Origen del perfil de mutaciones presente en las secuencias de SARS-CoV-2 en El Salvador
Keywords:
SARS-CoV-2, D614G, NGS, 2019- nCoV, COVID-19sAbstract
Introduction: this paper describes the mutation profile and analyzes the different mechanisms responsible for mutations in the first 6 complete sequences of the SARS-CoV-2 genome from samples of Salvadoran patients diagnosed with COVID-19. Objective: to analyze the mutation profile according to the mechanisms that give rise to the mutations present in SARS-CoV-2. Methodology: an analysis of the changes in the genome sequences of SARS- CoV-2 was performed using as reference the Wuhan sequence (NC_045512.2), once the mutations were known, we proceeded to tabulate and generate graphs of the SNPs and affected genes. The possible described mechanisms responsible for generating the mutations studied were also analyzed. Results: the analysis revealed that the mutations found have been reported worldwide, however, the sequences present greater similarity with the changes described in North America, added to this, the global analysis allowed classifying them in the GISAID GH broth, and pangolin lineage B.1.2 and B.1.370, both lineages with a high prevalence in the USA, which reinforces the hypothesis of the North American origin of the Salvadoran sequences. The pattern of changes in the SARS-CoV-2 genome in El Salvador suggests that the mutations are due to the action of APOBEC deaminase (C>T transition) and ADARs (A>G transition), to the effect of reactive oxygen species (ROS) (G>T transversion), to errors in the replication transcription complex (RTC) that escape the correction of the exonuclease activity of NSP14 and finally mutations as a result of recombination mechanisms.
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Alouane, T., Laamarti, M., Essabbar, A., Hakmi, M., Bendani, H., Laamarti, R., Ghrifi, F., Allam, L., Aanniz, T., Mentag, R., Sbabou, L., Nejjari, C., Amzazi, S., & Belyamani, L. (2020). SARS-CoV-2 Genomes: Moving Toward a Universal Vaccine for the “Confined Virus”? 1–19.
Angelini, M. M., Akhlaghpour, M., Neuman, B. W., & Buchmeier, M. J. (2013). Severe acute respiratory syndrome coronavirus nonstructural proteins 3, 4, and 6 induce double-membrane vesicles. MBio, 4(4), 1–10. https://doi.org/10.1128/mBio.00524-13
Becares, M., Pascual-iglesias, A., Nogales, A., Sola, I., Enjuanes, L., & Zuñiga, S. (2016). Mutagenesis of Coronavirus nsp14 Reveals Its Potential Role in. Journal of Virology, 90(11), 5399– 5414. https://doi. org/10.1128/JVI.03259-15.Editor
Brufsky, A. (2020). Distinct viral clades of SARS- CoV-2: Implications for modeling of viral spread. Journal of Medical Virology, 92(9), 1386–1390. https://doi.org/10.1002/ jmv.25902
Case, J. B., Ashbrook, A. W., Dermody, T. S., & Denison, M. R. (2016). Mutagenesis of S -Adenosyl-l-Methionine-Binding Residues in Coronavirus nsp14 N7- Methyltransferase Demonstrates Differing Requirements for Genome Translation and Resistance to Innate Immunity . Journal of Virology, 90(16), 7248–7256. https://doi.org/10.1128/ jvi.00542-16
Chen, Y., Cai, H., Pan, J., Xiang, N., Tien,P., Ahola, T., & Guo, D. (2009). Functional screen reveals SARS coronavirus nonstructural protein nsp14 as a novel cap N7 methyltransferase. Proceedings of the National Academy of Sciences of the United States of America, 106(9), 3484–3489. https://doi.org/10.1073/ pnas.0808790106
Chen, Y., Liu, Q., & Guo, D. (2020). Emerging coronaviruses: Genome structure, replication, and pathogenesis. Journal of Medical Virology, 92(4), 418–423. https://doi.org/10.1002/ jmv.25681
Di Giorgio, S., Martignano, F., Torcia, M. G., Mattiuz, G., & Conticello, S. G. (2020). Evidence for host-dependent RNA editing in the transcriptome of SARS- CoV-2. BioRxiv, June, 1–8. https://doi. org/10.1101/2020.03.02.973255
Eisenberg, E., & Levanon, E. Y. (2018). A-to-I RNA editing— immune protector and transcriptome diversifier. Nature Reviews Genetics, 19(8), 473–490. https:// doi.org/10.1038/ s41576-018-0006-1
Ferron, F., Subissi, L., De Morais, A. T. S., Le, N. T. T., Sevajol, M., Gluais, L., Decroly, E., Vonrhein, C., Bricogne, G., Canard, B., & Imbert, I. (2017). Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA. Proceedings of the National Academy of Sciences of the United States of America, 115(2), E162–E171. https://doi.org/10.1073/ pnas.1718806115
Gorbalenya, A. E., Baker, S. C., Baric, R. S., de Groot, R. J., Drosten, C., Gulyaeva, A. A., Haagmans, B. L., Lauber, C., Leontovich, A. M., Neuman, B. W., Penzar, D., Perlman, S., Poon, L. L. M., Samborskiy, D. V., Sidorov, I. A., Sola, I., & Ziebuhr, J. (2020). The species severe acute respiratory syndrome-related coronavirus: Classifying 2019- nCoV and naming it SARS-CoV-2. Nature Microbiology, 5(4), 536–544. https://doi. org/10.1038/s41564-020-0695-z
Gorbalenya, A. E., Enjuanes, L., Ziebuhr, J., & Snijder, E. J. (2006). Nidovirales: Evolving the largest RNA virus genome Virus Research, 117(1), 17–37. https://doi. org/10.1016/j.virusres. 2006.01.017
Gribble, J., Stevens, L. J., Agostini, M. L., Anderson-Daniels, J., Chappell, J. D., Lu, X., Pruijssers, A. J., Routh, A. L., & Denison, M. R. (2021). The coronavirus proofreading exoribonuclease mediates extensive viral recombination. PLoS Pathogens, 17(1), 1–28. https://doi. org/10.1371/journal.ppat.1009226
Harris, R. S., & Dudley, J. P. (2015). APOBECs and virus restriction. Virology, 479– 480, 131–145. https://doi.org/10.1016/j. virol.2015.03.012
Hernández Ávila, C. E., Ortega Pérez, C. A., Rivera, N. R., & López, X. S. (2021). Primeras seis secuencias del genoma completo de SARS-CoV-2 por NGS en El Salvador. Alerta, Revista Científica Del Instituto Nacional de Salud, 4(1), 61–66. https:// doi.org/10.5377/alerta.v4i1.10682
Huang, C., Wang, Y., Li, X., Ren, L., Zhao, J., Hu, Y., Zhang, L., Fan, G., Xu, J., Gu, X., Cheng, Z., Yu, T., Xia, J., Wei, Y., Wu, W., Xie, X., Yin, W., Li, H., Liu, M., … Cao, B. (2020). Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. The Lancet, 395(10223), 497–506. https://doi. org/10.1016/S0140-6736 (20)30183-5
Kuljić-Kapulica, N., & Budisin, A. (1992). Coronaviruses. Srpski Arhiv Za Celokupno Lekarstvo, 120(7–8), 215–218. https:// doi.org/10.4161/rna.8.2.15013
Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., Bi, Y., Ma, X., Zhan, F., Wang, L., Hu, T., Zhou, H., Hu, Z., Zhou, W., Zhao, L., Tan, W. (2020). Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding. The Lancet, 395(10224), 565–574. https://doi. org/10.1016/S0140-6736 (20)30251-8
Mercatelli, D., & Giorgi, F. M. (2020). Geographic and Genomic Distribution of SARS- CoV-2 Mutations. Frontiers in Microbiology, 11(July), 1–13. https://doi. org/10.3389/fmicb.2020.01800
Niocel, M., Appourchaux, R., Nguyen, X. N., Delpeuch, M., & Cimarelli, A. (2019). The DNA damage induced by the Cytosine Deaminase APOBEC3A Leads to the production of ROS. Scientific Reports, 9(1), 1–11. https://doi.org/10.1038/s41598- 019-40941-8
Perlman, S., & Netland, J. (2009). Coronaviruses post-SARS: Update on replication and pathogenesis. Nature Reviews Microbiology, 7(6), 439–450. https://doi. org/10.1038/nrmicro2147
Phuphuakrat, A., Kraiwong, R., Boonarkart, C., Lauhakirti, D., Lee, T.-H., & Auewarakul, P. (2008).Double-StrandedRNAAdenosine Deaminases Enhance Expression of Human Immunodeficiency Virus Type 1 Proteins. Journal of Virology, 82(21), 10864–10872. https://doi.org/10.1128/ jvi.00238-08
Pollpeter, D., Parsons, M., Sobala, A. E., Coxhead, S., Lang, R. D., Bruns, A. M., Papaioannou, S., McDonnell, J. M., Apolonia, L., Chowdhury, J. A., Horvath, C. M., & Malim, M. H. (2018). Deep sequencing of HIV-1 reverse transcripts reveals the multifaceted antiviral functions of APOBEC3G. Nature Microbiology, 3(2), 220–233. https://doi.org/10.1038/s41564-017-0063-9
Saberi, A., Gulyaeva, A. A., Brubacher, J. L., Newmark, P. A., & Gorbalenya, A. E. (2018). A planarian nidovirus expands the limits of RNA genome size. In PLoS Pathogens (Vol. 14, Issue 11). https://doi. org/10.1371/journal.ppat.1007314
Salter, J. D., & Smith, H. C. (2018). the Embrace of a Mutator: APOBEC Selection of Nucleic Acid Ligands. Trends in Biochemical Sciences, 43(8), 606–622. https://doi.org/10.1016/j. tibs.2018.04.013
Smith, E. C., & Denison, M. R. (2012). Implications of altered replication fidelity on the evolution and pathogenesis of coronaviruses. Current Opinion in Virology, 2(5), 519–524. https:// doi. org/10.1016/j.coviro.2012.07.005
Snijder, E. J., Limpens, R. W. A. L., de Wilde, A. H., de Jong, A. W. M., Zevenhoven-Dobbe, J. C., Maier, H. J., Faas, F. F. G. A., Koster, A. J., & Bárcena, M. (2020). A unifying structural and functional model of the coronavirus replication organelle: Tracking down RNA synthesis. PLoS Biology, 18(6), 1–25. https:// doi.org/10.1371/ journal.pbio.3000715
Sola, I., Almazán, F., Zúñiga, S., & Enjuanes, L. (2015). Continuous and Discontinuous RNA Synthesis in Coronaviruses. Annual Review of Virology, 2, 265–288. https://doi.org/10.1146/ annurev- virology-100114-055218
Sola, I., Mateos-Gomez, P. A., Almazan, F., Zuñiga, S., & Enjuanes, L. (2011). RNA-RNA and RNA-protein interactions in coronavirus replication and transcription. RNA Biology, 8(2), 237–248. https://doi. org/10.4161/rna.8.2.14991
Subissi, L., Imbert, I., Ferron, F., Collet, A., Coutard, B., Decroly, E., & Canard, B. (2014). SARS- CoV ORF1b-encoded nonstructural proteins 12-16: Replicative enzymes as antiviral targets. Antiviral Research, 101(1), 122–130. https://doi.org/10.1016/j. antiviral.2013.11.006
Tagliamonte, M. S., Abid, N., Borocci, S., Sangiovanni, E., Ostrov, D. A., Kosakovsky Pond, S. L., Salemi, M., Chillemi, G., & Mavian, C. (2021). Multiple recombination events and strong purifying selection at the origin of SARS-CoV-2 spike glycoprotein increased correlated dynamic movements. International Journal of Molecular Sciences, 22(1), 1–16. https://doi. org/10.3390/ijms22010080
Taylor, D. R., Puig, M., Darnell, M. E. R., Mihalik, K., & Feinstone, S. M. (2005). New Antiviral Pathway That Mediates Hepatitis C Virus Replicon Interferon Sensitivity through ADAR1. Journal of Virology, 79(10), 6291–6298. https://doi.org/10.1128/ jvi.79.10.6291-6298.2005
Wu, C., Liu, Y., Yang, Y., Zhang, P., Zhong, W., Wang, Y., Wang, Q., Xu, Y., Li, M., Li, X., Zheng, M., Chen, L., & Li, H. (2020). Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharmaceutica Sinica B, 10(5), 766–788. https://doi.org/10.1016/j. apsb.2020.02.008
Zahn, R. C., Schelp, I., Utermöhlen, O., & von Laer, D. (2007). A-to-G Hypermutation in the Genome of Lymphocytic Choriomeningitis Virus. Journal of Virology, 81(2), 457–464. https:// doi. org/10.1128/jvi.00067-06
Zhao, S.,& Chen, H.(2020).Modelingtheepidemic dynamics and control of COVID-19 outbreak in China. MedRxiv, 1–9. https:// doi.org/10.1101/2020.02.27.20028639
Zhou, P., Yang, X. Lou, Wang, X. G., Hu, B., Zhang, L., Zhang, W., Si, H. R., Zhu, Y., Li, B., Huang, C. L., Chen, H. D., Chen, J., Luo, Y., Guo, H., Jiang, R. Di, Liu, M. Q., Chen, Y., Shen, X. R., Wang, X., … Shi, Z. L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270–273. https://doi. org/10.1038/s41586-020-2012-7
Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., Niu, P., Zhan, F., Ma, X., Wang, D., Xu, W., Wu, G., Gao, G. F., & Tan, W. (2020). A Novel Coronavirus from Patients with Pneumonia in China, 2019. New England Journal of Medicine, 382(8), 727–733. https://doi.org/10.1056/ nejmoa2001017
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