The outbreak of COVID-19 has spread worldwide, causing great damage to the global economy. Raman spectroscopy is expected to become a rapid and accurate method for the detection of coronavirus. A classification method of coronavirus spike proteins by Raman spectroscopy based on deep learning was implemented. A Raman spectra dataset of the spike proteins of five coronaviruses (including MERS-CoV, SARS-CoV, SARS-CoV-2, HCoVHKU1, and HCoV-OC43) was generated to establish the neural network model for classification. Even for rapidly acquired spectra with a low signal-to-noise ratio, the average accuracy exceeded 97%. An interpretive analysis of the classification results of the neural network was performed, which indicated that the differences in spectral characteristics captured by the neural network were consistent with the experimental analysis. The interpretative analysis method provided a valuable reference for identifying complex Raman spectra using deep-learning techniques. Our approach exhibited the potential to be applied in clinical practice to identify COVID-19 and other coronaviruses, and it can also be applied to other identification problems such as the identification of viruses or chemical agents, as well as in industrial areas such as oil and gas exploration.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
F. Cui and H. S. Zhou, Biosens. Bioelectron., 165, Article ID 112349 (2020).
J. Huang, J. Wen, M. Zhou, S. Ni, W. Le, G. Chen, L. Wei, Y. Zeng, D. Qi, M. Pan, Anal. Chem., 93, No. 26, 9174–9182 (2021).
M. Asif, M. Ajmal, G. Ashraf, N. Muhammad, A. Aziz, T. Iftikhar, J. Wang, and H. Liu, Curr. Opin. Electrochem., 23, 174–184 (2020).
M. Shen, Y. Zhou, J. Ye, A. A. A. Al-Maskri, Y. Kang, S. Zeng, and S. Cai, J. Pharm. Anal., 10, 97–101 (2020).
V. M. Corman, O. Landt, M. Kaiser, R. Molenkamp, A. Meijer, D. K. W. Chu, T. Bleicker, S. Brünink, J. Schneider, M. L. Schmidt, et al., Eurosurveillance, 25, No. 3, Article ID 2000045 (2020).
M. N. Esbin, O. N. Whitney, S. Chong, A. Maurer, X. Darzacq, and R. Tjian, RNA, 26, No. 7, 771–783 (2020).
J. Huggett, K. Dheda, S. Bustin, and A. Zumla, Genes Immun., 6, 279–284 (2005).
M. L. Wong and J. F. Medrano, Biotechniques, 39, 75–85 (2005).
D. Jacofsky, E. M. Jacofsky, and M. Jacofsky, J. Arthroplasty, 35, S74–S81 (2020).
Q. Lin, D. Wen, J. Wu, L. Liu, W. Wu, X. Fang, and J. Kong, Anal. Chem., 92, 9454–9458 (2020).
G. Liu and, J. F. Rusling, ACS Sens., 6, 593–612 (2021).
C.-S. Ho, N. Jean, C. A. Hogan, L. Blackmon, S. S. Jeff rey, M. Holodniy, N. Banaei, A. A. Saleh, S. Ermon, and J. Dionne, Nat. Commun, 10, 1–8 (2019).
W. Lee, A. T. Lenferink, C. Otto, and H. L. Off erhaus, J. Raman Spectrosc., 51, 293–300 (2020).
D. Wrapp, N. Wang, K. S. Corbett, J. A. Goldsmith, C.-L. Hsieh, O. Abiona, B. S. Graham, and J. S. McLellan, Science, 367, 1260–1263 (2020).
Z. Li, A. C. Tomlinson, A. H. Wong, D. Zhou, M. Desforges, P. J. Talbot, S. Benlekbir, J. L. Rubinstein, and J. M. Rini, eLife, 8, Article ID e51230 (2019).
S. Abdul-Rasool and B. C. Fielding, Open Virol. J., 4, 76 (2010).
J. R. St-Jean, H. Jacomy, M. Desforges, A. Vabret, F. Freymuth, and P. J. Talbot, J. Virol., 78, 8824–8834 (2004).
P. C. Woo, S. K. Lau, C.-M. Chu, K.-H. Chan, H.-W. Tsoi, Y. Huang, B. H. Wong, R. W. Poon, J. J. Cai, and W.-K. Luk, J. Virol., 79, 884–895 (2005).
C. Drosten, S. Günther, W. Preiser, S. Van Der Werf, H.-R. Brodt, S. Becker, H. Rabenau, M. Panning, L. Kolesnikova, and R. A. Fouchier, N. Engl. J. Med., 348, 1967–1976 (2003).
R. J. De Groot, S. C. Baker, R. S. Baric, C. S. Brown, C. Drosten, L. Enjuanes, R. A. Fouchier, M. Galiano, A. E. Gorbalenya, and Z. A. Memish, J. Virol., 87, 7790–7792 (2013).
S. Su, G. Wong, W. Shi, J. Liu, A. C. Lai, J. Zhou, W. Liu, Y. Bi, and G. F. Gao, Trends Microbiol., 24, 490–502 (2016).
M. M. Kesheh, P. Hosseini, S. Soltani, and M. Zandi, Rev. Med. Virol., Article ID e2282 (2021).
Y. LeCun, L. Bottou, Y. Bengio, and P. Haff ner, Proc. IEEE, 86, 2278–2324 (1998).
K. He, X. Zhang, S. Ren, and J. Sun, Proc. IEEE Conf. Comput. Vision Pattern Recognit., 770–778 (2016).
D. X. Liu, J. Q. Liang, and T. S. Fung, Encycl. Virol., 428 (2021).
A. B. Gussow, N. Auslander, G. Faure, Y. I. Wolf, F. Zhang, and E. V. Koonin, Proc. Natl. Acad. Sci. USA, 117, 15193–15199 (2020).
H. Yao, Y. Song, Y. Chen, N. Wu, J. Xu, C. Sun, J. Zhang, T. Weng, Z. Zhang, and Z. Wu, Cell, 183, 730–738, Article ID e713 (2020).
C. Liu, Y. Yang, Y. Gao, C. Shen, B. Ju, C. Liu, X. Tang, J. Wei, X. Ma, and W. Liu, bioRxiv (2020).
K. Simonyan, A. Vedaldi, and A. Zisserman, arXiv preprint arXiv, Article ID 1312.6034 (2013).
C. Carlomagno, D. Bertazioli, A. Gualerzi, S. Picciolini, P. Banfi , A. Lax, E. Messina, J. Navarro, L. Bianchi, and A. Caronni, Sci. Rep., 11, 1–13 (2021).
H. Jinglin, Z. Minjie, L. Wei, C. Guo, N. Shuang, N. Gao, L. Zeyu, Z. Zongqing, H. Zhibing, and L. Bo, Qiangjiguang Yu Lizishu, 32, 069001–069002 (2020).
J. E. Sanchez, S. A. Jaramillo, E. Settles, J. J. V. Salazar, A. Lehr, J. Gonzalez, C. R. Aranda, H. R. Navarro-Contreras, M. O. Raniere, and M. Harvey, RSC Adv., 11, 25788–25794 (2021).
G. Yin, L. Li, S. Lu, Y. Yin, Y. Su, Y. Zeng, M. Luo, M. Ma, H. Zhou, and L. Orlandini, J. Raman Spectrosc., 52, 949–958 (2021).
Author information
Authors and Affiliations
Corresponding author
Additional information
Abstract of article is published in Zhurnal Prikladnoi Spektroskopii, Vol. 89, No. 6, p. 903, November–December, 2022.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Mo, W., Wen, J., Huang, J. et al. Classification of Coronavirus Spike Proteins by Deep-Learning-Based Raman Spectroscopy and its Interpretative Analysis. J Appl Spectrosc 89, 1203–1211 (2023). https://doi.org/10.1007/s10812-023-01487-w
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10812-023-01487-w