End-to-end system for rapid and sensitive early-detection of SARS-CoV-2 for resource-poor and field-test environments using a $51 lab-in-a-backpack

COVID-19 has exposed stark inequalities between resource-rich and resource-poor countries. International UN- and WHO-led efforts, such as COVAX, have provided SARS-CoV-2 vaccines but half of African countries have less than 2% vaccinated in their population, and only 15 have reached 10% by October 2021, further disadvantaging local economic recovery. Key for this implementation and preventing further mutation and spread is the frequency of voluntary [asymptomatic] testing. It is limited by expensive PCR and LAMP tests, uncomfortable probes deep in the throat or nose, and the availability of hardware to administer in remote locations. There is an urgent need for an inexpensive “end-to-end” system to deliver sensitive and reliable, non-invasive tests in resource-poor and field-test conditions. We introduce a non-invasive saliva-based LAMP colorimetric test kit and a $51 lab-in-a-backpack system that detects as few as 4 viral RNA copies per μL. It consists of eight chemicals, a thermometer, a thermos bottle, two micropipettes and a 1000–4000 rcf electronically operated centrifuge made from recycled computer hard drives (CentriDrive). The centrifuge includes a 3D-printed rotor and a 12 V rechargeable Li-ion battery, and its 12 V standard also allows wiring directly to automobile batteries, to enable field-use of this and other tests in low infrastructure settings. The test takes 90 minutes to process 6 samples and has reagent costs of $3.5 per sample. The non-invasive nature of saliva testing would allow higher penetration of testing and wider adoption of the test across cultures and settings (including refugee camps and disaster zones). The attached graphical procedure would make the test suitable for self-testing at home, performing it in the field, or in mobile testing centers by minimally trained staff.


Assay time for one sample and six samples
Our lab-in-backpack system can make a maximum of six samples at one time. The difference of assaying one sample and six sample is repeated protocol for adding regents and purifying the nuclei acid. The waiting time for incubation and evaporation and centrifugation are the same.

The hard drive centrifuge Recipe
The CentriDrive ( Fig S1) is a diagnostic 3D-printed hard drive centrifuge, at high rotational speeds of up to 10,000 RPM. Most importantly, at a cost of only $28 (See Appendix), this centrifuge is significantly cheaper than a standard centrifuge.

Procedure
Step 1: Opening the hard drive Using the T6 screwdriver, unscrew all T6 screws on the back of the hard drive, including one screw underneath the white label ( Fig S3). Once all screws have been removed, use a thin object to remove any glue between the edges. Then remove the back casing to expose the inside of the hard drive.
Step 2: Attaching the rotor Unscrew the T6 spindle screws located in the centre of the round spindle disk. The platter, spindle disk and actuator arm can now be removed as they are not needed ( Fig S4). Screw the 3D-printed centrifuge rotor onto the motor.
Step 3: Connecting the motor to the ESC This step involves the use of the soldering iron and the multimeter. Remove the green processor chip, revealing the motor with either three or four pins. Four-pin motors have three active pins and one common pin. To identify the common pin, measure the resistance between each pin using the multimeter (switch to the 200 Ω setting). The common pin (usually the farleft pin), will have half the resistance across it compared to the three active pins. Solder the three active pins to the three ESC motor pins.
Step 4: Setting up the CentriDrive By following the CentriDrive schematic shown in Fig S5, connect all the parts together using the appropriate pins (See Appendix) and breadboard wires. Finally, copy and paste the code provided (See Appendix) into the Arduino IDE software and upload it to the Geekcreit Nano via the USB input. Use the physical set-up in Fig S1 for reference.

Measurement of the Speed via IR Sensor
The CentriDrive uses an infrared (IR) sensor which operates as a digital tachometer to LED, onto a piece of metallic tape and receives the reflected light back using a photodiode (IR Receiver), at the frequency of the motor speed ( Fig S6).
[1] As part of the CentriDrive system, the IR sensor interacts with the Geekcreit Nano to measure the rotor rotation in revolutions per minute (RPM), displaying the speed on an inbuilt LCD. Similar to the way an encoder operates, the Geekcreit Nano records the time between each received IR ray collected by the IR sensor. The Geekcreit Nano then takes the reciprocal of this measure to obtain revolutions per second (RPS) and then multiplies that value by 60 to get RPM. Speed data was collected by the IR sensor, processed by the Geekcreit Nano and displayed on the LCD. However, the speed of the rotor could also be displayed directly using the Arduinos integrated development environment (IDE). This data could then be exported from the IDE to a spreadsheet (Excel) and filtered to only show speed values at specific intervals.
A 15-minute centrifuge maximum speed test was conducted at least three times to obtain 3 different data sets. Once the centrifuge was turned on, the potentiometer was turned to full and as soon as the centrifuge hits its maximum speed, it was timed for 15 minutes to investigate its consistency. An average was taken across all three data sets to obtain fifteen individual speed values and plotted on a graph of Speed (RPM) against Time (minutes) at 1-minute intervals. The results showed that the centrifuge did not go below its maximum speed during each 15-minute test, hence proving the consistency of the CentriDrive.
3. The consistency of the CentriDrive speed. Fig S7. Relationship between the CentriDrive speed and running time. The tests carried out with an attached rotor containing three water-filled microfuge tubes. Once the centrifuge was turned on, the potentiometer was turned to full and as soon as the centrifuge his its maximum speed, it was timed for 15 minutes to investigate its consistency. The error bar is within the size of the symbols.  Fig S11. The $51 lab-in-a-backpack system pictured in a small backpack, fitting the CentriDrive centrifuge, a 1000 cm 3 cooler/freezer box for reagents under the centrifuge, a thermos, digital thermometer, two pipettes, and room for additional storage (ruler for scale).