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COVID-19 detectors, $300 Real Time PCR & $50 LAMP

Real Time PCR (qPCR), LAMP and thermal cycler (PCR) are essential tools for COVID-19 testing. We are making open source ones.

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2 married hackers in Tokyo developed PCR machine years ago, USD50 LAMP in a week of April 2020 and now developing qPCR with helps from worldwide. Everything is opened under GPLv3 and parts price is less than USD300. Commercial qPCR machine used at COVID-19 testing costs USD20,000 to 200,000. COVID-19 detection test with Ninja qPCR PoC (Proof of Concept) and synthetic gene of unique sequence of virus is scheduled in Sep 2020.

Real Time PCR (qPCR)LAMP (Loop-mediated isothermal amplification) and thermal cycler (PCR) machines are essential tools used for COVID-19 testing.

This is my 20 minutes presentation at Virtually Maker Faire 2020 on May23. This article is updated on Aug28. Latest updates are added to the bottom.

PCR is essential

After COVID-19 pandemic, "PCR" is well-known word as testing method but it's not only for COVID-19. That's biological technique to get enough copies of specific part of DNA to see with naked eyes or fluorescence light sensors. DNA is too small and we cannot observe any results without PCR process.

By changing reagents, PCR machine can be used for any kinds of DNA testing including Malaria (200M people infected, 400K killed every year), food allergen (200K people needs in US), Science education, criminal investigation, paternity test and so on.

You may heard about other testing method like immunochromatography and antibody test. Here's pros and cons of all methods and these technique cannot replace PCR.

  • Immunochromatography : Cheap (<USD10/disposable shot) but less sensitive than PCR. Need more volume of virus sample than PCR and cannot be used for patients in early stage of infection.
  • Antibody test : Cheap (<USD10/disposable shot) but for later stage. Antibody is produced inside body only after weeks people get infected. Mainly used to know you were infected before.
  • PCR (thermal cycler) : Cheap (Sales price of NinjaPCR is USD499/piece) but bothering post-processes including electrophoresis and illuminator.
  • qPCR (Real Time PCR) : No need of post-process but expensive (Commercial one costs USD20K-200K). Mainly used for medical PCR testing now.
  • LAMP : Cheap (Parts price of NinjaLAMP is USD50/piece), fast and easy but not widely approved for medical diagnosis because it's latest technique. Hope it will be changed soon.

Why NinjaPCR

PCR can be done simply by changing temperature of plastic tubes reagents and samples in using heat elements like peltier, heater and fan. So there're already several kinds of open source PCR machines. But almost all of them (tell me if you know any exception) are not precise because they use thermistor value on heater or aluminium tube holder as the temperature of samples inside plastic tube. NinjaPCR is only one open source PCR machine with thermal simulation model.

Here's the result. Red line is output of our simulation and blue line is measured temperature inside tubes. NinjaPCR supports 16 PCR tubes (Single tube projects are not practical because they cannot compare results with poisitive/negative control). WiFi is also supported and you can use NinjaPCR with not only PC but iOS and Android. But this thermal simulation is most unique and important point we think because we failed some testing without this feature.

NinjaLAMP in Indonesia, New York, and more

This thermal simulation is imported into NinjaLAMP. LAMP is simpler than PCR and its parts price is only USD50. You can make your own NinjaLAMP by connecting Arduino, few resistors, MOSFET, heater to tube holder. We are sharing how to calibrate with any heaters and tube holders on GitHub.

NinjaLAMP is already manufactured in Indonesia by my friend Akbar, founder of LifePatch who is also a hacker and biologist. Just after he shared a paper about how to detect COVID-19 with LAMP method at the end of April, I started making Ninja LAMP and just a week later, it’s done! I shipped only core parts to him and he 3d printed these lovely pink enclosures. Ninja LAMP is really easy to extend and he added status LED.

Armen in Columbia University, New York made his own LAMP machine forked from Ninja LAMP adding LCD display. I heard that he successfully detected positive sample with it.

By COVID-19, so many papers are published by researchers but not all of them has access to required hardwares. Open...

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circuit_diagram.jpg

Circuit diagram of Ninja qPCR

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NinjaPCB_ver2.2-sch.jpeg

Circuit schematic of Ninja PCR

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NinjaPCB_ver2.2-brd.jpeg

Circuit layout of Ninja PCR

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schematic_lamp.png

Circuit schematic of Ninja LAMP

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layout_lamp.png

Circuit layout of Ninja LAMP

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  • 1 × Raspberry Pi as controller of Ninja qPCR
  • 1 × Arduino Micro as controller of Ninja LAMP
  • 1 × ESP WROOM-02 as controller of Ninja PCR

  • 1
    Assembly Instruction

    Ninja PCR BOM
    Please refer Support Site for detailed steps to build NinjaPCR from scratch.


    Ninja LAMP BOM
    Please refer GitHub for steps to build.

    Ninja qPCR
    It's still under development. We will share Bill of Materials and detailed assembly instructions like above links after we fix all 3D models and circuits.

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Discussions

Luke Gary wrote 10/21/2020 at 21:22 point

I am excited to see where this goes. I would take special care about low-noise design and proper shielding on the detector side of things, perhaps a modulated detection approach.

I have been designing real-time thermocyclers for about 6 years and the key factors here are the reagents and the dynamic range of the instrument for sure.

  Are you sure? yes | no

Bart wrote 09/20/2020 at 20:11 point

Hi shingo,

interesting product. I like that you want to provide scientific equipment to more people, but I  was wondering how you plan to provide the needed reagens, indeed the covid-19 primers but also the more general dNTPS, buffers etc.

Do you think it is feasible (and wise?) to provide these solutions in bulk to a mass of people of which a significant part not may not end up used or not used properly?

You would also need accurate pipette's (I believe these can also easily be a few hundred euro's) and some lab skill.

  Are you sure? yes | no

shingo wrote 09/24/2020 at 01:08 point

Hi Bart,

Wow your comment is best to come first. It's clearly unwise if cheap qPCR is provided to mass of people without skill right now only to give them fake relief or fake panic to make long line at testing sites to waste medical resources.

I think cheap qPCR is like Henry Ford's Model T in 1908. Where to get gas? Where to get driving skill? Who has responsibility for the accidents? Such discussions will never be happened without cheap car.


My suggestions:

1. Ninja qPCR should get FDA license as fast as possible to be used by doctors for diagnosis.

2. Establishment of new medical license for test site workers that can be acquired in shorter term.

3. Open source reagents without pipette at reasonable price at room temperature (Honestly I've been seeking how to achieve that for years. If you know some recipes, please share it here! I think freeze dry and such package are worth to try. https://lipitear.com/wp-content/uploads/2016/07/package-and-vials.jpg )

  Are you sure? yes | no

shingo wrote 08/27/2020 at 20:32 point

Ask me anything here or Facebook messenger
https://www.facebook.com/hisakawa

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