Unique SARS­CoV­2 variant exhibiting plenteous missense mutations in structural and nonstructural genes

Alnoura T.M.S., Ullah M.F., Elssaig E.H., Ahmed­Abakur E.H.

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.

Key words: COVID-19, genetic variation, homology, phy-logenetic, SARS-CoV-2

Tsitologiya i Genetika 2021, vol. 55, no. 5, pp. 69-71

1. Faculty of Medical Laboratory Science, Department of Microbiology and Immunology Alzaiem Alazhari University, Khartoum North, 11111, Sudan
2. Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, Tabuk, 71411, Saudi Arabia
3. Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia

E-mail: telnour ut.edu.sa, m.ullah ut.edu.sa, eelssaig ut.edu.sa,

eosman ut.edu.sa, eltayib1974 yahoo.com

Alnoura T.M.S., Ullah M.F., Elssaig E.H., Ahmed­Abakur E.H. Unique SARS­CoV­2 variant exhibiting plenteous missense mutations in structural and nonstructural genes, Tsitol Genet., 2021, vol. 55, no. 5, pp. 69-71.

In "Cytology and Genetics":
Tarig M.S. Alnour, Mohammad Fahad Ullah, Elmutuz H. Elssaig & Eltayib H. Ahmed-Abakur Unique SARS-CoV-2 Variant Exhibiting Plenteous Missense Mutations in Structural and Nonstructural Genes, Cytol Genet., 2021, vol. 55, no. 6, pp. 606–612
DOI: 10.3103/S0095452721060153

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