STUDY OF COVID-19 AND PREDICTION OF FUTURE MODEL USING MACHINE LEARNING
DOI:
https://doi.org/10.46243/jst.2022.v7.i02.pp112-120Keywords:
LSTM mode, Neural Network, Mutation rate, Gene sequence, SARS-Cov-2Abstract
SARS-CoV-2, a novel coronavirus mostly known as COVID-19 has created a global pandemic. The world is now immobilized by this infectious RNA virus. This RNA virus has the ability to do the mutation in the human body. This study explores the mutation rate of the whole genomic sequence gathered from the patient's dataset of different countries. The collected dataset is processed to determine the nucleotide mutation and codon mutation separately. It has been found that a huge amount of Thymine (T) and Adenine (A) are mutated to other nucleotides for all regions, but codons are not frequently mutating like nucleotides. Using this training and testing process, the nucleotide mutation rate of 400th patient in future time has been predicted. About 0.1% increment in mutation rate is found for mutating of nucleotides from T to C and G, C to G and G to T. While a decrement of 0.1% is seen for mutating of T to A, and A to C. It is found that this model can be used to predict day basis mutation rates if more patient data is available in updated time.
References
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293453
kaggle.com/paultimothymooney/coronavirus-genome-sequence
Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. The species severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nature Microbiology. 2020;5(4): 536‐544
Laboratory testing of 2019 novel coronavirus (2019-nCoV) in suspected human cases: interim guidance, 17 January 2020
Wang C., Horby P.W., Hayden F.G., Gao G.F. A novel coronavirus outbreak of global health concern. Lancet North Am Ed. 2020;395(10223): 470–473
Cucinotta D., Vanelli M. WHO declares COVID-19 a pandemic. Acta Bio-medica. 2020;91(1): 157–160
Huang C., Wang Y., Li X., Ren L., Zhao J., Hu Y., Cheng Z. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet North Am Ed. 2020;395(10223): 497–506
Lu R., Zhao X., Li J., Niu P., Yang B., Wu H., Bi Y. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet North Am Ed. 2020;395 (10224): 565–574
Wu A., Peng Y., Huang B., Ding X., Wang X., Niu P., Sheng J. Genome composition and divergence of the novel coronavirus (2019nCoV) originating in China. Cell Host Microbe
Graham R.L., Baric R.S. Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission. J Virol. 2010;84(7): 3134–3146
Cui J., Li F., Shi Z.L. Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol. 2019;17(3): 181–192
Yang J. Inhibition of SARS-CoV-2 replication by acidizing and RNA lyase-modified carbon nanotubes combined with photodynamic thermal effect. J Explor Res Pharmacol. 2020: 1–6
Fehr A.R., Perlman S. Coronaviruses. Humana Press; New York, NY. Coronaviruses: an overview of their replication and pathogenesis. 2015: 1–23
Pachetti M., Marini B., Benedetti F., Giudici F., Mauro E., Storici P., Zella D. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med. 2020;18(1): 1–9
Lodish H., Berk A., Zipursky S.L., Matsudaira P., Baltimore D., Darnell J. Mutations: types and causes. Mol Cell Biol. 2000; 4
Sanjuán R., Nebot M.R., Chirico N., Mansky L.M., Belshaw R. Viral mutation rates. J Virol. 2010;84(19): 9733–9748
Pfeiffer J.K., Kirkegaard K. Increased fidelity reduces poliovirus fitness and virulence under selective pressure in mice. PLoS Pathog. 2005;1(2)
Vignuzzi M., Stone J.K., Arnold J.J., Cameron C.E., Andino R. Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population. Nature. 2006;439(7074): 344–348
Biswas A., Bhattacharjee U., Chakrabarti A.K., Tewari D.N., Banu H., Dutta S. Emergence of Novel Coronavirus and COVID-19: whether to stay or die out? Crit Rev Microbiol. 2020; 1–12
Das R., Ghate S.D. Investigating the likely association between genetic ancestry and COVID-19 manifestation. medRxiv
Bhowmik D., Pal S., Lahiri A., Talukdar A., Paul S. Emergence of multiple variants of SARS-CoV-2 with signature structural changes. bioRxiv
Wrapp D., Wang N., Corbett K.S., Goldsmith J.A., Hsieh C.L., Abiona O., McLellan J.S. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science. 2020;367(6483): 1260–1263
Kumar G.V., Jeyanthi V., Ramakrishnan S. A short review on antibody therapy for COVID-19. New Microbes New Infect
Ojosnegros S., Beerenwinkel N. Models of RNA virus evolution and their roles in vaccine design. Immunome Res. 2010;6(S2): S5




