Determining the variations in SARS-CoV-2 variant is considered main factor for understanding the pathogenic mechanisms, aid in diagnosis, prevention and treatment. The present study aimed to determine the genetic variations of SARS-CoV-2. The sequences of SARS-CoV-2 were ob-tained from National Center for Biotechnology Information (NCBI) and studied according to the time of isolation and their origin. The genome sequence of SARS-CoV-2 accession number NC_045512 which represented the first isolated sequence of SARS-CoV-2 (Wuhan strain) was used as the reference sequence. The obtained genome sequences of SARS-CoV-2 were aligned against this Wu-han strain and variations among nucleotides and proteins were examined. The sequence of SARS-CoV-2 accession number MT577016 showed very low homology 98.75 % compared to Wuhan strain NC_045512. The analysis identified 301 nucleotide changes, which correspond to 258 different mutations; most of them 80 % (207/258) were missense point mutations followed by 17.1 % (44/258) silent point mutations. The critical mutations occurred in viral structural genes; 16.7 % (43/258) mutations reported in S gene and 1 missense mutation was observed in E gene. Our finding showed the lowest homology and relatively distant phylogenetic relation of this SARS-CoV-2 variant with Wuhan strain along with high frequency of mutations including those in spike S and envelope E genes.
Keywords: COVID-19, genetic variation, homology, phy-logenetic, SARS-CoV-2

Full text and supplemented materials
References
1. Ahmed-Abakura, E.H., Challenge of COVID 19: pathogenicity, genetic variations and laboratory diagnosis, AJBSR, 2020, vol. 11, no. 1. https://doi.org/10.34297/AJBSR.2020.11.001604
2. Ahmed-Abakur, H.E. and Alnour, T.M.S., Genetic variations among SARS-CoV-2 strains isolated in China, Gen. Rep., 2020, vol. 21, p. 100925. https://doi.org/10.1016/j.genrep.2020.100925
3. Ceraolo, C. and Giorgi, F.M., Genomic variance of the 2019-nCoV coronavirus, J. Med. Virol., 2020, vol. 92, no. 5, pp. 522–528. https://doi.org/10.1002/jmv.25700
4. Chang, H.W., Egberink, H.F., Halpin, R., et al., Spike protein fusion peptide and feline coronavirus virulence, Emerg. Infect. Dis., 2012, vol. 18, no. 7, pp. 1089–1095. https://doi.org/10.3201/eid1807.120143
5. Deng, X., Gu, W., Federman, S., et al., Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California, Science, 2020, vol. 369, no. 6503, pp. 582–587. https://doi.org/10.1126/science.abb9263
6. European Centre for Disease Prevention and Control, Rapid Increase of a SARS-CoV-2 Variant with Multiple Spike Protein Mutations Observed in the United Kingdom 20 December 2020, Stockholm: ECDC, 2020. https://www.ecdc. europa.eu/sites/default/files/documents/SARS-CoV-2-variant-multiple-spike-protein-mutations-United-Kingdom.pdf.
7. Felsenstein, J., Confidence limits on phylogenies: an approach using the bootstrap, Evolution, 1985, vol. 39, pp. 783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
8. Khailany, R.A., Safdar, M., and Ozaslan, M., Genomic characterization of a novel SARS-CoV-2, Gene Rep., 2020, vol. 19, p. 100682 https://doi.org/10.1016/j.genrep.2020.100682
9. Kumar, S., Stecher, G., Li, M., et al., MEGA X: Molecular evolutionary genetics analysis across computing platforms, Mol. Biol. Evol., 2018, vol. 35, no. 6, pp. 1547–1549. https://doi.org/10.1093/molbev/msy096
10. Lokman, S.M., Rasheduzzaman, Salauddin, A., et al., Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: a computational biology approach, Infect. Genet. Evol., 2020, vol. 84, p. 104389. https://doi.org/10.1016/j.meegid.2020.104389
11. Lu, R., Zhao, X., Li, J., et al., Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding, Lancet, 2020, vol. 395, no. 10224, pp. 565–574. https://doi.org/10.1016/S0140-6736(20)30251-8
12. Naqvi, A.A.T., Kisa, F., Taj, M., et al., Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies: structural genomics approach, Biochim. Biophys. Acta Mol. Basis Dis., 2020, vol. 1866, no. 10, art. 165878. https://doi.org/10.1016/j.bbadis.2020.165878
13. Raza, H., Wahid, B., Rubi, G., et al., Molecular epidemiology of SARS-CoV-2 in Faisalabad, Pakistan: a real-world clinical experience, Infect. Genet. Evol., 2020, vol. 84, art. 104374. https://doi.org/10.1016/j.meegid.2020.104374
14. Saitou, N. and Nei, M., The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol., 1987, vol. 4, pp. 406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
15. Shu, B. and Gong, P., Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation, Proc. Natl. Acad. Sci. U. S. A., 2016, vol. 113, no. 28, art. E4005-14. https://doi.org/10.1073/pnas.1602591113
16. Tamura, K., Nei, M., and Kumar, S., Prospects for inferring very large phylogenies by using the neighbor-joining method, Proc. Natl. Acad. Sci. U. S. A., 2004, vol. 101, no. 30, pp. 11030–11035. https://doi.org/10.1073/pnas.0404206101
17. Uddin, M., Mustafa, F., Rizvi, T.A., et al., SARS-CoV-2/ COVID-19: viral genomics, epidemiology, vaccines, and therapeutic interventions, Viruses, 2020, vol. 12, no. 5, p. 526. https://doi.org/10.3390/v12050526
18. van Pesch, V., van Eyll, O., and Michiels, T., The leader protein of Theiler’s virus inhibits immediate-early alpha/beta interferon production, J. Virol., 2001, vol. 75, no. 17, pp. 7811—7817. https://doi.org/10.1128/jvi.75.17.7811-7817.2001
19. Wang, C., Liu, Z., Chen, Z., et al., The establishment of reference sequence for SARS-CoV-2 and variation analysis, J. Med. Virol., 2020, vol. 92, no. 6, pp. 667–674. https://doi.org/10.1002/jmv.25762
20. Wu, F., Zhao, S., Yu, B., et al., A new coronavirus associated with human respiratory disease in China, Nature, 2020, vol. 579, no. 7798, pp. 265–269. https://doi.org/10.1038/s41586-020-2008-3