistics.

Sorry, poor wording on my part.

Ahh, didn’t think about it from that angle, apologies.

What would "illicit testing" even mean? Any lab with the right equipment can test for the virus. There was an article in the NYT the other day talking about how these celebrities got tests before everyone else, and in some of the cases they were paying private labs.

As I understand, an illicit would mean the test materials and process are not approved or regulated by the CDC.

I'm not sure what laws could/would apply.

Almost completely OT but:

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

(Disclaimer: No medical training. Former analytical chemist.) Rapid test kits like these are your best bet if you want to go the DIY route. The only caveats I have are:

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.

I did a ctrl-f to see if anyone had posted anything about testing for antibodies. As I read the symptoms and think back a bit, I am 70/30 I have had it already. I would LOVE to know if I have had it already. I can do so much more for those around me, it would also motivate me to actaully write my scathing review that I have replayed in my head about how much it sucks to not be treated with tussin-x or similar opiate when symptoms were so bad that I had. Instead I just replay it in my mind on occasion.

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.

Out of curiosity, what changes if you have had it, recovered and been symptom free for 2 weeks? Is there something different in what you’re supposed to do.

No, not really any enormous changes. But here in Sweden we don’t have proper lockdowns (yet), and my office isn’t completely shut dow, we are just strongly recommended to work from home.

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.

Keep in mind that even if you have had it, people are infectious on average for 20 days from before symptoms appear [1], so it might be good to self-quarantine for a while.

[1] https://www.scmp.com/news/china/society/article/3076022/coro...

There is also the possibility it is biphasic, although this could also be more of a problem with testing.

https://www.nytimes.com/2020/02/29/health/coronavirus-reinfe...

https://theguardian.com/world/2020/feb/27/japanese-woman-tes...

Assuming immunity, you could take care of your parents, grandparents and other high-risk people. You’d have to balance the risk of a false-positive test and wrong assumptions about immunity against the risk of someone from a high risk group running errands.

You're likely immune, at least for a while. You could live more normally, or join studies, or volunteer and help people out, etc.

Btw, these samekind of test kits seem to be available in alibaba (in large quantaties that is)

I'm a Stanford newbie. This is completely believable, but of the stories The Fountain Hopper breaks, what's the accuracy rate?

If it's so easy, then is it so hard to ramp up testing?

At least in my country (PL), I was told the laboratory needs to be certified for work with infectious material at a certain standard (you don't want the virus to spread to the people running the test). So while most hospitals have a rt-pcr thermocycler, there are only a handful of labs equipped with personal protection systems for working with live viruses and having the established protocols to avoid sample contamination etc.

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.

One thing others don't seem to have mentioned: While you can do this with any qPCR machine, you would not be allowed to actually use a random qPCR machine for medical testing. You need a special qPCR machine which is installed by the company, then run through a calibration procedure "certify-in-place" which is invalidated if the machine is moved. There is currently a waiting list to buy one of these machines (at least in the U.S.) and they are much more expensive than normal qPCR machines.

If it's so easy to build a website. Why doesn't everyone scale to the size of Google?

My guess: non trivial to do it safely and non trivial to get accuracy rates you'd get from a professional lab.

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.

Comparison is flawed.

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 mean if you transferred $500 billion to my bank account and said “clone Google” I would not get very far.

You might not, but many of us are capable to developing the systems and features that are core to google's business, and for any parts we don't know, we know where to find the people we need.

But why do you assume that someone like you rather than someone like me is in charge here? Statistically there are orders of magnitude more mes than yous. And empirically, it seems as though the people in charge right now are even more catastrophically incompetent than anyone thought.

Hire the right people with all that money and you could.

I wouldn’t be able to evaluate people well enough to hire the right ones.

That right there is the problem we face as a nation, Mr President.

That doesn't take away from the point that there probably exists a non-zero number of people who could convert $500B into something of the scale of Google.

I’d be curious to the answer to that too. I can think of quite a few reasons, but I’m sure there are nuances that are completely unknown to me.

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?

It boils down to people, logistics, and efficiency:

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.

I appreciate what's going on at UW regarding this and realize that it must have been a huge amount of work to say the least. However, I'd like to point out that most of what you've described is related to the bureaucracy and paperwork of certified medical procedures. Under ordinary circumstances that's all well and good, but given the severity of the situation it seems like it would have been better to eliminate much of that at least a month ago. Put another way, combat medics don't let someone die just because they're short some official FDA approved widget.

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.

> 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.

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.

My calculation (1000 tests per day) left space for 12 controls per batch - is that not sufficient under the circumstances? Alternatively, at 500 tests per day (again, this is _per_ low-end machine!) you could run each sample twice in addition to the 12 controls. (And I would _never_ dismiss controls as an inefficiency, even the most trivial exploratory experiment is highly suspect without one.)

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.

You're saying a lot of things here that don't make any sense.

> 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.

I'm fairly certain that everything I said makes sense, so I'll try to clarify a bit.

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.)

If you're basing your sample throughput calculations on instrument throughput (1000/day), you're implicitly assuming that instrument run time is the limiting factor, and the rest of the operations can match it.

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 was attempting to illustrate the absurdity of the past month and a half by performing a back-of-the-envelope calculation, not provide a detailed business plan for launching a biotech startup. FFS

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.

What was described above wasn't "US Administrative Bureaucracy" so much as "this is how busy labs are run." It can be challenging to understand that if you're coming from a small research lab where QA/QC boils down to recalibrating when you feel like it, and sample records are maintained by transcribing loose paper into Excel.

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.

Then let's be about it. South korea did this, why can't we?

Supply chain issues, for one.

Eg. Not enough cotton swabs: https://www.politico.com/news/2020/03/16/coronavirus-testing...

Yeah, by a bit of absolutely terrible luck, the preferred swabs for this are produced by a factory in Lombardy, Italy. There are other manufacturers of swabs that could be used but they don't seem to have the production capacity.

Seriously? There are approximately 1 Billion cotton swabs in this country (U.S.). This is not the issue. The issue is gross federal gov't incompetence.

It's somewhat more nuanced than that. The currently approved swabs have limited availability, and indeed there are others (unapproved) that would work. However it seems you can't use just any - they have to consist of synthetic fiber, can't have a wooden shaft, and can't contain calcium alginate. This rules out many of the swabs that a healthcare facility might have on hand.

(https://khn.org/news/as-coronavirus-testing-gears-up-special...)

Indeed given many lives lie in the balance, shouldn't there be something like a bootcamp get smart people up to speed on this quickly?

I doubt it's the lab techs that are in short supply. It's probably the consumables and reagents that go into the test that are out of stock. Lab procedures scale pretty well (to an extent - not the scale of the pandemic). Lab work is often feast or famine in terms of sample volume. During normal times, spikes usually just means the folks running the assays will be particularly busy.

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 one thing, the Qiagen kits are in short supply.

Which is why the FDA recently approved the Roche extraction kit, but honestly you don't even need a kit. (For example: https://primerdigital.com/rna.html)

This this this. YOU DO NOT NEED A KIT. You just don't. The kit is just basically a small tube of Trizol reagent that you can just buy by the ton, and oligos that you can order for overnight delivery, in a nice fancy package.

You don’t even need Trizol - us old school Molecular Biologists used phenol.

For something like snot you probably don’t need any extraction process beyond heating to 100C in buffer.

It is easy. S. Korea did it in about a week. The only reason it hasn't happened in the U.S. is incompetence and lack of leadership.

Not anyone can do the test, professionals are needed to administer it.

Ha ha. Professionals are needed to design it, test it, and validate it. All of which can be done in a day (or two or three to be fair). THe "professionals" who actually administer these types of tests at your average quest or labcorp testing center are not highly skilled workers. Most of their training involves how to fill out paperwork.

Edit: it seems the idea is to possibly catch asymptomatic people so they can self isolate (if they otherwise wouldn't) or tell their contacts to keep an eye out

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.

I’m not sure why your getting down voted. It is irresponsible.

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.

IANAL, but it seems like a grey area. He's not passing his test off as a "real" test, dispensing any medication, or otherwise acting as a doctor.

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?

Either this is a genius hack (saving lives) or a genius scam!

How does it save lives? If someone took this test and popped positive, would it increase the likelihood of receiving effective treatment or of reducing transmission? I'm trying to figure out the value.

If the tests could be done on someone who is asymptomatic, then it could be hugely beneficial.

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 best case scenario for controlling this epidemic is containment through contract tracing. That means we find people who have it, figure out who they got and from and gave it to, and get those people to quarantine. This strategy is failing in the US due to insufficient testing.

We're past that stage. It's purely about flattening the curve so the health system can cope while protecting the the vulnerable.

The official statistics have a lag in them due to only showing confirmed cases.

You'd hope that someone with a positive test is more careful about isolating themselves and perhaps tells their contacts to do the same.

Besides, if you test someone and he tests negative, you should ideally keep him isolated for a few days and do the test again (cause he might have just caught the virus and be still below detection threshold). It seems impractical.

Depends on their accuracy. A positive illicit test will result in somewhat reduced transmission. A false negative in possibly significantly increased transmission.

Also depends on whether you're testing suspected cases or merely hypochondriacs.

It might reduce transmission if the patient chooses to self-isolate and otherwise would not have.

What's the point of getting a "bootleg" unofficial test -- why would you trust the results (positive or negative)?

You trust the Stanford whiz kid with access to the lab.

Perhaps we need an open source effort for this? The main obstacle is sample collection and safety handling. given however the demand for testing, maybe a group of scientists could come up with specifications for ad hoc sample testing centers and perhaps recommend best practices and off the shelf products to minimize the risk. There are tons of graduate students who could volunteer and lots of unused pcr machines. It would be far better to organize these bootleggers as an open community sharing their standards rather than each person doing their own setup.

People seem to be caught up in a frenzy of the importance of PCR testing.

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.

I am buying a used RT-PCR machine for that, will get it home in the next few days. I have an account at Sigma-Aldrich as a hobbyist researcher, so I can order primers and other reagents.

Kudos! Several dozen US labs in the US claimed similar capability in January. But ponderous accuracy certification from the FDA kept them unofficial until March.

Also this probably doesnt scale well to the thousands per day states need now.

Hmmm I swear I heard a story about a Stanford student doing bogus blood tests before ... can't remember where though.

Please tell us about the time you most successfully hacked some (non-computer) system to your advantage?

Can we trust "Stanford Students" with medical tests? The school has a history of encouraging bad behavior in this area, as well as a history of letting people bribe athletic coaches to gain entrance.

I would not trust this organization. They're tainted.

Elizabeth Holmes 2.0?

> according to GroupMe messages obtained by FoHo

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.

GroupMe is still extensively used at universities. I only know a few undergrads who prefer to use it, but most seem to use it as a compromise. I personally hate its UI.

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