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Open source, BeagleBone-based diagnostics computer to add Covid-19 testing

Mar 17, 2020 — by Eric Brown — 1802 views

Chai is prepping a Coronavirus Environmental Testing Kit for its open source, BeagleBone-based Open qPCR system. The kit can test surfaces for Covid-19 from swab samples and return results within the hour.

BeagleBoard.org announced that it will be donating BeagleBone Black SBCs for Chai’s project to widely deploy a Covid-19 environmental test kit that will work on its BeagleBone-based Open qPCR computer. Launched on Kickstarter back in 2014, the Linux-driven OpenqPCR medical diagnostics computer enables relatively low-cost polymerase chain reaction (PCR) testing — a common technique for testing DNA sequences.



Open qPCR and software interface
(click images to enlarge)

As explained in a brief announcement by Adafruit about Chai’s presentation on its coronavirus kit at the Open Hardware Summit, the upcoming kit will use the primers and probe information recently released by the CDC for performing PCR tests for Covid-19, also known as the novel coronavirus. Chai’s test kit will use a “soon to be open sourced RNA extraction control system and internal amplification control system” to enable DIY researchers to test environmental surfaces, says Adafruit.

The Coronavirus kit can test swabs used on doorknobs, seats, phones, computers, and other hard surfaces. Results are available within the hour, including specifics on the quantity of the virus.

Inside the Open qPCR RNA extraction chamber, the virus is prepped and a fraction is sent to the RT -qPCR test. Here, the sample’s RNA is converted to DNA and then amplified for easier detection.


BeagleBone
Black

It’s unclear if the BeagleBoard.org’s BeagleBone donations are designed to discount the cost of the Open qPCR machines and test kits or simply to expand production of the systems. Considering that the BeagleBone costs only $60 and the Open qPCR costs $4,499 for the single-channel model and $6,499 for the dual-channel model, that won’t do much to reduce the cost of the system. However, the Open qPCR hardware and software are open source, and Chai will be open sourcing the RNA Extraction Control and Internal Amplification Control systems. The company is also soliciting public donations for the project.

Chai is encouraging hackerspaces and community labs to take the portable system out into the community to test surfaces. Chai is aiming at an end-user cost of $10 to $15 per test. The test kits are aimed primarily at public spaces like schools, libraries, senior systems, and other public institutions, but can also be used in offices and any other environment.

The Open qPCR system is used by thousands of customers for research, food safety, water quality, and pathogen detection. Comparable commercial qPCR test instruments cost $30K+, although part of that costs covers the cost of the medical certification processes required for use in hospitals, which Open qPCR does not possess.



Open qPCR internal detail view (left) and optical subystem
(click images to enlarge)

Both the single- and dual-channel versions of the Open qPCR contain heat blocks that hold 16 reaction wells for processing 100 or 200 uL tubes or strips. The heat block ramps between 0 and 100 degrees C at 5 C/s, allowing many PCR protocols to be completed in as little as 30 minutes. Each of the 16 wells has its own LED and photodiode detector.

An optical subsystem detects one spectral band for the single-channel model and two spectral bands for the dual-channel model. Both models can detect many green fluorophores like FAM in the 510-545 nm range. The dual-channel version can also detect HEX/VIC/JOE fluorophores in the 560-610 nm region.



Open qPCR detail view and legend
(click images to enlarge)

The Open qPCR’s BeagleBone mainboard controls a WiFi radio, Ethernet and USB ports, and a 5-inch capacitive touchscreen. The system’s REST-enabled web interface supports access from all major mobile and desktop platforms.

The 280 x 240 x 190mm, 4 kg box is portable, but can be battery powered only for low-power mode isothermal DNA detections using as little as 45W. The Open qPCR accepts 100-240V input and typically consumes 75W, with peak consumption of 350W. The 10 to 35°C tolerant system is fan cooled and features an innovative design that provides simultaneous heating and cooling of different components.

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The blog announcement and related video from BeagleBoard.org’s Jason Kridner includes other updates, such as upcoming collaborations with Seeed on a PocketBeagle Grove Kit and a Cape for the Machinekit community for building 3D printers and CNC machines. There’s also a collaboration with KiCAD to migrate the design of the new BeagleBone AI SBC from Allegro to KiCAD “so that people can use open source tools to edit the design and collaborate and help move that design forward.”




Jason Kridner’s YouTube video version of BeagleBoard.org’s blog update, including the Open qPCR Coronovirus kit

 
Further information

The Chai Coronavirus Environmental Test should be available soon. It’s unclear to what extent the Open qPCR systems and test kits might be discounted for public institutions if at all. More information may be found on Chai’s Coronavirus Environmental Testing page, where you can sign up for notifications on availability, as well as the Open qPCR product and shopping page.

The BeagleBoard blog announcement may be found here.

 

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