Increase CoVid-19 testing capacity to >10K/day

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Demonstrate a CoVid-19 testing rate of >10K tests/day using lab automation infrastructure.

The UK and Europe have a COVID crisis with cases increasing exponentially. At opencell we will deploy a testing system that uses liquid handling robots and molecular assays in order to increase testing capacity to >10K/day in 2 weeks. 

The Situation
We are facing a once in a century global pandemic. We have more world wars than pandemic case studies. We need to act quickly and efficiently to limit public harm. At the current exponential growth rate we will be seeing a daily increase of 1,000-10,000 infected people by the end of the month. The health service does not have the ability to complete that volume of testing. Testing is one way to reduce pressure on healthcare systems and to ensure that those infected undertake appropriate isolation procedures. 

Our Plan
We will be creating this groundbreaking work from OpenTrons. They describe an automated and scalable approach to massively increase sample testing by >10K/day per lab unit. By completing this rapid scale up we will be capable of guiding other lab facilities on adding this capability. 

The process and experiment
The process involves a core procedure: reverse transcription polymerase chain reaction (RT-qPCR), which acts to amplify a section of  DNA (or RNA) molecules in a sample to a measurable level and complete a quantitative read out optically.
At opencell, as well as the core lab infrastructure for micro/molecular bio, we have 2 x 96 well qPCR units. To perform the qPCR we would need to complete a sample collection, perform preparation steps and finally undertake the measurement. 
First, we swab a cheek (or send a prepaid envelope with a swab) and place it in a viral inactivation buffer. 
Second, we prepare the sample for RNA extraction and this is where the opentrons liquid handling unit enters. The effort of doing one measurement is the same effort to do 96 (+~10%). We have been donated 2 OT2 liquid handling units (from the wondrous OpenTrons Team!) and could access a further unit. 
Third we remove the RNA from solution using magnetic beads. The RNA attaches to these beads and then we resuspend in wash buffers and finally elute. Again this is something best done in bulk using the OpenTrons. 
Finally we take our eluted RNA and prepare by mixing with the qPCR reagents and place in a compatible 96 well plate. Again, go robot go. 
The qPCR can give a valid output in as little as an hour and the total process flow could take as little as 5 hours. The system will complete 400-500 runs in a day if operated at maximum load. 
By optimally configuring layout, adding additional robotic units and providing sufficient caffeinated beverages we could then scale to >10K runs/day by replicating the system 20 times.

This is a technically challenging project requiring substantial support in the lab, locally along with remote expert guidance. We may additionally need to be able to deliver this system to NHS facilities using shipping container labs. We may need to advise policy makers on reducing current testing restrictions and support on this process is vital.

What YOU can help with?

We are facing a once in a century global pandemic. This challenge exceeds anything the NHS will be able to stomach  by itself. To reach our goal of testing 10.000 samples a day we need the help of a wide range of specialists and passionate people to help on the challenges below.

Do you think you can contribute to the challenge?
Email or fill in the form below.

Note suggestions and ideas have come from discussions or publications from Opentrons, Biohackspace London, BentoBio, Mammoth Bio, and JOGL. If we forgot to mention you sincerest apologies! 
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1) OpenTrons programming
We need all the help we can on planning/writing executing protocols (Python)

2) OpenTrons tools and add on expertise.
We would appreciate additional opentrons accessories like magnetic bead system, heating system and additional multichannel arms. 

3) Reagent suppliers
We need a range of reagent and consumables to complete this work. We are reaching out to all suppliers to request materials, discounts and any support possible in the areas of DNA/primers, PCR+other 96 well plates, kits/reagent/buffer for rtqPCR preparation.

4) Appropriate experimental controls
We need advice from existing facilities and labs that work with RNA to devise appropriate controls (for instance the IDT control resources).

5) qPCR and rtqPCR experience
We need help in running qPCR experiments, cross contamination and data analysis.

6) Molecular protocol design
What is the best protocol to run? We need people who can guide us in designing the best process. Standard kits? E.g., QIAamp viral RNA extraction Kit or maybe we need to think outside the box e.g., Mammoth.

7) RNA expertise
We need support in working with RNA and preventing cross contamination.

8) Data Science and Bioinformatics
We will have a LOT of data and we need help managing, securing, maintaining and mining that data. 

9) Privacy (Data)
Our preference is OPENDATA so that the whole world can benefit and we would need help on how that can be delivered alongside peoples right to privacy

10) Regulatory expertise
We will work ethically and legally at all times. This is an unprecedented crisis and we need help on knowing what the regulations are and if we need to give policy makers advice to suspend and/or adjust them temporarily. 

11) Patient Sampling
We need medical professional advice on how sampling might be achieved safely, ethically, legally, and REMOTELY to prevent additional spread. Current UKGov guidelines (and more guidelines). Could this be a mail order system? E.g., 23andme cheek swabs?

12) Patient support
Psychological, and emotional support needs to be put in place to help anyone planning to test, getting a test or awaiting a test result.