Mutations in the sequence of the three structural proteins of this virus may have a significant impact on the progression of the pandemic.
📌 3 Key Takeaways
🎯
Objective & Hypothesis:Background: SARS-CoV-2 associated with severe acute respiratory syndrome is a common, rapidly growing infectious disease with high morbidity and mortality.
📊
Key Findings & Data:Background: SARS-CoV-2 associated with severe acute respiratory syndrome is a common, rapidly growing infectious disease with high morbidity and mortality.
💡
Conclusion & Impact:Mutations in the sequence of the three structural proteins of this virus may have a significant impact on the progression of the pandemic.
🔬Design:Araştırma Makalesi
📍Scope:Comprehensive Sample
⚙️Variables:R programlama dili · SARS-CoV-2 · Dizi Hizalama
Abstract
Background: SARS-CoV-2 associated with severe acute respiratory syndrome is a common, rapidly growing infectious disease with high morbidity and mortality. Mutations in the sequence of the three structural proteins of this virus may have a significant impact on the progression of the pandemic.
Özet
Amaç: Şiddetli akut solunum sendromu ile ilişkili SARS-CoV-2, yüksek morbidite ve mortaliteye sahip, yaygın, hızla büyüyen bir enfeksiyon hastalığıdır. Bu virüsün üç yapısal proteininin dizisindeki mutasyonlar, pandeminin ilerlemesi üzerinde önemli bir etkiye sahip olabilir.
Tutkun, G., Özgen, A. O., Bilge, U. (2022). Models of spike, envelope and membrane proteins of SARS-CoV-2 variants for possible therapeutics. Journal of Medical Topics and Updates, Cilt: 1 Sayı: 3, 133–141. https://ajindex.com/articles/1618899
Alsulami, A. F., Thomas, S. E., Jamasb, A. R., Beaudoin, C. A., Moghul, I., Bannerman, B., Copoiu, L., Vedithi, S. C., Torres, P., & Blundell, T. L. (2021). SARS-CoV-2 3D database: Understanding the coronavirus proteome and evaluating possible drug targets. Briefings in Bioinformatics, 22(2), 769–780. https://doi.org/10.1093/bib/bbaa404
Arabi, Y. M., Asiri, A. Y., Assiri, A. M., Balkhy, H. H., Al Bshabshe, A., Al Jeraisy, M., Mandourah, Y., Azzam, M. H. A., Bin Eshaq, A. M., Al Johani, S., Al Harbi, S., Jokhdar, H. A. A., Deeb, A. M., Memish, Z. A., Jose, J., Ghazal, S., Al Faraj, S., Al Mekhlafi, G. A., Sherbeeni, N. M., … Saudi Critical Care Trials Group. (2020). Interferon Beta-1b and Lopinavir-Ritonavir for Middle East Respiratory Syndrome. The New England Journal of Medicine, 383(17), 1645–1656. https://doi.org/10.1056/NEJMoa2015294
Bayrakdar, F., Cosgun, Y., Yalcin, S., & Korukluoglu, G. (2021). HCoV-19/Turkey/HSGM-F10304/2021 (GISAID EpiCoV EPI_ISL_8082633). Ministry of Health Turkey. https://www.epicov.org/epi3/frontend#3f63b7
Buxbaum, E. (2015). Protein Structure. In E. Buxbaum, Fundamentals of Protein Structure and Function (pp. 15–64). Springer International Publishing. https://doi.org/10.1007/978-3-319-19920-7_2
Cao, Y., Wang, J., Jian, F., Xiao, T., Song, W., Yisimayi, A., Huang, W., Li, Q., Wang, P., An, R., Wang, J., Wang, Y., Niu, X., Yang, S., Liang, H., Sun, H., Li, T., Yu, Y., Cui, Q., … Xie, X. S. (2021). Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Nature. https://doi.org/10.1038/d41586-021-03796-6
Cao, Y., Yang, R., Lee, I., Zhang, W., Sun, J., Wang, W., & Meng, X. (2021). Characterization of the SARS-CoV-2 E Protein: Sequence, Structure, Viroporin, and Inhibitors. Protein Science, 30(6), 1114–1130. https://doi.org/10.1002/pro.4075
Cubuk, J., Alston, J. J., Incicco, J. J., Singh, S., Stuchell-Brereton, M. D., Ward, M. D., Zimmerman, M. I., Vithani, N., Griffith, D., Wagoner, J. A., Bowman, G. R., Hall, K. B., Soranno, A., & Holehouse, A. S. (2021). The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. Nature Communications, 12(1), 1936. https://doi.org/10.1038/s41467-021-21953-3
de Oliveira, O. V., Rocha, G. B., Paluch, A. S., & Costa, L. T. (2021). Repurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screening. Journal of Biomolecular Structure and Dynamics, 39(11), 3924–3933. https://doi.org/10.1080/07391102.2020.1772885
Enjuanes, L., Smerdou, C., Castilla, J., Antón, I. M., Torres, J. M., Sola, I., Golvano, J., Sánchez, J. M., & Pintado, B. (1995). Development of protection against coronavirus induced diseases. A review. Advances in Experimental Medicine and Biology, 380, 197–211. https://doi.org/10.1007/978-1-4615-1899-0_34
Good, D. J. (2020). A low-cost, in silico nutritional genomics course-based undergraduate research experience applicable to multiple disciplines. Biochemistry and Molecular Biology Education, 48(4), 320–328. https://doi.org/10.1002/bmb.21352
Huang, Y., Yang, C., Xu, X., Xu, W., & Liu, S. (2020). Structural and functional properties of SARS-CoV-2 spike protein: Potential antivirus drug development for COVID-19. Acta Pharmacologica Sinica, 41(9), 1141–1149. https://doi.org/10.1038/s41401-020-0485-4
Iannarella, R., Lattanzi, C., Cannata, G., Argentiero, A., Neglia, C., Fainardi, V., Pisi, G., & Esposito, S. (2020). Coronavirus infections in children: From SARS and MERS to COVID-19, a narrative review of epidemiological and clinical features. Acta Biomedica Atenei Parmensis, 91(3), e2020032–e2020032. https://doi.org/10.23750/abm.v91i3.10294
Kardani, K., Bolhassani, A., & Namvar, A. (2020). An overview of in silico vaccine design against different pathogens and cancer. Expert Review of Vaccines, 19(8), 699–726. https://doi.org/10.1080/14760584.2020.1794832
Li, Y., Zhang, Z., Yang, L., Lian, X., Xie, Y., Li, S., Xin, S., Cao, P., & Lu, J. (2020). The MERS-CoV Receptor DPP4 as a Candidate Binding Target of the SARS-CoV-2 Spike. IScience, 23(6), 101160. https://doi.org/10.1016/j.isci.2020.101160
McIntosh, K., Dees, J. H., Becker, W. B., Kapikian, A. Z., & Chanock, R. M. (1967). Recovery in tracheal organ cultures of novel viruses from patients with respiratory disease. Proceedings of the National Academy of Sciences of the United States of America, 57(4), 933–940. https://doi.org/10.1073/pnas.57.4.933
Mousavizadeh, L., & Ghasemi, S. (2021). Genotype and phenotype of COVID-19: Their roles in pathogenesis. Journal of Microbiology, Immunology and Infection, 54(2), 159–163. https://doi.org/10.1016/j.jmii.2020.03.022
Omrani, A. S., Saad, M. M., Baig, K., Bahloul, A., Abdul-Matin, M., Alaidaroos, A. Y., Almakhlafi, G. A., Albarrak, M. M., Memish, Z. A., & Albarrak, A. M. (2014). Ribavirin and interferon alfa-2a for severe Middle East respiratory syndrome coronavirus infection: A retrospective cohort study. The Lancet. Infectious Diseases, 14(11), 1090–1095. https://doi.org/10.1016/S1473-3099(14)70920-X
Portelli, S., Olshansky, M., Rodrigues, C. H. M., D’Souza, E. N., Myung, Y., Silk, M., Alavi, A., Pires, D. E. V., & Ascher, D. B. (2020). Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource. Nature Genetics, 52(10), 999–1001. https://doi.org/10.1038/s41588-020-0693-3
Pulliam, J. R. C., Schalkwyk, C. van, Govender, N., Gottberg, A. von, Cohen, C., Groome, M. J., Dushoff, J., Mlisana, K., & Moultrie, H. (2021). Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa (p. 2021.11.11.21266068). https://doi.org/10.1101/2021.11.11.21266068
Raghav, S., Ghosh, A., Turuk, J., Kumar, S., Jha, A., Madhulika, S., Priyadarshini, M., Biswas, V. K., Shyamli, P. S., Singh, B., Singh, N., Singh, D., Datey, A., Avula, K., Smita, S., Sabat, J., Bhattacharya, D., Kshatri, J. S., Vasudevan, D., … Sherpa, T. (2020). Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. Frontiers in Microbiology, 11, 2847. https://doi.org/10.3389/fmicb.2020.594928
Shamsi, A., Mohammad, T., Anwar, S., Amani, S., Khan, M. S., Husain, F. M., Rehman, Md. T., Islam, A., & Hassan, M. I. (2021). Potential drug targets of SARS-CoV-2: From genomics to therapeutics. International Journal of Biological Macromolecules, 177, 1–9. https://doi.org/10.1016/j.ijbiomac.2021.02.071
Shen, L., Bard, J. D., Triche, T. J., Judkins, A. R., Biegel, J. A., & Gai, X. (2021). Emerging variants of concern in SARS-CoV-2 membrane protein: A highly conserved target with potential pathological and therapeutic implications. Emerging Microbes & Infections, 10(1), 885–893. https://doi.org/10.1080/22221751.2021.1922097
Siu, Y. L., Teoh, K. T., Lo, J., Chan, C. M., Kien, F., Escriou, N., Tsao, S. W., Nicholls, J. M., Altmeyer, R., Peiris, J. S. M., Bruzzone, R., & Nal, B. (2008). The M, E, and N structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles. Journal of Virology, 82(22), 11318–11330. https://doi.org/10.1128/JVI.01052-08
Swain, S. S., Rout, S. S., Sahoo, A., Oyedemi, S. O., & Hussain, T. (2021). Antituberculosis, antioxidant and cytotoxicity profiles of quercetin: A systematic and cost-effective in silico and in vitro approach. Natural Product Research, 0(0), 1–5. https://doi.org/10.1080/14786419.2021.2008387
Toparslan, E., Karabag, K., & Bilge, U. (2020). A workflow with R: Phylogenetic analyses and visualizations using mitochondrial cytochrome b gene sequences. PLOS ONE, 15(12), e0243927. https://doi.org/10.1371/journal.pone.0243927
Troyano-Hernáez, P., Reinosa, R., & Holguín, Á. (2021). Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Viruses, 13(2), 243. https://doi.org/10.3390/v13020243
Wormser, G. P., & Aitken, C. (2010). Clinical Virology, 3rd Edition Edited by D. D. Richman, R. J. Whitley, and F. G. Hayden Washington, DC: ASM Press, 2009. 1408 pp, Illustrated. $259.59 (hardcover). Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America, 50(12), 1692. https://doi.org/10.1086/652862
Zhang, C., Zheng, W., Huang, X., Bell, E. W., Zhou, X., & Zhang, Y. (2020). Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1. Journal of Proteome Research, 19(4), 1351–1360. https://doi.org/10.1021/acs.jproteome.0c00129
Zheng, W., Zhang, C., Li, Y., Pearce, R., Bell, E. W., & Zhang, Y. (2021). Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. Cell Reports Methods, 1(3), 100014. https://doi.org/10.1016/j.crmeth.2021.100014