Hefnawi

Detect SARS-CoV-2 virus using Near-infrared spectroscopy

This work is still-in-progress; originally started on 25 March, 2020. And, interestingly gained some interest during that time on-wards.

This work is NOT affiliated with any group, organisation or team.

The HackADay project page.

Prologue

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.

A list of published research papers is available at the end of this post.


⚕ The project ⚕

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.

Note: You can follow the latest updates and/or collaborate on the project, please check the HackADay project page.

STOP_PRESS Updates will be added below, enjoy and discuss 😄 STOP_PRESS


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 AS7263 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 was not sure it’s the best way forward. That’s why I published 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 a brilliant scientist, professor Miguel José Yacamán from NAU; his work is featured in 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.”


Update [02 April 2020]

The AS7263 NIR sensor breakout and the TSL235R Light-to-Frequency converter sensors have been ordered and should arrive soon.

I will start experimenting with them for starters before I can acquire the TSL237T which will probably require some PCB design beforehand.


Reach Out! 😷

I’m reaching out and sharing all the resources I have and will continue to do so. Please assist in any way possible!

My goal is to make this test method available for everyone for free, I do not accept any work done on this project either by me or the community to be used for financial gain. At the current situation of COVID-19, it’s time for everyone to unite and fight against illness together.

Please reach out to anyone you think can help or provide guidance to this project.

Also, feel free to suggest the best platform to host communications on (for example slack) and of course, all the work done will be published on Github so everyone can collaborate.

More updates will be posted on my weblog, twitter and HackADay project page as more progress is reported.


Published research papers

  • 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. Full Article
  • 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. Full Article
  • 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. Full Article
  • 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. Full Article
  • 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. Full Article
  • 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. Full Article
  • 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. Full Article
  • 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. Full Article

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