Portable Spectrum Devices to Detect COVID-19

Backround

• Near-infrared spectroscopy: Promising diagnostic tool for viral infections

[ref: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092872/ ]

Although several methods, including enzyme-linked immunosorbent assay, polymerase chain reaction, immunofluorescent assay, and Western blotting, have been used for the diagnosis of viral infections, none of them is ideal in terms of cost-effectiveness, speed, and accuracy. Currently, the rate of outbreak of emerging viruses is increasing and therefore the development and establishment of analytical methods for such viral infections are becoming more important. Near-infrared (NIR) spectroscopy is a fast, multicomponent assay that enables non-invasive, non-destructive analysis. Recently, the diagnosis of viral infections using NIR spectroscopy has been attempted.

[ref: https://phys.org/news/2017-11-nir-driven-h2-evolution-wavelength-range.html ]

• Recent developments and problems in the diagnosis of viral infections

Early and sensitive detection of viral infection is necessary for the maintenance of a safe blood supply, treatment of viral infections, and prevention of transmission. Several methods such as ELISA and PCR have been used for the detection of viruses from individuals during the pre-seroconversion window period. ELISA is commercially available, reliable, and specific. However, ELISA covers only a narrow range of virus antigens, and is time-consuming and expensive. PCR is sequence-specific. The sensitivity of PCR is several orders of magnitude higher than those of conventional serological tests. However, PCR may be not suitable for large-scale routine screening. To reduce the cost of PCR, pooled plasma has been used to screen large numbers of samples, but the pooling method reduces the sensitivity to the same level as that of ELISA.

To concentrate virus particles, ultracentrifugation has been used, but ultracentrifugation causes a high rate of false-positive results. Furthermore, a high rate of false-positive results and false-negative results due to the mismatch of the primers for subtypes of viruses has also been reported for the PCR method. Moreover, particular precautions are required to avoid cross-contamination in PCR analyses. Recently, multiplex PCR assays for viruses have been developed. That method is slightly improved in terms of cost-effectiveness and time, but does not address the other limitations of PCR. Thus, the development of an accurate, fast, and low-cost method for the diagnosis of viruses based on novel concepts is needed.

• COVID-19 Disease Testing; Utilising Fluorescence During a Pandemic

[ref: https://www.edinst.com/us/blog/covid-19-disease-testing-utilising-fluorescence-during-a-pandemic/ ]

While the world continues to endure loss and hardship due to the outbreak of COVID-19, caused by a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), researchers are scrambling to provide test kits that are accurate, fast, sensitive, and widely available, especially as symptoms vary broadly and may not appear for days if at all. To this end, several diagnostic methods have been designed and tested, and one USA FDA approved test kit utilises fluorescence based reverse transcript real-time polymerase chain reaction (rRT-PCR) technique. The rRT-PCR test works by detecting replicated nucleic acid copies from the SARS-CoV-2 virus through a bound fluorescence probe that is released from its quencher counterpart upon primer replication.

The rRT-PCR fluorescence generating process utilising a bound fluorescence and quencher pair of molecules as the probe for specific types of cDNA.

Once an appropriate specimen is taken from an individual’s respiratory system, the RNA is isolated and reverse transcribed into complementary DNA (cDNA), which then undergoes the PCR process to amplify the number of cDNA copies, with several sets of SARS-CoV-2 primer and probe detection targets. Incorporated into the probe detection sets are a pair of molecules that are bound in tandem as a fluorescence emitter and dark quencher (non-emissive); 5(6)-carboxyfluorescein (FAM) as the emitter, and Black Hole Quencher – 1 (BHQ1) as the dark quencher (Figure 2). When the PCR cycle reaches the extension phase, the Taq polymerase primer nuclease activity on the 5’ end ruptures the FAM from the BHQ-1 in the probe and its fluorescence is then measured as a function of each cycle, increasing in intensity for positive diagnoses.

FAM emission spectrum overlaid with the BHQ-1 absorption spectrum with their associated structures. Data obtained from BioSeach Technologies and AAT Bioquest. Molecular structures are from Sigma Aldrich (FAM) and ATDBio, Ltd. (BHQ-1).

Our design of NIR spectrum

• Objectives

Design and verify a fast and cheap method for near infrared spectroscopy detection for rapid diagnosis of COVID-19;Quickly (in seconds) detect the infrared spectral characteristics of the sample to be tested;Provide low-cost and fast detection infrared spectrum detection hardware products;Help anyone with conditional analysis of new coronavirus and other viruses to detect infrared spectrum characteristics;Provide tools for any infrared spectroscopy related researchers.

• COVID-19 detection

The current control of the spread of COVID-19 coronaviruses and the identification of infected persons are essential to restore the normal operation of the entire society. The method for detecting COVID-19 coronavirus is mainly PCR analysis. But these methods are either accurate but expensive and time-consuming, or fast but expensive and less reliable.The unique molecular structure of the virus determines its special spectral characteristics. We predict that based on the near-infrared spectroscopy technology, a swab secretion sample can be obtained through the nose or throat with a cotton swab, and then the COVID-19 detection can be analyzed by accurate, fast and economical infrared spectroscopy.The characteristics of NIR spectroscopy are accuracy, speed, and lower analysis cost, while not destroying or changing the characteristics of the sample. This can greatly improve the speed of COVID-19 virus detection and reduce the cost of COVID-19 virus detection. In addition, because of the ease of operation of near-infrared spectroscopy, it also makes COVID-19 virus detection operators safer.Near-infrared spectroscopy is a complex technique that can infer the basic composition of a substance from the absorption spectrum characteristics of a sample. The applied pulses of light energy penetrate its surface and cause molecular vibrations, scattering in all directions depending on the composition of the sample. Vibration corresponds to different molecular bonds and reactive groups of matter. The spectrum obtained in the near-infrared range is complex and requires application analysis through data processing.

A Bit of a Disclaimer

This device/project is only an attempt to detect Covid-19, providing an exploration idea! Used for precise medical diagnosis at your own risk.

The Electronics

• LDO SGM2036
  Input 1.6V~5.5V，
  output 3.3V

• AT25SF041
  Memory size 4Mbit
  Interface type SPI
  Package type SOIC
  Number of pins 8
  Minimum operating supply voltage 2.5 V
  Maximum operating supply voltage 3.6 V
  Dimensions 5.4 x 5.35 x 1.91mm
  Maximum random access time 8ns

• CB-M02-CH340G
  Convert from USB to TTL
  VCC 5.0V
  TX/RX/GND

• AS7263
  Using new manufacturing technology, the nano-light interference filter is directly attached to the CMOS silicon wafer with extreme precision. The interference filter technology used by this sensor has extremely high accuracy and stability. Infrared characteristics of near infrared spectrum 610nm, 680nm, 730nm, 760nm, 810nm and 860nm.
  For example, bulky laboratory-grade analytical equipment can now be replaced by convenient handheld devices. At the factory, the samples produced today have to be sent from the production line to the laboratory for chemical analysis. Future quality inspections can be completed on the production line by a new compact, robust optical spectrum analyzer based on multi-spectral sensors.

• CB-M01-BLE
  CB-M01 is a development board based on Nordic Bluetooth chip nRF52832, which supports Bluetooth Low Energy (BLE), and provides a hardware development platform for developers to help engineers quickly understand and learn the nRF52832 BLE features and realize the development work of the product prototype stage.
  This module realizes the transparent transmission of data from Bluetooth to the serial port. Signal pins include: VCC\GND\RX\TX.

Building the Device Step-By-Step

Here is a step-by-step walkthrough of how to build this project.

1. Circuit design

• AS7263
  Pin 8 I2C_ENB is pulled low.
  In this mode, pins 11/12 respectively represent RX/TX, which is in serial UART working mode;
  When pin 2 RESN is pulled high, the chip is in a normal working state.
  When RESN is pulled low, the chip enters the reset state and the system restarts.
  Communication with flash memory AT25SF041 through MOSI/MISO/SCK/CSN_EE using SPI bus;
  After the LDO voltage regulation, the power supply to VDD.
• AT25SF041
  Store the AS7263 firmware program, which can be burned offline and online, and the AS7263 Pin RESN should be pulled down during online burning, otherwise the chip will be burned.
• LDO-SGM2036
  In order to make the AS7263 work normally under a stable voltage, the LDO is used to stabilize the input voltage and supply power to the AS7263.

2. Overall hardware plan

Option One

• CB-M02-CH340G module:
  Through the CH340G module, the USB serial bus is converted to a TTL serial bus. The CH340G module supplies power to LDO and AS7263 through 5.0V. The RX/TX signal uses 3.3V level, which is connected to the RX/TX of AS7263.
• Power Supply:
  The entire AS7263 module is powered by a USB serial port, the maximum absorption current of the AS7263 is 5mA, and the typical operating current of the LED indicator is 4mA;When working, the host computer sends a UART serial command to the AS7263 through the USB serial port. The AS7263 returns the infrared spectrum detection result to the host computer through the USB serial port. At the same time, the initial state configuration of the AS7263 is also configured through the serial port command when it starts working.
• Host Computer:
  With USB, Device can be connected to PC or other systems with the operating system can be Ubuntu, windows10, or etc. UART driver is installed, programming is based by Python, the corresponding library is

import serial.tools.list_ports
import numpy as np

Option two

• Bluetooth module CB-M01-BLE:
  The module realizes the data transparent transmission function through Bluetooth and supports UART serial communication. Use the most popular BLE5.0 low power Bluetooth technology stack.At this time, the host computer can be a mobile phone and other mobile communication devices and any device equipped with a Bluetooth module.
  The host computer controls the AS7263 through the Bluetooth transparent transmission module to perform infrared detection. This solution can be powered by a rechargeable battery. It is a very simple and portable device that is suitable for daily use anytime and anywhere.
• Host computer:
  Through the wireless Bluetooth module, the device can be easily connected with Android phones, iPhone phones and other portable devices. The device does not need to install any drivers, it can directly transfer data to mobile phones and other portable devices.

3. Overall software solution

AS7263 configuration

• ATINTTIME :
  Set the integration time of the spectral sensor
  ATINTTIME=60, Integration time = <value> * ~2.8 ms
• ATGAIN :
  sets the gain of the spectral sensor channel
  ATGAIN=2, specific correspondence: 0=1X, 1=3.7X, 2=16X, 3=64X
• ATINTRVL :
  ATINTRVL=2, Set the sampling rate, every two cycles, sampling once

AS7263 control

• AT :
  serial communication test command.
  If the serial communication is normal, return OK
• ATTEMP :
  read the current temperature of the chip;
• ATBURST:
  sets the number of consecutive samples in burst mode
  ATBURST=10, continuous sampling 10 times

Host computer control

Option One

The host computer is connected to the spectrum sensor module through the USB serial bus. Taking the operation of the PC under Windows 10 as an example,

• Start a serial port and configure the baud rate and communication timeout time of the corresponding serial port communication;
• Configure AS7263 to make it enter the normal working state;
• Control AS7263, detect near infrared spectrum data;

serial.Serial("COM7", 115200, timeout=1) #open a serial port with bauterate=115200

result = ser.write(serialcmd.encode("ascii")) #send AT command to AS7263

resultcmd = ser.readline().decode("ascii").replace("\n", "") #read the result of AS7263 detection NIR

Option two

The host computer is connected to the spectrum sensor module through the Bluetooth module. Take the operation under the IOS system iphone as an example:

• Configure the serial communication parameters of the Bluetooth module;
• Start Bluetooth module realizes the transparent transmission of serial port UART communication data;
• send the serial port command directly;

4. Near infrared detection process

A transmission scheme is used to detect the absorption characteristics of the measured object to near infrared light. The specific process of detection is as follows:

• step1. Fix the light source to the set position.The spectrum emitted by the selected light source must have sufficient intensity in the near-infrared spectral range. In actual measurement, the mobile phone flash meets the requirements.
• step2. Fix the near-infrared spectrum detection device.The spectrum device is on the opposite side of the light source, and the light hole of the device directly faces the light source.
• step3. Select a set of standard utensils with good near-infrared light transmittance to prepare different samples.Considering the professionalism and danger of Covid-19 virus detection, we use different daily items to verify the feasibility of near infrared spectroscopy.
• step4. Establish a sample library of near infrared spectroscopy.Put different measured samples between the light source and the spectral sensor, record the original spectral data, and after data processing, generate a near-infrared spectral sample library.
• step5. Detect unknown test objects.Place the unknown test object between the light source and the spectral sensor, record the original spectral data, and after data processing, compare with the data in the infrared spectrum sample library to determine the type of the unknown test object.

5. Near infrared data processing

• step1. Background near infrared spectrum acquisition X0
• step2. The near-infrared spectrum collection of the measured object Xi
• step3. Subtract the background near-infrared spectrum from the near-infrared spectrum of the measured object to obtain the near-infrared spectrum absorption characteristic of the measured object, Yi=Xi-X0
• step4. Noise judgment - Set a threshold L according to the actual test environment. If the L2 norm of Yi is greater than L, the signal is considered valid; otherwise, the signal is considered invalid and is basically background noise
• step5. Relevance judgment - Take any standard signal in the sample library and do correlation analysis with the rest of the signals, ie

Find the similarity between the near infrared spectrum of the measured object and each signal of the standard sample library, Get R=[r1, r2, …, ri, …, rn], Then the category of the measured object is m, rm = max{R|i=1, …, n}

irvaluee = np.subtract(irvalue0, irvalue1)  # Eliminate the influence of background light on near infrared spectrum detection

np.sum(np.power(irvaluee, 2)) < 600  # Check if the detected signal exceeds the effective threshold

np.corrcoef(irmeasurement) # Calculate the similarity between the standard sample signals of the sample library

Print Case and Assembly

The wireless case is divided into two parts:

• The lower side. The circuit board contains all devices such as AS7263 sensors, rechargeable batteries and wireless modules. Fix the circuit board to the lower part of the housing with screws through four screw holes;
• The upper side. There is an opening for the Type-C USB plug to charge the device; there is also a small toggle switch for starting and shutting down the device. A small hole is opened above the housing, directly facing the near infrared spectrum sensor, so that the spectrum sensor AS7263 can receive the measured light.

Done! That's all!

If you have any questions or suggestions don't hesitate to leave a comment below and contact me. or participate in our open source project https://github.com/sacrohu/NIRDevelopment. Thank you!