The Official Coronavirus Discussion

[harryklippton]

In addition to working at a university, I've been taking welding classes there part time for almost the last year. I don't have any idea how they expect us to do that remotely. I feel bad for the other guys in the class who are paying for it and/or expect to get a job in a few months.

[lars]

This is so incredibly ironic and fitting to a discussion about COVID-19:

[somnif]

I've been seeing a lot people asking "How are celebrities getting tested when there are no tests available?!?!" and going off on conspiracy theories, so I thought I'd offer an some info of how the test works.

Short answer, you can order the test supplies from any decent biotech supplier, provided you have the money and equipment. Let me explain.

Currently, the way the virus is detected in people is via RT-PCR. This stands for "Reverse transcriptase - Polymerase chain reaction". PCR is how we make copies of DNA, you make a tiny bit of DNA that "targets" the section you want to copy (these targeting bits are called Primers), mix them with DNA Polymerase (an enzyme that makes DNA) and the stuff it needs to work (nucleotides and buffers), and the piece of DNA you're building from (called the template). You then place this mix in a machine (thermocycler) that cycles the reaction so it happens over and over and over, and after a few hours, you have thousands if not millions of copies of your piece of DNA.

Now SARS-CoV-2 is an RNA virus, no DNA to work from, so we have to add a second enzyme called Reverse Transcriptase. This makes a DNA copy of the RNA that our normal PCR mix can work on. Our template is a sample from the patient, a sputum sample (deep cough phlegm), sinus swab, and/or throat swab.

The Enzyme mix is easy, you can order it in bulk, about a thousand bucks for 100 reactions worth. The machinery is also easy but not cheap, a decent thermocycler will run you several thousand dollars (though I'm seeing them on ebay as low as 250$). Honestly the only really tricky bit is designing those Primers so that they will only target a specific bit of genetic material only found in the SARS virus.

But, those primers? The design of them is publicly available. https://meridianlifescience.com/primers-and-probes-described-by-who Right there, all the sequences as approved by the WHO you'd need to ID the virus. You can order them from a dozen places on the web and get them overnighted. Pretty cheap honestly, a few hundred reactions worth of primer is about 10$ (plus shipping). You need 2 primers per reaction, and you'd probably want to check several genes at once just for verification sake, but still not terrible.

So you swab the patient, concentrate down the material, add it to your enzyme and primer mix, and put it in the machine. Come back in 3-4 hours, and then visualize the results (this is done by running the sample on a slab of gel, takes about an hour). It does take some skill, but any benchmonkey with a few hours training can do this. I've taught undergrads to run PCRs in a 3 hour lab and gotten good results, the underlying technology may be amazing but the hands-on work is drudgery.

Now, what we don't currently have here in the US is a government approved, all-in-one boxed up kit to send out to hospitals and doctors for this (or at least, very limited supplies). This is the stumbling block for large scale testing. But the fact that private doctors are getting tests run isn't some great conspiracy, it's just DIY. I've seen that Bill Gates is trying to fund an "At Home" test to be sent out in bulk, but that is literally just the swab. Samples are collected and sent off to labs to be run just like normal.

I do agree our government is being rather.... incompetent with its handling of this situation, but I prefer to think of it as a case of Hanlon's Razor. Don't ascribe to malice that which is adequately described by stupidity. Maybe I'm being naive, but god knows I need something to keep me sane.


(Oh and if you're curious, the Probes with FAM---BBQ on that primer page are for use with a somewhat more advanced version of PCR that lets you get results in real-time, and lets you know how much template you started with, which requires more expensive materials, more expensive machinery, and more expertise to run. My description was for the simple set up)

[Bio77]

Somnif:  I am a scientist at a biotech company.  We have developed  a few in-vitro diagnostic tests, not for Covid-19, but in general.   You are right, the principal of the test are simple.  In fact, we ordered the primers and supplies for Covid-19 a few days ago, just so we can test ourselves if need be.  The trick is to validate the test and prove that it is giving accurate results.  This is what is required to have an FDA registered test, and it is cumbersome.  For example, the swabs you are describing are not FDA approved for OTC test. This regulation is typically a good thing.  It keeps the claims and performance of a test in check. 

A work around to an FDA registered test is a lab developed test (LDT). The law is such that a hospital can run their own LDT, but only for their patients.  They would not be able to market the test outside of their hospital, although there are ways to bend this rule.  The tests you are talking about are most likely this and not a conspiracy.  The system is designed to protect people from bad tests (i.e., false positive and  false negative results), however, in crisis the system is not nimble. 

The bigger problem with our system is the dependance on industry to do these things.  There isn't a profit incentive (unless you are a celebrity and willing to pay) for companies to make these type of public heath tests and go through all the FDA hoops.  The CDC is supposed to be able to pick up this slack, amongst their other responsibilities, but their version of the test didn't work as expected.  In my opinion, todays announcement was basically, that the US is willing to pay Quest to do tests and not scrutinize the accuracy (or protect them from liability, I'm not sure how emergency authorization works exactly).   

[davent]

I've read a couple times in newspapers here in Ontario Canada that more of our population of 14.5 million have been tested for the virus than the number of people tested in all of the US at this point in time, 10  hours ago the published number of positives  was 79.
dave

[somnif]

This regulation is typically a good thing.  It keeps the claims and performance of a test in check. 

You're absolutely right, I was just commenting as I've been seeing people getting legitimately angry in my town that our Basketball players were getting tested while nurses were not. Commenting on the "how" of people could get tested, rather than the logistical hurdles.

I wholeheartedly agree that testing is important (I did a semester long project on Thalidomide at one point, waiting for better data is awesome). But the fact a few people are doing a run around doesn't mean the government is "holding out on us" as I've heard said. Just means some people are willing to brute force the issue for self-quarantine purposes.

[EBK]

Once everything calms down again, can we all converge on Tennessee with our musical gear and celebrate with a Beanstock (Beanstalk?) festival? 

[EBK]

2nd positive test result in my city.  Local emergency declared.

[matmosphere]

So, being an expat at the moment I'm curious about honest opinions how things are going in the states. From the outside looking in it seems like things are going a little cuckoo, but i suspect that isn't really the case. Just curious.

Where I'm at schools have been closed, large events cancelled, they're locking down the borders and asking people to not travel within the country. But there are only a handful of confirmed cases. The locals seem to be handling things well. Everyone seems to be at ease and I think people thought I was crazy to be stocking up on food and stuff whatnot.

I imagine it's not to different there, just checking

[thesmokingman]

I'm troubled that there's been a run on literally everything BUT the beer/wine aisle ... if this is the end times or you're stuck at home with your kids until the 30th like me you only have so long before Lloyd is serving you imaginary drinks at the bar

[Scruffie]

I'm troubled that there's been a run on literally everything BUT the beer/wine aisle ... if this is the end times or you're stuck at home with your kids until the 30th like me you only have so long before Lloyd is serving you imaginary drinks at the bar

What do you mean, imaginary, I was just talking to my 'pal Grady here about some people that need to be... corrected.

[somnif]

Welp, tis official, my university is telling students to not come back after spring break, all classes moving to Online through the end of the semester. They're giving dorm dwellers 3 days to either collect their stuff and move out, or provide proof they have nowhere else to go and get permission to stay on campus.

Wheeee. Probably means I'm going to be doing 72 students worth of plate culturing so they have enough data to do their term projects on. (Unless we just decided to fake it and make up data for them, director is still undecided on the matter)

[CodeMonk]

21 cases reported in Nevada, with 9 in my area, Washoe County (Reno area).
I know of at least one casino closing. Don't know about the rest of them, but i think its likely they will follow suit.
Casinos are a major source of tax revenue here and employee a massive amount of people.

Tesla, where I work is still operating. Several thousand people work there (I've been off on medical leave for a few months (unrelated to the virus).

[CodeMonk]

Went to Walmart to do my normal shopping and get some health related things.
They are now only open 6AM - 11PM.

And this is unrelated, but relevant.
I live practically a stones throw away from Hwy 80 (maybe not a stone, but could hit it with a BB gun).
Its a MAJOR trucking/shipping route.
Its been closed at the California/Nevada border for 2 days now due to a storm.

[EBK]

My agency announced yesterday that employees should telework to the extent possible until further notice, up to 80 hours per biweek.  Our buildings are closed to the public.  Daycare is still open for now.

Edit: daycare just closed.