Creating an open-source detection method for SARS CoV-2

Neither diagnosis of cases of SARS-CoV-2 nor detection of environmental contamination by the virus are yet simple. Complicated techniques of molecular amplification, requiring serious infrastructure and biosafety procedures, limit people everywhere from knowing whether the virus is really in their environment or not.

The 'Do-It-Together SARS CoV-2 Detective' project (more info here) will develop a strategy similar to that used for the ‘GMO Detective’ method, in order to detect the virus causing Covid-19. Done not only without complicated equipment but with a simple +/- readout, the #CoronaDetective is predicted to be very specific. Furthermore, controls to ensure sensitive detection, without false positives or negatives, are intrinsic to this solution. The final product, strips of tubes with dry reagents, could be readily supplied anywhere, without cold-chain dependence; and monitoring tests could be run by ordinary people, without any background in medicine or biology, just some ability to follow simple instructions and common sense. In the future the project will try 'multiplexed' fluorescent detection, using an inexpensive (even DIY) detector, but with a partner project (Slack #proj-neb-lamp-test), would also be glad to find out whether a simpler color change reaction will be sufficient for valid results.

Human or clinical samples should only be run in settings with access to appropriate biosafety facilities, of course. This project is in full compliance with the OpenCovid-19 Initiative's Biosafety and Biosecurity Guidelines, and is fortunate to include appropriate labs for all levels of validation. Using openly available information, targeted regions of the virus have already been analysed, and one even shown to be identifiable by team members with such molecular techniques. Now we aim to optimise components and to make a validated method for anyone to use.

This project is part of the JOGL OpenCovid19 initiative which aims as a program is to collectively develop open-source and low-cost tools and methodologies that are safe and easy to use to fight the COVID-19 pandemic, and is being developed as part of the Covid19 Diagnostic and Detection Challenge. It was recently funded in first wave of grantees from the JOGL open peer review micro-grant system. Anyone can play a role!

Open participatory research, together, can help solve today's problems! Your help is welcome!

How to contribute

You can join us via this Slack channel: #proj-nucleic-acid-amplification of the JOGL Open Covid-19 Initiative. All this is being discussed in: #proj-nucleic-acid-amplification, and more widely in #chlg-detection-diagnostic. Related work is also being done on different methods of RNA extraction in: #proj-rna-extraction.

More work is being done on producing and testing open source versions of the required enzymes in #proj-enzyme-production #freegenes, which are related to : https://openbioeconomy.org/projects/open-enzyme-collections/ and https://biobricks.org/freegenes/

Ali Bektas, a collaborator from the Oakland Genomics Center in California is actively trying to package this all into a small cartridge see https://app.jogl.io/project/187. And others here also working on similar methods https://app.jogl.io/project/163. These two projects, were also funded in first wave of grantees from the JOGL open peer review micro-grant system