Coronavirus testing project

profbraino

Hi All.

I have an idea for a public project, or at least an extended though exercise. Let's engineer a solution to address the need for hundreds of millions of tests for coronavirus and complimentary tests for antibodies that defeat the virus. You read this far, hear me out.

I was thinking that someplace like hackaday would have information on the well understood method to detect the virus itself,
https://hackaday.com/2020/03/24/coronavirus-testing-just-the-facts/
and/or would have links to new methods to detect the antibodies in a patient
https://www.sciencemag.org/news/2020/03/new-blood-tests-antibodies-could-show-true-scale-coronavirus-pandemic
which might contain a reprint of the new method
https://www.medrxiv.org/content/10.1101/2020.03.17.20037713v1
Incidentally, this last is just an example on a preprint server and has not been peer reviewed and might not be a valid solution, but you get the general idea.

These methods might be viewed as primarily process control. Most of the Parallax community has some experience with process control to varying degrees.

While most community member do not has expertise in all areas of, for example RT-qPCR (from the hackaday article), many will have expertise in at least one aspect of this process.

My thought is, since we’re all staying home anyway, why not start a distributed project build a home version of one of these?

A similar approach was applied to 3D printing, now everybody has one; laser cutting, most folks that have one are not blind; pick and place, folks that really want one can have one; and reflow soldering, (I think I recall folks were able to make something that does this with an oven). Now that we have all these technologies, can we try to combine them into a home brew virus test rig?

All we need to do is define and understand each step of the process, and identify an implementation of each process step. It changes from a medical problem to an engineering challenge. If we can fill in the blanks end to end, anybody can build one. Many of the Parallax community would be the type to give it a try. If only one succeeds, we still all succeed. Most of the community has spare Props, Arduinos, Raspberry Pi’s, 3D printers, and toaster ovens. Why not put them to good use?

Clearly, I have too much time on my hands.

Would this be of interest to anyone?

Cheers!

JD

I was thinking the same thing over the past couple days. There is a "signature" that this virus has, everything does. That being the case, there could be a digital fingerprint created from that information that could be used to test against.

I saw some Arduino respirator creations used in the hospitals the other day on the news, which got me thinking about this idea. Seriously, it was breadboards and project boxes next to patients, so the idea that everyday builders could create a device that is used in real life applications is not far off. Hospitals are looking for any help they can get. I have to admit, the medical field is not a specialty of mine by far; I agree with you in that, there are plenty of absurdly smart people on here, that we if we pooled together ideas, we might find a option.

I do see a hurdle that could be hard to overcome. Blood samples can last up to 3 weeks, which isn’t great time frame for each sample. Do we know anyone that could give a sample that is positive for COVID-19? If I’m not mistaken, those patients are hard to get to these days and I don’t think a hospital will give us any samples. Humorously, I can imagine someone going up and asking, “Hey, do you have any COVID-19 positive samples I could get?”. I believe that would create more questions than assistance.

I did find a couple articles about DIY COVID-19 tests and the CDC isn't very helpful (no fault of theirs, it's still new) on what they are actually looking for during testing. Simply saying "There are laboratory tests that can identify the virus that causes COVID-19 in respiratory specimens. State and local public health departments have received tests from CDC while medical providers are getting tests developed by commercial manufacturers." and "Limited information is available to characterize the spectrum of clinical illness associated with coronavirus disease 2019 (COVID-19). No vaccine or specific treatment for COVID-19 is available; care is supportive. The CDC clinical criteria for considering testing for COVID-19 have been developed based on what is known about COVID-19 and are subject to change as additional information becomes available."

Getting information about what to test for in sample, and a valid sample to test against is really the first hurdle. After that, we need a person/s who is/are positive until development is completed. The CDC has us at a real advantage in this area, they have a lot of patients to continuously to run tests on. The hobbyist community might be the last to be "served" this information unless it's leaked. Perhaps there is someone on here who could help get, or provide information on what to test for.

Since we all have time on our hands, we could spend it in worse ways than trying to find ways to help. I like your “out-of-the-box” thinking

pmrobert

A very early step is using PCR with very specific primers to identify and replicate enough very specific genetic material from the sample to be able to proceed further. The PCR procedure does require very specific temperatures and times to work. Microcontrollers are used very heavily in these devices. Take a look at this: https://en.wikipedia.org/wiki/Polymerase_chain_reaction

JD

pmrobert wrote: »

A very early step is using PCR with very specific primers to identify and replicate enough very specific genetic material from the sample to be able to proceed further. The PCR procedure does require very specific temperatures and times to work. Microcontrollers are used very heavily in these devices. Take a look at this: https://en.wikipedia.org/wiki/Polymerase_chain_reaction

Do you think that would extend the lifespan of the original sample past the 3 weeks or would it degrade the sample to quickly after replication? I read that there must be enough knowledge about the sample for PCR to work properly. If we're trying to recreate a COVID-19 sample, we would need to know what to look for to make sure it was being recreated. Though it does state that "The DNA used for PCR amplification can be partially degraded. As long as a few DNA molecules are intact between the two primers, amplification can occur."

Source: Polymerase Chain Reaction

pmrobert

The sample itself will last indefinitely when stored at very low temps- think liquid N2 temps. The procedure for producing the primers is dependent on RNA or DNA sequencing. That’s where you get the fingerprint but that’s a whole world in and of itself. There’s only four possible base pairs but there’s a LOT of those pairs on each nucleus acid molecule.

JD

Well that adds another level of complexity, keeping something so consistently cold is itself a challenge, even to get supplies to do it. It sounds like you have some background in this area, do you think it's possible?

pmrobert

Possible though likely not practical. Nothing's impossible as we in the Prop world know! My background in this is several microbiology/virology classes, classroom and lab, courtesy of a MS in biology. I was very much more in the clinical field but have a rough idea of how this stuff works. The really cold storage is for an indefinite storage time. There are commonly used freezers that don't require a regular Dewar bottle topoff. I'm not sure how long they would preserve a specimen but it's likely far longer than three weeks. See https://www.pro-lab-direct.com/category-s/1926.htm?gclid=CjwKCAjwvZv0BRA8EiwAD9T2VZc3-6_bQ0EoRQvuNlDS5zcrj0neNG73qefqt9fglNxw3wufcchYHBoCSusQAvD_BwE

JD

Agreed, all things are possible if enough effort is thrown at it. I was looking at the Dewar Flask for Extended-Time Storage, but those fridges are way better. Thanks for your specialized opinion about the project.

profbraino

Perhaps scope could be limited to testing (for the presence of the virus or antibody, and exclude cryogenic storage. Indefinite storage could be a a follow-on task, if we end up with something to store.

If we limit to two options: 1) detect virus, and 2) detect antibodies, these would be useful outcomes and narrow in scope.

1) Detect Virus seem like a logical start, as 2) detect Antibodies extends the process used to detect virus.

The main challenge seems to be a) defining the PCR reaction process, and b) defining the PCR reagents or consumables.

Simplistically, the process is:
1. prepare test vial
2. get sample
3. add reagent(s)
4. cook sample
5. attempt detection
6. destroy sample (if it has virus)

"Get sample" would be obtaining a q-tip cotton swab of saliva, etc

Thoughts?

pmrobert

I'm not being negative just realistic. I do have some classwork in the immunoassay realm and know several people well who work in this field. It's not easy or simple in any way. To detect antibodies: https://www.assaygenie.com/rapid-covid19-antibody-detection-tests-principles-and-methods and here's a link that accurately describes the process. https://academic.oup.com/labmed/article-pdf/32/3/142/24958149/labmed32-0142.pdf This is PhD level stuff guys.

pmrobert

I'm not being negative just realistic. Here's a decent description of a process for detecting viral load of HIV: https://academic.oup.com/labmed/article-pdf/32/3/142/24958149/labmed32-0142.pdf Here's a link to immunoassay methodology: https://www.assaygenie.com/rapid-covid19-antibody-detection-tests-principles-and-methods This is very complex, very difficult to replicate stuff that requires very specific conditions at every step. You screw up the temp curve while doing a PCR cook? You now have an expensive vial of random nonrecoverable nucleic and amino acids. I absolutely love and truly respect the desire you guys have. The DIY vent project is definitely doable. One thing that's missing from that so far in that thread is sensors - you need EtCO2, FiO2, SpO2, pressure and flow sensors, there's a bunch of stuff involved for even a rudimentary device in that realm.

profbraino

If it was easy, some high school kids would have done it already.
Thanks for the references, I'll give those a look.

JD

I found a forum where there is a contest going on for this very topic. It's on the Arduino's project site. If you are interested in pursuing the idea, might be worth looking into. Might just find additional people there willing to help and come up with something.

THE COVID-19 DETECT & PROTECT CHALLENGE