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Article

Convolutional Neural Network Applied to SARS-CoV-2 Sequence Classification

1
Bioinformatics Multidisciplinary Environment (BioME), Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
2
Laboratory of Machine Learning and Intelligent Instrumentation, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
3
Federal Institute of Education, Science and Technology of Rio Grande do Norte, Paraiso, Santa Cruz 59200-000, RN, Brazil
4
Department of Pharmacy and Pharmaceutical Technology, University of Granada, 18071 Granada, Spain
5
Department of Computer Engineering and Automation, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Marcin Woźniak
Sensors 2022, 22(15), 5730; https://doi.org/10.3390/s22155730
Received: 29 June 2022 / Revised: 28 July 2022 / Accepted: 28 July 2022 / Published: 31 July 2022
COVID-19, the illness caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus belonging to the Coronaviridade family, a single-strand positive-sense RNA genome, has been spreading around the world and has been declared a pandemic by the World Health Organization. On 17 January 2022, there were more than 329 million cases, with more than 5.5 million deaths. Although COVID-19 has a low mortality rate, its high capacities for contamination, spread, and mutation worry the authorities, especially after the emergence of the Omicron variant, which has a high transmission capacity and can more easily contaminate even vaccinated people. Such outbreaks require elucidation of the taxonomic classification and origin of the virus (SARS-CoV-2) from the genomic sequence for strategic planning, containment, and treatment of the disease. Thus, this work proposes a high-accuracy technique to classify viruses and other organisms from a genome sequence using a deep learning convolutional neural network (CNN). Unlike the other literature, the proposed approach does not limit the length of the genome sequence. The results show that the novel proposal accurately distinguishes SARS-CoV-2 from the sequences of other viruses. The results were obtained from 1557 instances of SARS-CoV-2 from the National Center for Biotechnology Information (NCBI) and 14,684 different viruses from the Virus-Host DB. As a CNN has several changeable parameters, the tests were performed with forty-eight different architectures; the best of these had an accuracy of 91.94 ± 2.62% in classifying viruses into their realms correctly, in addition to 100% accuracy in classifying SARS-CoV-2 into its respective realm, Riboviria. For the subsequent classifications (family, genera, and subgenus), this accuracy increased, which shows that the proposed architecture may be viable in the classification of the virus that causes COVID-19. View Full-Text
Keywords: SARS-CoV-2; COVID-19; deep learning; CNN SARS-CoV-2; COVID-19; deep learning; CNN
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MDPI and ACS Style

Câmara, G.B.M.; Coutinho, M.G.F.; Silva, L.M.D.d.; Gadelha, W.V.d.N.; Torquato, M.F.; Barbosa, R.d.M.; Fernandes, M.A.C. Convolutional Neural Network Applied to SARS-CoV-2 Sequence Classification. Sensors 2022, 22, 5730. https://doi.org/10.3390/s22155730

AMA Style

Câmara GBM, Coutinho MGF, Silva LMDd, Gadelha WVdN, Torquato MF, Barbosa RdM, Fernandes MAC. Convolutional Neural Network Applied to SARS-CoV-2 Sequence Classification. Sensors. 2022; 22(15):5730. https://doi.org/10.3390/s22155730

Chicago/Turabian Style

Câmara, Gabriel B. M., Maria G. F. Coutinho, Lucileide M. D. da Silva, Walter V. do N. Gadelha, Matheus F. Torquato, Raquel de M. Barbosa, and Marcelo A. C. Fernandes. 2022. "Convolutional Neural Network Applied to SARS-CoV-2 Sequence Classification" Sensors 22, no. 15: 5730. https://doi.org/10.3390/s22155730

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