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Analysis of C-terminal Domain ORF6 for Mutation Pattern SARS-Cov-2 using Slicing Index

by Rini Arianty, Ety Sutanty, Esti Setiyaningsih
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International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 186 - Number 27
Year of Publication: 2024
Authors: Rini Arianty, Ety Sutanty, Esti Setiyaningsih
10.5120/ijca2024923746

Rini Arianty, Ety Sutanty, Esti Setiyaningsih . Analysis of C-terminal Domain ORF6 for Mutation Pattern SARS-Cov-2 using Slicing Index. International Journal of Computer Applications. 186, 27 ( Jul 2024), 8-12. DOI=10.5120/ijca2024923746

@article{ 10.5120/ijca2024923746,
author = { Rini Arianty, Ety Sutanty, Esti Setiyaningsih },
title = { Analysis of C-terminal Domain ORF6 for Mutation Pattern SARS-Cov-2 using Slicing Index },
journal = { International Journal of Computer Applications },
issue_date = { Jul 2024 },
volume = { 186 },
number = { 27 },
month = { Jul },
year = { 2024 },
issn = { 0975-8887 },
pages = { 8-12 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume186/number27/analysis-of-c-terminal-domain-orf6-for-mutation-pattern-sars-cov-2-using-slicing-index/ },
doi = { 10.5120/ijca2024923746 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-07-09T00:35:29.506922+05:30
%A Rini Arianty
%A Ety Sutanty
%A Esti Setiyaningsih
%T Analysis of C-terminal Domain ORF6 for Mutation Pattern SARS-Cov-2 using Slicing Index
%J International Journal of Computer Applications
%@ 0975-8887
%V 186
%N 27
%P 8-12
%D 2024
%I Foundation of Computer Science (FCS), NY, USA
Abstract

This study is to ascertain the extent to which ORF6 affects the rate at which the SARS-CoV-2 virus spreads as well as the variables that may contribute to the ORF6 protein's propensity to do so. If the virus with one or more mutations has a different phenotypic from the original virus, then the SARS-CoV-2 virus may have undergone a mutation. The genetic coding of the virus contains mutations. Compared to DNA viruses and bacteria, the SARS-CoV-2 virus is a single-stranded positive RNA virus with a fragile structure that is simple to modify. As a result, RNA viruses in vitro have a greater capacity for mutation. This research will analysis the ORF6 Protein SARS-CoV-2 dataset, which has mutations or not in the C-terminal section. Proteins that do not have their own mutations have a much higher replication capacity than those that have mutations. The present study employs Biopython and Slicing Index technique to investigate the ORF6 protein's interaction with cells and its impact on the immune system by means of visualizing the protein group data on string pieces by dividing the data based on the mutation index.

References
  1. E. Mohammadi, F. Shafiee, K. Shahzamani, and M. Mehdi, “Biomedicine & Pharmacotherapy Novel and emerging mutations of SARS-CoV-2 : Biomedical implications,” vol. 139, 2021.
  2. [D. N. Aisyah, C. A. Mayadewi, H. Diva, Z. Kozlakidis, Siswanto, and W. Adisasmito, “A spatial-temporal description of the SARSCoV-2 infections in Indonesia during the first six months of outbreak,” PLoS One, vol. 15, no. 12 December, pp. 1–14, 2020, doi: 10.1371/journal.pone.0243703.
  3. Y. Yang et al., “SARS-CoV-2: characteristics and current advances in research,” Virol. J., vol. 17, no. 1, pp. 1–17, 2020, doi: 10.1186/s12985-020-01369-z.
  4. [A. Rauf et al., “COVID-19 pandemic: Epidemiology, etiology, conventional and non-conventional therapies,” Int. J. Environ. Res. Public Health, vol. 17, no. 21, pp. 1–32, 2020, doi: 10.3390/ijerph17218155.
  5. S. M. Sadat, M. R. Aghadadeghi, M. Yousefi, A. Khodaei, M. Sadat Larijani, and G. Bahramali, “Bioinformatics Analysis of SARS-CoV-2 to Approach an Effective Vaccine Candidate Against COVID-19,” Mol. Biotechnol., vol. 63, no. 5, pp. 389–409, 2021, doi: 10.1007/s12033-021-00303-0.
  6. R. A. Khailany, M. Safdar, and M. Ozaslan, “Genomic characterization of a novel SARS-CoV-2,” Gene Reports, vol. 19, no. March, 2020, doi: 10.1016/j.genrep.2020.100682.
  7. E. Volz et al., “Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data,” medRxiv, vol. 4, no. 2, pp. 47–49, 2021, doi: 10.1101/2020.12.30.20249034.
  8. K. Hukma, A. Putri, K. P. Sari, and M. Y. Safitri, “Analisis Variasi Genetik Sekuen Gen Surface Glycoprotein ( S ) Pada SARS – CoV-2 Popset : 1843471817 Menggunakan RFLP Secara In- Sillico,” Pros. Semin. Nas. Biol., vol. 1, no. 1, pp. 44–52, 2021, [Online]. Available: https://semnas.biologi.fmipa.unp.ac.id/index.php/prosiding/article/view/8
  9. Y. Miyamoto et al., “SARS-CoV-2 ORF6 disrupts nucleocytoplasmic trafficking to advance viral replication,” Commun. Biol., vol. 5, no. 1, pp. 1–15, 2022, doi: 10.1038/s42003-022-03427-4.
  10. [M. Sedegah et al., “Cellular interferon-gamma and interleukin-2 responses to SARS-CoV-2 structural proteins are broader and higher in those vaccinated after SARS-CoV-2 infection compared to vaccinees without prior SARS-CoV-2 infection,” PLoS One, vol. 17, no. 10 October, pp. 1–23, 2022, doi: 10.1371/journal.pone.0276241.
  11. D. A. Jamison et al., “A comprehensive SARS-CoV-2 and COVID-19 review, Part 1: Intracellular overdrive for SARS-CoV-2 infection,” Eur. J. Hum. Genet., vol. 30, no. 8, pp. 889–898, 2022, doi: 10.1038/s41431-022-01108-8.
  12. R. Hall et al., “SARS-CoV-2 ORF6 disrupts innate immune signalling by inhibiting cellular mRNA export,” PLoS Pathog., vol. 18, no. 8, pp. 1–24, 2022, doi: 10.1371/journal.ppat.1010349.
  13. R. Zhou, R. Zeng, A. von Brunn, and J. Lei, “Structural characterization of the C-terminal domain of SARS-CoV-2 nucleocapsid protein,” Mol. Biomed., vol. 1, no. 1, pp. 1–11, 2020, doi: 10.1186/s43556-020-00001-4.
  14. G. Quéromès et al., “Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France,” Emerg. Microbes Infect., vol. 10, no. 1, pp. 167–177, 2021, doi: 10.1080/22221751.2021.1872351.
  15. P. V. Markov et al., “The evolution of SARS-CoV-2,” Nat. Rev. Microbiol., vol. 21, no. June, 2023, doi: 10.1038/s41579-023-00878-2.
  16. B. Cosar et al., “SARS-CoV-2 Mutations and their Viral Variants,” Cytokine Growth Factor Rev., vol. 63, no. July 2021, pp. 10–22, 2022, doi: 10.1016/j.cytogfr.2021.06.001.
  17. [M. Rashighi and J. E. Harris, 乳鼠心肌提取 HHS Public Access, vol. 176, no. 3. 2017. doi: 10.1053/j.gastro.2016.08.014.CagY.
  18. K. Kryukov, L. Jin, and S. Nakagawa, “Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format,” Patterns, vol. 3, no. 9, p. 100562, 2022, doi: 10.1016/j.patter.2022.100562.
  19. D. M. Kristensen, Y. I. Wolf, and E. V Koonin, “ATGC database and ATGC-COGs : an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation,” vol. 45, no. October 2016, pp. 210–218, 2017, doi: 10.1093/nar/gkw934.
  20. A. Banerjee et al., “Single-Molecule Analysis of DNA Base-Stacking Energetics Using Patterned DNA Nanostructures,” 2022.
  21. NCBI, “No Title,” ORF6 Protein Dataset, 2023. https://www.ncbi.nlm.nih.gov/gene/1489673
  22. R. Sanjua, “Mechanisms of viral mutation ´,” pp. 4433–4448, 2016, doi: 10.1007/s00018-016-2299-6.
  23. M. Linxweiler, B. Schick, and R. Zimmermann, “Let ’ s talk about Secs : Sec61 , Sec62 and Sec63 in signal transduction , oncology and personalized medicine,” no. January, pp. 1–10, 2017, doi: 10.1038/sigtrans.2017.2.
  24. S. Sun, M. Mariappan, Y. W. Campus, and W. Haven, “C-terminal tail length guides insertion and assembly of membrane proteins,” vol. 295, no. 21, pp. 15498–15510, 2020, doi: 10.1074/jbc.RA120.012992.
  25. S. E. Turvey, “NIH Public Access,” no. June, 2018, doi: 10.1016/j.jaci.2009.07.016.
  26. M. Moustaqil et al., “SARS-CoV-2 proteases cleave IRF3 and critical modulators of inflammatory pathways ( NLRP12 and TAB1 ): implications for disease presentation across species and the search for reservoir hosts .,” vol. 3, 2020.
  27. S. Fung, K. Siu, H. Lin, M. L. Yeung, and D. Jin, “SARS-CoV-2 main protease suppresses type I interferon production by preventing nuclear translocation of phosphorylated IRF3,” vol. 17, 2021, doi: 10.7150/ijbs.59943.
  28. W. Dejnirattisai et al., “The antigenic anatomy of SARS-CoV-2 receptor binding domain,” Cell, vol. 184, no. 8, pp. 2183-2200.e22, 2021, doi: 10.1016/j.cell.2021.02.032.
  29. D. Ellis et al., “Stabilization of the SARS-CoV-2 Spike Receptor-Binding Domain Using Deep Mutational Scanning and Structure-Based Design,” Front. Immunol., vol. 12, no. June, pp. 1–17, 2021, doi: 10.3389/fimmu.2021.710263.
  30. [L. Miorin, T. Kehrer, M. T. Sanchez-aparicio, K. Zhang, and P. Cohen, “SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling,” 2020, doi: 10.1073/pnas.2016650117.
Index Terms

Computer Science
Information Sciences
Bio-informatics

Keywords

Biopython; ORF6; SARS-CoV-2; Slicing; Viral

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