Detecting SARS-CoV-2: Near-infrared spectroscopy

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Near-infrared spectroscopy (NIRS) is nothing new, however, it’s a relatively new method deployed in the field of virology. It has been successfully used before to identify HIV-1 and Influenza virus. In addition, it doesn’t require any reagents, enzymes or test kits that take at least an hour to perform the test like the PCR (Polymerase chain reaction) or RT-PCR (Reverse transcription polymerase chain reaction) and in most cases 2+ hours.
This is a proposal for a new technique for testing COVID-19 patients for the SARS-CoV-2 virus using a near-infrared spectroscopy device and then analysing the spectra using Machine Learning classification algorithms like PCA (Principle Component Analysis) or other algorithms.

I started working on the design and would be very glad to hear from prospect collaborators. I have no plans at the moment on how to proceed with actual testing and validation at local hospitals or private labs, so any information would be very appreciated.

Research papers published on the use of Near-infrared spectroscopy in the field of virology

[Also outlined with links to the full articles at the end of my weblog post here:]

  • Santos, M.C., Morais, C.L., Nascimento, Y.M., Araujo, J.M. and Lima, K.M., 2017. Spectroscopy with computational analysis in virological studies: A decade (2006–2016). TrAC Trends in Analytical Chemistry, 97, pp.244-256.
  • Sakudo, A., Tsenkova, R., Onozuka, T., Morita, K., Li, S., Warachit, J., Iwabu, Y., Li, G., Onodera, T. and Ikuta, K., 2005. A Novel Diagnostic Method for Human Immunodeficiency Virus Type‐1 in Plasma by Near‐Infrared Spectroscopy. Microbiology and Immunology, 49(7), pp.695-701.
  • Fernandes, J.N., Dos Santos, L.M., Chouin-Carneiro, T., Pavan, M.G., Garcia, G.A., David, M.R., Beier, J.C., Dowell, F.E., Maciel-de-Freitas, R. and Sikulu-Lord, M.T., 2018. Rapid, noninvasive detection of Zika virus in Aedes aegypti mosquitoes by near-infrared spectroscopy. Science advances, 4(5), p.eaat0496.
  • Kobayashi, T., Kato, Y.H., Tsukamoto, M., Ikuta, K. and Sakudo, A., 2009. Portable visible and near-infrared spectrophotometer for triglyceride measurements. International journal of molecular medicine, 23(1), pp.75-79.
  • von Lühmann, A., Herff, C., Heger, D. and Schultz, T., 2015. Toward a wireless open source instrument: functional near-infrared spectroscopy in mobile neuroergonomics and BCI applications. Frontiers in human neuroscience, 9, p.617.
  • Rinnan, Å., Van Den Berg, F. and Engelsen, S.B., 2009. Review of the most common pre-processing techniques for near-infrared spectra. TrAC Trends in Analytical Chemistry, 28(10), pp.1201-1222.
  • Marques, A.S., Moraes, E.P., Júnior, M.A., Moura, A.D., Neto, V.F., Neto, R.M. and Lima, K.M., 2015. Rapid discrimination of Klebsiella pneumoniae carbapenemase 2–producing and non-producing Klebsiella pneumoniae strains using near-infrared spectroscopy (NIRS) and multivariate analysis. Talanta, 134, pp.126-131.
  • Sakudo, A., Suganuma, Y., Kobayashi, T., Onodera, T. and Ikuta, K., 2006. Near-infrared spectroscopy: promising diagnostic tool for viral infections. Biochemical and biophysical research communications, 341(2), pp.279-284. 

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  • 1 × TSL237T High-Sensitivity Light-to-Frequency Converter

  • Cross-posting Updates from my blog

    Ahmed Hefnawi (Volta)06/06/2020 at 13:25 0 comments

    Cross-posting updates from my blog for those of you following up on this project :)

    Update [06 June 2020]

    Some people offered support

    The idea for this project was to spread the data collected and share it with as many people as possible because I don’t have enough time to work on it on my own. It would be selfish to withhold ideas when others could possibly start implementing it, right?

    I was reached by two gentlemen on LinkedIn, one of them offered to support the project where it requires medical trials and approvals and the other offered to support through his medical background and connections. This is great news to me and also one of them mentioned that he also has a team working on a similar project using NIRS in virology, which was very exciting as well.

    A new sensor, countless possibilities 🤔

    Hamamatsu Sensor

    In addition, I received a quote for a very high-sensitivity very compact spectrometer that would possibly be a game-changer compared to the AS726 sensor; however, I cannot afford it at the moment so will have to save to perform any testing with it, I thought about starting a campaign to fund it, but then I thought I might not have the time to devote to testing it so that could be wasted. That’s why I include the details here in the update.

    It’s specifically the Hamamatsu C14398MA-01 sensor, the sales team at Hamamatsu were very helpful to provide technical specifications and price details, so if you are interested in more details please reach out. Also, the initial lead time is 8 weeks.

    Possible new technique

    I also learned about the Terahertz technology, which is very promising in the field of spectroscopy.

    Update [03 June 2020]

    🧬 Learned about the Loop-mediated isothermal amplification (LAMP) technique for the amplification of DNA.

    🌟 Also, learned about this brilliant guy, professor Miguel José Yacamán from this article

    “In his previous work, José Yacamán has used surface-enhanced Raman spectroscopy to detect glycoproteins and sialic acid as a method of testing for breast cancer, which is now in the final approval stage for commercial use.”

  • Ordered some items

    Ahmed Hefnawi (Volta)04/01/2020 at 19:51 0 comments

    So today I ordered the following items for initial testing:

    1. Sparkfun AS7263 NIR breakout board to start testing the AS7263 chip
    2. Light to Frequency Converter - TSL235R
    3. various passive components and prototyping stuff.

    I'm still planning to get my hands on TSL237T but it might take sometime to design and get a PCB to test that chip.

    Will keep you posted.

    Thanks =)

  • Researching the sensor to use

    Ahmed Hefnawi (Volta)03/30/2020 at 16:05 0 comments

    I'm looking into Light to Frequency converters and other light sensing options.

    So far, I'm focused on TSL 237

    Datasheet here

    What do you think, have you worked with spectrophotometers before, can you recommend a better sensor?


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dipteshlala wrote 07/19/2020 at 20:52 point

Ahmed Hefnawi (Volta) currently i am going to participate in a hackathon and i have been working on the similar idea also .

Currently my team is trying to analyze by bioinformatics tool the optical symmetries , as u know that already the virus is proved to be Raman positive and detected in a very well manner ; so there is a chance that it may be positive for IR or may not based on molecular rather centroid symmetry.

Data is very much needed by experiments on known positive samples with IR spectrometer and then we should try to minimize the cost and size of the spectrometer and the Deep neural network for interpretation 

  Are you sure? yes | no

V Daita wrote 04/30/2020 at 13:05 point

What are your opinions on the Public Lab Smartphone-based spectrometer? If you were to make some modifications to your camera, you might be able to get Vis-NIR spectra on your smartphone...

  Are you sure? yes | no

Ahmed Hefnawi (Volta) wrote 06/06/2020 at 13:30 point

That would be very interesting project to experiment with and check out.

But with the optical window required for a reliable application in virology, I'm not sure that would be a reliable option at least not during the phase of collecting correct spectra using a calibrated sensor along with NIR LEDs or Laser Diodes. What do you think?

  Are you sure? yes | no

V Daita wrote 06/06/2020 at 17:28 point

Potentially - there are some papers that mention the 650-1050 range being adequate for such thing - this would not be done on a phone but something more along the lines of OpenMV, etc.

  Are you sure? yes | no

Ahmed Hefnawi (Volta) wrote 06/06/2020 at 19:39 point

Yes exactly, that is the optical window that is quoted by most of the published papers also in my list above.

That's interesting, I wonder how would an OpenMV handle NIR and would be interested in testing it after establishing the spectra, and I think it might not be a match for specialised sensor with a decent spectral response range of 640 - 1050 nm, not only that but a spectral resolution of 17-20 nm, but still could be used in different other applications outside of virology.

Also, I wonder how would the Raspberry Pi NoIR camera would do as well, endless possibilities once we have established spectra and then I would be very interested in making comparisons between OpenMV, RPi NoIR, etc against the readings of the spectrometer sensors.

Would you be interested to work on this project with me? As per my latest update I don't have enough time to proceed so I'm openly sharing every bit of information I have on this project so that others can pick up and move it forward :)



  Are you sure? yes | no

V Daita wrote 07/10/2020 at 21:38 point

Hey Ahmed, 

I would be really excited to work with you on this, and sorry for the late reply. I am currently talking with someone who is working on implementing NIRS for real-world devices, and he also seems interested. Would you mind emailing me ( and putting me in touch with anyone else you know working on NIRS-based COVID-19 detection? I might be able to help them with their research.

Also, quick sidenote, for a hackathon, I gathered a team that was able to build a model that could analyze COVID-19 Raman spectra using PCA, and we are planning to add noise reduction.

Thank you,


  Are you sure? yes | no

Ahmed Hefnawi (Volta) wrote 07/11/2020 at 15:05 point

Thank you Vijay for your reply.

That sounds very interesting, I will drop you an email and would be looking forward to collaborating with you or your team.

The analysis of Raman spectra using PCA sounds like a good start regarding your hackathon, let me know also if I can lend a hand at any time over weekends, I'm currently a bit busy with other stuff, but can always spare an hour or two every weekend.


  Are you sure? yes | no

Marcrbarker wrote 03/30/2020 at 21:48 point

How are you differentiating in the spectral domain ? Are you using a diffraction grating and precision optics?  Or maybe you have a narrowband tunable wavelength infrared source?  This is the single most important aspect of the hardware design.   I would say easily trumps over the choosing an infrared sensor.  

STOP PRESS - EDIT   I've just seen this 18 slot channelised spectrometer on here

For example the last spectrometer I did was 30 years ago fixed band only looking at one pair of absorption wavelength. It had used precision thinfilm narrow bandpass optical filters built at 185 nm and (??can't remember nm) spot frequencies. Optical design at UV was a challenge because ordinary glass couldn't be used , not much a problem at nearinfrared.     

I expect that once there's a prototype detecting things OK, interest and serious support will then really kick off.      

  Are you sure? yes | no

Ahmed Hefnawi (Volta) wrote 03/31/2020 at 09:33 point

Thank you so much for the suggested spectrometer project, there are a number of open source spectrophotometer designs as well available and one of them in my listed literature. I would say they are a very helpful source. Specially the AS7265x chip, I will look into it indeed!

Speaking of the spectral domain, I'm not planning on using diffraction grating, I want this prototype to be easy to build and in the future easy to manufacture. I would go with a very low spectral bandwidth of less than 30nm probably play with some laser IR emitters for various wave lengths in the range of 650nm to 1000nm which is the most useful range for biological samples called the "optical window" as suggested by the literature as well. Anything less than 650nm or greater than 1000nm will be greatly distorted by the high absorption of water and if we are using red blood cells by hemoglobin. And yes, I will be working with near-infrared at least during the current phase, things could change in the future.

That's great to know :) Yeah, I'm looking forward to having a prototype that can produce very reliable spectra and would really appreciate your comments and suggestions along the way since you have already worked with spectrometer.

Stay tuned and have a great day!


  Are you sure? yes | no

Ahmed Hefnawi (Volta) wrote 03/30/2020 at 16:47 point

The literature is not about SARS-CoV-2 but one of the researches tackled HIV-1.

There is no exact fingerprint for the spectra of the SARS-CoV-2 available yet, but this will be extracted from the spectra and data analysis done on samples after constructing the first prototype. Also, the protein structure of the virus is now available and I can use this to infer the fingerprint, but again it will depend on the sensitivity we can reach with the sensor and the spectra produced.

The plan is to test samples from PCR or RT-PCR confirmed patients (both positive and negative) and start correlating the output from the spectrophotometer.
Thank you for asking and I would be happy to hear back from you.

  Are you sure? yes | no

Dan Maloney wrote 03/30/2020 at 16:40 point

Can you give a quick summary of the literature? What's the signature that you'll be looking for that's specific to SARS-CoV-2 in an infected patient?

  Are you sure? yes | no

Ahmed Hefnawi (Volta) wrote 03/30/2020 at 16:50 point

Wrt literature summary, I'm writing my thoughts from all the literature that I have gone through so far, and hope it helps. Also please feel free to suggest or ask or comment on any future project log or anything that doesn't seem right. I'm very open to feedback and ideas.

  Are you sure? yes | no

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