Comment by joshuamcginnis | Hacker News Reader

Comment by joshuamcginnis | Hacker News Reader

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Five days ago, it was reported that a German biotech company had already produced 4 million tests.[0]

"The tests use what’s called the polymerase chain reaction, a diagnostic method recommended by the WHO that amplifies the virus’s genetic code so it can be detected before the onset of symptoms. The kit comes with two vials: a primer to help detect an infection, and a synthetically engineered piece of the virus, which labs use to produce a surefire positive match to ensure their machines are working correctly. A lab technician combines these ingredients with a patient’s mucus sample—usually from a throat or nasal swab—and results are usually available in a few hours."

Coincidentally, I recently discovered the burgeoning biohacking scene in which many folks are already using affordable PCR thermocyclers in their home labs to do DNA amplification and crispr-cas experiments. I do fungal sequencing for phylogeny myself.

Given the simplicity of the testing process using PCR, why does it seem like the US is moving so slowly with getting tests in peoples hands? Is it the primer or control virus synthesis? Is it the manufacturing process? Is it red tape? If so, which specifically? Is it poor communication? Is it a confluence of factors?

Why isn't every local university or lab working together to at the least, copy the Germans protocol and get to work on manufacturing ASAP? Why isn't there a line of people outside these labs ready to drop-off their sample and get the results online? Where is the American version of the aforementioned biotech startup?

This epidemic and the general response has only reinforced my belief in the future of citizen science and the widespread accessibility of indie biohacking tools and methodologies. There are just too many misaligned incentives in pharma research, leaving huge gaps in the ability to bring new tests and drugs to the market. Look no further than the antibiotic resistant drug problem.

[0]https://www.msn.com/en-us/finance/companies/a-berlin-biotech...

As far as I can tell, and admittedly this is conjecture based on piecing together a bunch of off-hand comments by official spokespersons and a few industry insiders I talk to regularly, it's because the U.S. decided that everyone needs to use the same exact test. There is some validity to that approach in that it makes the data a lot better for comparison tracking. But, they compounded that somewhat defensible decision to require that everyone uses the same exact test kit. This turned into a disaster when the chosen supplier couldn't produce the reagents in the required time/amount.

This an aside, but this seems like a textbook example of government regulation of healthcare not only failing but getting in the way and actively causing harm. There are literally 1000s of generally certified labs that they could have said very early on "go to it if you have this certification" and instead they plodded through this top-down heavy handed mess and made this pandemic many times worse.

In the US you have this combination of heavy over-regulation and lack of public provisioning. It's like the worst of both combined. Between this, cannabis, ketamine, and the opioid crisis, I absolutely do not understand why there isn't an uproar over overregulation in healthcare getting in the way.

None of those generally certified labs have any clue how to develop a new test. Not even a test that is exactly the same as a test they already have. There are 1000's of them, because you need very little training to push some buttons and enter data into forms. Those generally certified labs did what they are supposed to do. They looked to the government for guidance on what to test and how. The gov't made many mistakes: disbanding of the CDC pandemic response team. Putting anti-science Pence in charge. Forming a CDC team that was heavy on science and management but light on epidemiology. Not following the WHO's lead on their already established and working test. Listening to pharma's explanation about what they will be able to do in 12-18 months and confusing that with a statement about what they can do now. These are all mistakes that didn't have to happen and happened because morons are in charge.

As others have mentioned, false negatives and false positives are both annoying problems. The standard diagnostic kit for example comes with a positive control, which frankly is absolutely essential. Synthesizing a primer is trivial, a positive control is not as trivial (especially if it's an RNA sample). It's also an RT PCR, which means it's extremely easy to contaminate samples among each other (so you can never be sure if even one of your samples actually has the virus whether ALL of the samples have it or not). Further, you can't trust regular gel results too much, you need a qRT-PCR cycler which most labs would have but probably not these hackers.

Also were talking about a virulent pathogen sample. Do you truly want to stand in line and collect random snot samples with covid virus without proper training and PPE?

There's no stopping anyone from getting the primers (small pieces of DNA) and doing a qPCR yourself. You'll also need reverse transcriptase (the RT, converts RNA->DNA) and a way to purify RNA from a mix of cells/spit/junk. These are all relatively inexpensive, standard molecular biology reagents. There are some shortages of RNA extraction kits, but a good molecular biologist can do without one.

What you might be missing is consistency, which is what the medical system is worried about. You want to avoid false negatives AND false positives when it really counts. Getting that consistency is where the regulations come in. Nowadays I think it's appropriate to relax them a little in the interest of the emergency.

It's going to be hard to get the assay working and trusting without a positive control though

Correct! Though making that template isn't that difficult either, you can order the DNA version and generate the RNA from that.

> Given the simplicity of the testing process using PCR, why does it seem like the US is moving so slowly with getting tests in peoples hands?

This has already happened in the US, with 1.5 million tests ready to ship, with emergency approval from the US government. In April they will be producing 5 million tests per week. https://ir.thermofisher.com/investors/news-and-events/news-r...

Ready to ship and April are much different than the countries who have been, and continue to test, upwards of 10Ks+ folks a day. As of today, the CDC is reporting only N=4225 completed tests in CDC labs and N=20907 in other US labs.

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