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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.qiag

• voldacar 7y ago
  Would this be easy to do yourself if you were able to find (or make) a PCR machine?
  • mjfl 7y ago
    You would also need a microcentrifuge and pipettes and stuff, but yes.
    • gravelc 7y ago
      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.
      • copperx 7y ago
        Why is that? Is it really impossible to do the test on a simple PCR machine, or is it just too slow?
        • gravelc 7y ago
          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).
      • mjfl 7y ago
        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.
      • jevinskie 7y ago
        I saw a whole kit including laptop, software, and license for $3,500 buy-it-now on eBay last week.
      • hcknwscommenter 7y ago
        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.
        • 7y ago
  • joshuamcginnis 7y ago
    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.
    • TheSpiceIsLife 7y ago
      Governments could open source all patents and design specifications for all relevant technology.
    • voldacar 7y ago
      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
      • subroutine 7y ago
        You need a set of pipettes, a thermal cycler (i.e. https://www.ebay.com/b/PCR-Thermal-Cyclers/185231/bn_115383501 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/ https://www.minipcr.com/products/p51-molecular-glow-lab/
        • voldacar 7y ago
          thanks so much, this will be a fun rabbit hole i think
  • asdff 7y ago
    You can make your own pcr machine with thermometers, 3 pots of water on your stove, and a stop watch
  • hcknwscommenter 7y ago
    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.
    • juuul 7y ago
      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.
• salemh 7y ago
  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-botched-its-coronavirus-testing/ 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?
  • jjeaff 7y ago
    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.
    • leereeves 7y ago
      As others have said, it's a huge problem if it leads people to think they're now immune to the coronavirus.
  • Symmetry 7y ago
    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.
• deleted 7y ago
  [deleted]
• gravelc 7y ago
  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....
  • jey 7y ago
    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?
    • gravelc 7y ago
      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.
    • danarlow 7y ago
      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.)
  • mullingitover 7y ago
    > 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.
• foobaw 7y ago
  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.
  • lordnacho 7y ago
    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.
    • kolinko 7y ago
      As someone who had experience in both - PCR is similar, if not simpler to setting up NN. You just need equipment.
      • omar_a1 7y ago
        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.)
• rllin 7y ago
  it's a specialized swab shortage
• downshun 7y ago
  You ruined the Clickbait \s 100+ disappointments
• puzzlingcaptcha 7y ago
  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-panel-primer-probes.pdf https://www.cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-p...
  • hcknwscommenter 7y ago
    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.
• buboard 7y ago
  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
• chippy 7y ago
  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"
  • buboard 7y ago
    no it isn't . there are lot of research labs that can do the test. the problem is safety, not the test itself.
    • jjoonathan 7y ago
      ...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.
      • buboard 7y ago
        risk tolerance changes in times of crisis though
        • LanceH 7y ago
          Statutes of limitation run past the crisis when the lawsuits phrased, "you should have known" come out.
          • Balgair 7y ago
            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.
  • archi42 7y ago
    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.
• duchenne 7y ago
  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.
  • _delirium 7y ago
    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.
• Tepix 7y ago
  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?
• superpermutat0r 7y ago
  > 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.
  • est31 7y ago
    > 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-Wir-brauchen-Abkuerzungen-bei-der-Impfstoffzulassung,podcastcoronavirus140.html https://www.ndr.de/nachrichten/info/16-Coronavirus-Update-Wi... [1]: https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.3.2000045 https://www.eurosurveillance.org/content/10.2807/1560-7917.E...