Re: [DIYbio] DIY COVID-19 PCR test

It's possible that I could provide an RNA standard that I have developed for the coronavirus (based on using MS2 phage as a cage for packaged, something called "Armoured RNA"). At the moment it is just the N gene, but I am planning to make for the Env gene as well (depending on what route the diagnostic herd goes). Just not sure how sharing works outside of the research community (or if I would be allowed to share it).

It would probably serve as a much better standard than just using plasmid and it is more stable than a plasmid too I think.

Michael

On Sunday, March 1, 2020 at 11:31:06 PM UTC, Reginald Smith wrote:

If you get these working let us know. It seems that it is a huge cocktail with the first two primer pairs (1-4) in the BioBasic kit being the ones originally developed and recommended by the Chinese government in late January, the last four (9-12) are two pairs from the WHO recommendations and (5-11) it is unclear where they are from (no Google matches). Maybe they developed independently at BioBasic using conserved genome regions. Interesting the CDC recommended primers aren't in there. I have seen so many different primer sets, some with huge overlap in the coronavirus family, that I am not sure if a gold standard is agreed upon yet. I'm sure they all work to some extent though.

Reggie

On Saturday, February 29, 2020 at 5:59:29 AM UTC-5, Derek wrote:

To be clear I am in no way advocating testing of possible infected individuals in a community lab setting.

My primary goal here is to do environmental testing. Right now there is a lot of fear around this virus and there is a high likelihood that it is not yet present in most of our communities. I fear by the time it is actually present that response fatigue will have set in and people will have become more lax in self-protection. With the long latency period, while virus is being shed, it is likely that sampling of public banisters, buses, etc. may show evidence of community spread of the virus prior to showing active cases in any particular area. This would be an indication of the need to take stronger self-protective measures or at least get an updated "go to the hospital and get tested if you're ill" message out there.

In terms of primers and evidence of their working, during the initial calibration of the test I expect will have to spread some of the positive control on surfaces in the lab and see if they can be picked up, sensitivity, etc.

In terms of safety considerations, I think that this is helpful to public safety and the safety of individuals involved in the effort. Since we are discussing sampling of public spaces that are generally presumed safe, or at least safe pending mitigation such as frequent hand washing, it would seem that no additional safety risk is presented. And the act of sampling itself increases awareness of the possible vectors for infection. If we included primers for something more common, rhinovirus for instance, that we could expect to see in many places it would further the awareness of which surfaces tend to promote contagion.

It would be great if there were a test that people could do at home if they felt that they were infected, but as noted above that could have nothing to do with infected individuals or their samples entering a community lab. One approach that is promising is the dipstick-based isothermal amplification approach coming out of the Zhang lab. https://www.broadinstitute.org/files/publications/special/COVID-19%20detection%20(updated).pdf

In terms of links, I am collecting others and will update but here are a couple of the sources I mentioned:

https://www.biobasic.com/coronavirus-covid-19-primers/

https://www.molecularcloud.org/How-to-detect-the-2019-novel-coronavirus.html

https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-detection-instructions.html

and a couple different kit approaches:

https://www.idtdna.com/pages/landing/coronavirus-research-reagents

https://www.sciencellonline.com/PS/7038.pdf

Derek

On Saturday, 29 February 2020 00:20:49 UTC-8, Thomas Landrain wrote:

I think we all agree on not transforming DIYbio labs into local diagnosis medical labs for contagious diseases. Way too dangerous and irresponsible :/

However, I'm seeing an opportunity for this community to perform "safe" research projects to develop cheap and easily implementable methodologies to detect the presence of the virus. Such as the one proposed by Derek where he uses a small piece of its DNA sequence. 

The approach would be the same as for the open insuline project, the research can be done safely, but the implementation has to be done in a controlled environment which cannot obviously be DIY labs. The goal is to obtain scientific and technological commons that can be used and improved by the global community, medical scientists and international health organizations included. 

BioCurious, OpenCell and Derek's pioneering efforts in trying to contribute to understanding and fighting Covid-19 need to be continued and this crisis is an important opportunity to mobilize safely our community around it. 

Thomas 

On 29 Feb 2020 at 08:23 +0100, Jonathan Cline <jnc...@gmail.com>, wrote:

This is a terrible idea.  No one in a DIY community should be actively going within 50' of someone who wants a covid swab test.  This is a highly contagious virus.  It is not something you want to do for the LoL's or the rep's.  The first medical doctor (and others, probably) who treated patients in China is now dead himself.  It is not something you want to do in a community environment, where, once you are infected from the DIY patient solicitations, you also infect others in the ad hoc unprotected community lab, since you may not show outward symptoms for a week or more.  Do some critical thinking, eh?   This is not the DIY project you are looking for.

On Friday, February 28, 2020 at 4:20:57 PM UTC-8, Thomas Landrain wrote:

Hi there from Paris, France,

Great initiative! 

I'd love to help organize a community of contributors aiming to design a DIY 2019-nCoV diagnosis test. I'm a biologist myself

... 

I also believe we should start organizing our DIYbio community around this very goal and research various ways to provide DIY/cheap 2019-nCoV testing abilities and methodologies that are well documented and that can be reviewed by the international community too. 

Let me know if you like this idea and if yes, we can start documenting the projects on JOGL and mobilize people around them. 

-- 

## Jonathan Cline

## jcl...@ieee.org

## Mobile: +1-805-617-0223

########################

 

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