Open Science: tackling Corona virus head on

Accurate affordable testing is crucial for lifting the burden of the SARS-CoV-2 virus and associated CoViD-19 disease from our communities, and economies.

With testing you can find the virus. And with contact tracing you can allow people to effectively quarantine themselves, breaking the chain of infections and stopping the spread. With no new hosts the virus will quickly disappear from your communities.

So accurate affordable testing is crucial.

Proprietary

Most groups of people find themselves in companies which often need investment to perform R&D (research & development), manufacture and sell their product.

Investment driven companies need to make a profit, and often a large one. This is not bad, it’s just the way it is.

Aiming to make a large profit is an inherent property of investment. Investors take risks: some of the companies they invest in fail. The more companies that fail, the more money investors loose and the higher the profit margin those other investments need to return to the investors. Otherwise the investors go broke and stop being investors. It’s a pretty self selecting process and at its core is risk and need for profit.

Open-source

As in software, every once in a while a group of people come along who develop an idea into a robust technology. And then, for various fortuitous and noble reasons, release it for free. This is open-source at it’s best.

Technically patents are open-source too as they’re meant to document all the necessary components of an innovation and expire 20 years later, at which point they’re also free to copy. The time delay is justified by saying they need to recuperated the costs & risks they put into R&D. One of the problems with patents is that they often don’t include all the details, leaving important trade secrets undisclosed for years after the patent expires. This is not open-source.

Open-source SARS-CoV-2 testing

There are now three inspirational open-source projects, two of which I’ve been tremendously grateful to interact with the teams behind the technologies.

1. BOMB.bio Open-source RNA purification

A crucial step in testing for the virus often involves extracting viral RNA from the patient sample and purifying it to remove enzymes like RNases (that can destroy the viral RNA before you get a chance to measure it) and other contaminants (that can interfere with the process of measuring it by inhibiting the RT-PCR reactions).

Early on in this pandemic, members of the international BOMB.bio team in New Zealand quickly partnered with New Zealand’s largest diagnostic lab to produce an updated protocol suitable for extracting RNA from SARS-CoV-2. This is now being used by multiple labs all over the world. With improvements being made daily.

2. Crick Institute

The Crick institute put together and validated an automated protocol for SARS-CoV-2 detection along with all the well thought through standard operating procedures (SOPs) you need to run it.

3. OpenCell London

Finally, last but not least, OpenCell London started waving the flag earlier than *anyone else* I know.

As you can see I eventually caught up with them. And after they assembled a large international team of volunteers, together we have released their our (still getting used to that) paper on an open-source mobile testing lab in-a-shipping-container. Complete with all the code you need to run the RNA purification protocol and the setup and analysis steps.

All open-source. All free. Anyone one the planet can copy this code and experimental design, start improving it for us and everyone else.

This marks the end of the beginning of this journey. The path is long and I hope the proprietary companies can make sure we don’t have to travel much further along this road. In case they can’t, let’s stack the deck against this virus. Together we’ve made some important steps along that road to accurate affordable testing for as many people as possible.

Some of the other people who have directly helped so far

Catherine Moore and Rocio Martinez-Nunez have been sources of immense wisdom, shared it widely to help others, whilst also doing a heavy workload, and done so patiently, kindly, with dedication. We all owe you a big debt of gratitude.

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