Re: [DIYbio] DIY COVID-19 PCR test

Hi Tyler,


I'm interested in talking with you on your data sharing platform, do you have a website with more information?  I too am working on software for citizen science to share and collaborate 

James

Sent from my iPhone

On Feb 29, 2020, at 9:05 PM, Tyler Quarton <tquarton@gmail.com> wrote:


Hi Maria,

I'm currently developing a platform that facilitates data sharing and collection for citizen scientists. I told my development team about this diy covid initiative and we are now working rapidly to get a minimally functioning prototype in hopes to create that centralized database for tracking. I'll keep the group in the loop as we move forward. 


On Friday, February 28, 2020 at 7:43:00 PM UTC-5, Maria Chavez wrote:
Hey Derek,

So I did a mental walk through of doing some RT PCR sort of testing but there are many big question for me.

-  what value does this give?  The two reasons for testing is to identify it for treatment and containment.  Community labs dont have the ability to treat or training in dealing with people with positive infections who might come in so it could make them a place highly likely to put the community lab members at risk, for epidemiology its needed to have central tracking so where does this data go to?
- are the primers any good? I know the WHO tests seem to the better ones, the CDC initial test was a multi disease test that didnt work right so they are in the midst of switching systems, and need to centralize where the data is kept for tracking of outbreaks.  
- What are the possibilities for safety considerations?

Overall I want to find ways for the DIY bio community to serve their communities during such times but I also want to make sure we keep ourselves and communities safe.  

Thoughts on this?

On Fri, Feb 28, 2020 at 9:19 AM Derek <der...@gmail.com> wrote:
Hey Tito,

Been doing some research on this. With the long incubation time I'd like to know when it's circulating in the community before cases are seen. Have found an rt-pcr protocol and located a company that will sell me a plasmid with part of the capsid envelope to use as a positive control. Biobasic has all the primers cheaply. Still working on a collection protocol to allow me to swab banisters, etc. A bunch of folks at the victoria makerspace are interested in helping so will eventually be documenting our steps. Happy to share any details.

Derek

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Re: [DIYbio] DIY COVID-19 PCR test

In my opinion the Zhang lab post is not great. It ignores everything that would actually make it clinically relevant (e.g. sample processing). It's completely unrealistic to give people the idea that you can just have a viral load high enough to do a SHERLOCK assay without any sample processing. And the sample processing is the most difficult part. Their intention seems to be just to get a little bit of PR.

There are many issues when dealing with the virus that need to be considered. The current testing is only around 40% accurate because the viral load from throat swabs is unreliable. Even then, you need to have a sample processing step before you do the RT-PCR. The next problem is scaling. Most laboratories are not equipped to perform thousands of tests in a day. In China, regular biology labs at universities are doing the testing and they couldn't do more than 2000 a day with 50 staff. This is because sample processing is done in a P3 biosafety setting. RT-qPCR is just not readily scaleable and there will also be massive problems when African countries have to try and test large portions of the population. The current mainstays (Roche and Abbott) can only perform around 1000 tests in an automated fashion in a shift and they are dependent on their own reagents.

When trying to do community led research it needs to be planned out. Adding a bit of plasmid to a lab bench and then seeing if you can amplify it ignores many of the aspects of the virus that make it clinically relevant. What's a relevant concentration? How does DNA plasmid compare to an RNA virus? How stable is DNA compared to RNA? How do you know how many copies you're adding to the lab bench (260/280 is horribly unreliable when determining copy number)? What are really the questions that you would like to answer and how would they make a difference?

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