Novel CRISPR-Cas9 approach to combat with COVID-19

Jahanzaib Ali

Abstract

Background: The recent outbreak of Corona Virus has affected people all over the world so that WHO declared it a pandemic. This pandemic has become a major problem for people, health professionals, and research institutes that how to combat SARS-CoV-2. The objective of this review article is to provide a brief study that CRISPR/Cas9 can be used to combat SARS-CoV-2. Methods: The comparison of three genome editing techniques (ZNF, TALEN, and CRISPR/Cas9) is done. The mechanism of action of CRISPR/Cas9 is discussed. Results: The studies provided in this review article suggest that it is difficult to recognize this virus as they have their own metabolic machinery and they replicate their selves in the host cell and consume host cellular products to perform their own functions. The COVID-19 proteins may contain some specific areas that are suitable targets for therapy, such as tiny inhibitor molecules for viral polymerase, or impede the attachment of viruses to the receptor sites, for example, viral coat proteins can be used for vaccination purposes. Conclusion: CRISPR-Cas9 can be used to control the SARS-CoV-2 genome from replication and spread to other parts of the body as it can edit the genome quite efficiently. This proposed model will help in targeting the SARS-CoV-2 genome more precisely in the future.

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References

Amin, M. (2021). COVID-19 and the liver: overview. Eur J Gastroenterol Hepatol, 33(3), 309-311. doi: 10.1097/meg.0000000000001808
Anka, A. U., Tahir, M. I., Abubakar, S. D., Alsabbagh, M., Zian, Z., Hamedifar, H., . . . Azizi, G. (2021). Coronavirus disease 2019 (COVID-19): An overview of the immunopathology, serological diagnosis and management. Scand J Immunol, 93(4), e12998. doi: 10.1111/sji.12998
Bhaya, D., Davison, M., & Barrangou, R. (2011). CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet, 45, 273-297. doi: 10.1146/annurev-genet-110410-132430
Böger, B., Fachi, M. M., Vilhena, R. O., Cobre, A. F., Tonin, F. S., & Pontarolo, R. (2021). Systematic review with meta-analysis of the accuracy of diagnostic tests for COVID-19. Am J Infect Control, 49(1), 21-29. doi: 10.1016/j.ajic.2020.07.011
Chen, J. S., Ma, E., Harrington, L. B., Da Costa, M., Tian, X., Palefsky, J. M., & Doudna, J. A. (2018). CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science, 360(6387), 436-439. doi: 10.1126/science.aar6245
Cho, S. W., Kim, S., Kim, Y., Kweon, J., Kim, H. S., Bae, S., & Kim, J. S. (2014). Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res, 24(1), 132-141. doi: 10.1101/gr.162339.113
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., . . . Zhang, F. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science, 339(6121), 819-823. doi: 10.1126/science.1231143
Cui, J., Li, F., & Shi, Z. L. (2019). Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol, 17(3), 181-192. doi: 10.1038/s41579-018-0118-9
Doudna, J. A., & Charpentier, E. (2014). Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science, 346(6213), 1258096. doi: 10.1126/science.1258096
Drosten, C., Preiser, W., Günther, S., Schmitz, H., & Doerr, H. W. (2003). Severe acute respiratory syndrome: identification of the etiological agent. Trends Mol Med, 9(8), 325-327. doi: 10.1016/s1471-4914(03)00133-3
Esbin, M. N., Whitney, O. N., Chong, S., Maurer, A., Darzacq, X., & Tjian, R. (2020). Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection. Rna, 26(7), 771-783. doi: 10.1261/rna.076232.120
Freije, C. A., Myhrvold, C., Boehm, C. K., Lin, A. E., Welch, N. L., Carter, A., . . . Sabeti, P. C. (2019). Programmable Inhibition and Detection of RNA Viruses Using Cas13. Mol Cell, 76(5), 826-837.e811. doi: 10.1016/j.molcel.2019.09.013
Gaj, T., Gersbach, C. A., & Barbas, C. F., 3rd. (2013). ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol, 31(7), 397-405. doi: 10.1016/j.tibtech.2013.04.004
Gaj, T., Guo, J., Kato, Y., Sirk, S. J., & Barbas, C. F., 3rd. (2012). Targeted gene knockout by direct delivery of zinc-finger nuclease proteins. Nat Methods, 9(8), 805-807. doi: 10.1038/nmeth.2030
Giovanetti, M., Benedetti, F., Campisi, G., Ciccozzi, A., Fabris, S., Ceccarelli, G., . . . Ciccozzi, M. (2021). Evolution patterns of SARS-CoV-2: Snapshot on its genome variants. Biochem Biophys Res Commun, 538, 88-91. doi: 10.1016/j.bbrc.2020.10.102
Habibzadeh, P., & Stoneman, E. K. (2020). The Novel Coronavirus: A Bird's Eye View. Int J Occup Environ Med, 11(2), 65-71. doi: 10.15171/ijoem.2020.1921
Harrison, A. G., Lin, T., & Wang, P. (2020). Mechanisms of SARS-CoV-2 Transmission and Pathogenesis. Trends Immunol, 41(12), 1100-1115. doi: 10.1016/j.it.2020.10.004
Hossain, M. G., Javed, A., Akter, S., & Saha, S. (2021). SARS-CoV-2 host diversity: An update of natural infections and experimental evidence. J Microbiol Immunol Infect, 54(2), 175-181. doi: 10.1016/j.jmii.2020.06.006
Hryhorowicz, M., Lipiński, D., Zeyland, J., & Słomski, R. (2017). CRISPR/Cas9 Immune System as a Tool for Genome Engineering. Arch Immunol Ther Exp (Warsz), 65(3), 233-240. doi: 10.1007/s00005-016-0427-5
Hsieh, P. K., Chang, S. C., Huang, C. C., Lee, T. T., Hsiao, C. W., Kou, Y. H., . . . Chang, M. F. (2005). Assembly of severe acute respiratory syndrome coronavirus RNA packaging signal into virus-like particles is nucleocapsid dependent. J Virol, 79(22), 13848-13855. doi: 10.1128/jvi.79.22.13848-13855.2005
Hsu, P. D., Lander, E. S., & Zhang, F. (2014). Development and applications of CRISPR-Cas9 for genome engineering. Cell, 157(6), 1262-1278. doi: 10.1016/j.cell.2014.05.010
Hu, B., Guo, H., Zhou, P., & Shi, Z. L. (2021). Characteristics of SARS-CoV-2 and COVID-19. Nat Rev Microbiol, 19(3), 141-154. doi: 10.1038/s41579-020-00459-7
Hu, W., Kaminski, R., Yang, F., Zhang, Y., Cosentino, L., Li, F., . . . Khalili, K. (2014). RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection. Proc Natl Acad Sci U S A, 111(31), 11461-11466. doi: 10.1073/pnas.1405186111
Janik, E., Niemcewicz, M., Ceremuga, M., Krzowski, L., Saluk-Bijak, J., & Bijak, M. (2020). Various Aspects of a Gene Editing System-CRISPR-Cas9. Int J Mol Sci, 21(24). doi: 10.3390/ijms21249604
Jin, Y., Yang, H., Ji, W., Wu, W., Chen, S., Zhang, W., & Duan, G. (2020). Virology, Epidemiology, Pathogenesis, and Control of COVID-19. Viruses, 12(4). doi: 10.3390/v12040372
Kang, Y., & Xu, S. (2020). Comprehensive overview of COVID-19 based on current evidence. Dermatol Ther, 33(5), e13525. doi: 10.1111/dth.13525
Kennedy, E. M., & Cullen, B. R. (2015). Bacterial CRISPR/Cas DNA endonucleases: A revolutionary technology that could dramatically impact viral research and treatment. Virology, 479-480, 213-220. doi: 10.1016/j.virol.2015.02.024
Khalili, K., Kaminski, R., Gordon, J., Cosentino, L., & Hu, W. (2015). Genome editing strategies: potential tools for eradicating HIV-1/AIDS. J Neurovirol, 21(3), 310-321. doi: 10.1007/s13365-014-0308-9
Khan, I., Ahmed, Z., Sarwar, A., Jamil, A., & Anwer, F. (2020). The Potential Vaccine Component for COVID-19: A Comprehensive Review of Global Vaccine Development Efforts. Cureus, 12(6), e8871. doi: 10.7759/cureus.8871
Khan, S., Ullah, M. W., Siddique, R., Nabi, G., Manan, S., Yousaf, M., & Hou, H. (2016). Role of Recombinant DNA Technology to Improve Life. Int J Genomics, 2016, 2405954. doi: 10.1155/2016/2405954
Kim, Y. G., Li, L., & Chandrasegaran, S. (1994). Insertion and deletion mutants of FokI restriction endonuclease. J Biol Chem, 269(50), 31978-31982.
Lauer, S. A., Grantz, K. H., Bi, Q., Jones, F. K., Zheng, Q., Meredith, H. R., . . . Lessler, J. (2020). The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application. Ann Intern Med, 172(9), 577-582. doi: 10.7326/m20-0504
Ludwig, S., & Zarbock, A. (2020). Coronaviruses and SARS-CoV-2: A Brief Overview. Anesth Analg, 131(1), 93-96. doi: 10.1213/ane.0000000000004845
Luk, H. K. H., Li, X., Fung, J., Lau, S. K. P., & Woo, P. C. Y. (2019). Molecular epidemiology, evolution and phylogeny of SARS coronavirus. Infect Genet Evol, 71, 21-30. doi: 10.1016/j.meegid.2019.03.001
Majumder, J., & Minko, T. (2021). Recent Developments on Therapeutic and Diagnostic Approaches for COVID-19. Aaps j, 23(1), 14. doi: 10.1208/s12248-020-00532-2
Mali, P., Aach, J., Stranges, P. B., Esvelt, K. M., Moosburner, M., Kosuri, S., . . . Church, G. M. (2013). CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol, 31(9), 833-838. doi: 10.1038/nbt.2675
Mali, P., Esvelt, K. M., & Church, G. M. (2013). Cas9 as a versatile tool for engineering biology. Nat Methods, 10(10), 957-963. doi: 10.1038/nmeth.2649
Memi, F., Ntokou, A., & Papangeli, I. (2018). CRISPR/Cas9 gene-editing: Research technologies, clinical applications and ethical considerations. Semin Perinatol, 42(8), 487-500. doi: 10.1053/j.semperi.2018.09.003
Mohamadian, M., Chiti, H., Shoghli, A., Biglari, S., Parsamanesh, N., & Esmaeilzadeh, A. (2021). COVID-19: Virology, biology and novel laboratory diagnosis. J Gene Med, 23(2), e3303. doi: 10.1002/jgm.3303
Pairo-Castineira, E., Clohisey, S., Klaric, L., Bretherick, A. D., Rawlik, K., Pasko, D., . . . Baillie, J. K. (2021). Genetic mechanisms of critical illness in COVID-19. Nature, 591(7848), 92-98. doi: 10.1038/s41586-020-03065-y
Petrosillo, N., Viceconte, G., Ergonul, O., Ippolito, G., & Petersen, E. (2020). COVID-19, SARS and MERS: are they closely related? Clin Microbiol Infect, 26(6), 729-734. doi: 10.1016/j.cmi.2020.03.026
Phan, M. V. T., Ngo Tri, T., Hong Anh, P., Baker, S., Kellam, P., & Cotten, M. (2018). Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains. Virus Evol, 4(2), vey035. doi: 10.1093/ve/vey035
Rabaan, A. A., Al-Ahmed, S. H., Haque, S., Sah, R., Tiwari, R., Malik, Y. S., . . . Rodriguez-Morales, A. J. (2020). SARS-CoV-2, SARS-CoV, and MERS-COV: A comparative overview. Infez Med, 28(2), 174-184.
Ran, F. A., Hsu, P. D., Lin, C. Y., Gootenberg, J. S., Konermann, S., Trevino, A. E., . . . Zhang, F. (2013). Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell, 154(6), 1380-1389. doi: 10.1016/j.cell.2013.08.021
Richardson, C. D., Ray, G. J., DeWitt, M. A., Curie, G. L., & Corn, J. E. (2016). Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat Biotechnol, 34(3), 339-344. doi: 10.1038/nbt.3481
Salian, V. S., Wright, J. A., Vedell, P. T., Nair, S., Li, C., Kandimalla, M., . . . Kandimalla, K. K. (2021). COVID-19 Transmission, Current Treatment, and Future Therapeutic Strategies. Mol Pharm, 18(3), 754-771. doi: 10.1021/acs.molpharmaceut.0c00608
Sanyal, S. (2020). How SARS-CoV-2 (COVID-19) spreads within infected hosts - what we know so far. Emerg Top Life Sci, 4(4), 371-378. doi: 10.1042/etls20200165
Satija, N., & Lal, S. K. (2007). The molecular biology of SARS coronavirus. Ann N Y Acad Sci, 1102(1), 26-38. doi: 10.1196/annals.1408.002
Shen, B., Zhang, W., Zhang, J., Zhou, J., Wang, J., Chen, L., . . . Skarnes, W. C. (2014). Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects. Nat Methods, 11(4), 399-402. doi: 10.1038/nmeth.2857
Shi, Y., Wang, G., Cai, X. P., Deng, J. W., Zheng, L., Zhu, H. H., . . . Chen, Z. (2020). An overview of COVID-19. J Zhejiang Univ Sci B, 21(5), 343-360. doi: 10.1631/jzus.B2000083
Stadler, K., Masignani, V., Eickmann, M., Becker, S., Abrignani, S., Klenk, H. D., & Rappuoli, R. (2003). SARS--beginning to understand a new virus. Nat Rev Microbiol, 1(3), 209-218. doi: 10.1038/nrmicro775
Veres, A., Gosis, B. S., Ding, Q., Collins, R., Ragavendran, A., Brand, H., . . . Musunuru, K. (2014). Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. Cell Stem Cell, 15(1), 27-30. doi: 10.1016/j.stem.2014.04.020
White, M. K., Hu, W., & Khalili, K. (2015). The CRISPR/Cas9 genome editing methodology as a weapon against human viruses. Discov Med, 19(105), 255-262.
Wiersinga, W. J., Rhodes, A., Cheng, A. C., Peacock, S. J., & Prescott, H. C. (2020). Pathophysiology, Transmission, Diagnosis, and Treatment of Coronavirus Disease 2019 (COVID-19): A Review. Jama, 324(8), 782-793. doi: 10.1001/jama.2020.12839
Wright, D. A., Li, T., Yang, B., & Spalding, M. H. (2014). TALEN-mediated genome editing: prospects and perspectives. Biochem J, 462(1), 15-24. doi: 10.1042/bj20140295
Xu, X., Chen, P., Wang, J., Feng, J., Zhou, H., Li, X., . . . Hao, P. (2020). Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Sci China Life Sci, 63(3), 457-460. doi: 10.1007/s11427-020-1637-5
Yamayoshi, S., Sakai-Tagawa, Y., Koga, M., Akasaka, O., Nakachi, I., Koh, H., . . . Kawaoka, Y. (2020). Comparison of Rapid Antigen Tests for COVID-19. Viruses, 12(12). doi: 10.3390/v12121420
Yang, L., Grishin, D., Wang, G., Aach, J., Zhang, C. Z., Chari, R., . . . Church, G. (2014). Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells. Nat Commun, 5, 5507. doi: 10.1038/ncomms6507
Yi, Y., Lagniton, P. N. P., Ye, S., Li, E., & Xu, R. H. (2020). COVID-19: what has been learned and to be learned about the novel coronavirus disease. Int J Biol Sci, 16(10), 1753-1766. doi: 10.7150/ijbs.45134
Yüce, M., Filiztekin, E., & Özkaya, K. G. (2021). COVID-19 diagnosis -A review of current methods. Biosens Bioelectron, 172, 112752. doi: 10.1016/j.bios.2020.112752
Zhou, P., Yang, X. L., Wang, X. G., Hu, B., Zhang, L., Zhang, W., . . . Shi, Z. L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270-273. doi: 10.1038/s41586-020-2012-7

Authors

Jahanzaib Ali
writter1008@gmail.com (Primary Contact)
Ali, J. (2023). Novel CRISPR-Cas9 approach to combat with COVID-19. BIOEDUSCIENCE, 7(2), 182–191. https://doi.org/10.22236/jbes/12275

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