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Detecting SARS-CoV-2: Near-infrared spectroscopy

https://hefnawi.me/posts/detect-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: https://hefnawi.me/posts/detect-sars-cov-2-near-infrared-spectroscopy/]

  • 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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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...  https://spectralworkbench.org/

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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    https://hackaday.io/project/143014-compact-25-spectrometer

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.      

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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!

Ahmed

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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.

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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?

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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.

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