Análisis molecular y filogenético de SARS-CoV-2 presente en Colombia
| datacite.rights | http://purl.org/coar/access_right/c_16ec | eng |
| dc.contributor.advisor | Arquéz Mendoza, Moisés Alberto | |
| dc.contributor.advisor | Lozano Solano, Dayan | |
| dc.contributor.author | Rivera Roca, Sirly Johanna | |
| dc.date.accessioned | 2022-02-14T20:40:23Z | |
| dc.date.available | 2022-02-14T20:40:23Z | |
| dc.date.issued | 2022 | |
| dc.description.abstract | l SARS-CoV-2 es un virus que constituye una importante amenaza para la salud a nivel mundial, debido a las altas tasas de infección y mortalidad que presenta. Pese a esto sus rasgos genéticos y los procesos evolutivos a los que está sometido aún son desconocido y es poca la información que existe en nuestro país. Para poder entender los procesos evolutivos a los que está sometido este nuevo virus, es importante obtener una filogenia de las diferentes variantes circulantes, analizar esta variabilidad entre otras características, tanto en nuestro territorio como en el mundo. En esta investigación, se realizó un análisis bioinformático de los genes de importancia estructural y funcional del virus, determinando de esta forma características genómicas y filogenéticas, de los subtipos de SARS-CoV-2 circulantes, mediante el método de inferencia bayesiana, adicionalmente se exploraron las relaciones entre las proteínas de algunas cepas y el grado de conservación total de la proteína E en todos los continentes. | spa |
| dc.description.abstract | SARS-CoV-2 is a virus that has caused major health threats in the world. The genetic traits and evolutionary processes of each of its proteins in Colombia are still largely unknown. In order to have more information on their phylogeny, variability or evolutionary mutability, in the strains that circulate in Colombia, in relation to the strains of the world, a bioinformatic analysis of the genes that translate to structural and accessory proteins was carried out, determining in this way genomic and phylogenetic characteristics of the circulating SARS-CoV-2 subtypes, through Bayesian inference methods and thus be participants in the construction of important bases, for the advancement of new diagnostic and treatment methods, finding relationships between the proteins of some strains and the total conservation of protein E in all continents. | eng |
| dc.format.mimetype | spa | |
| dc.identifier.uri | https://hdl.handle.net/20.500.12442/9364 | |
| dc.language.iso | spa | spa |
| dc.publisher | Ediciones Universidad Simón Bolivar | spa |
| dc.publisher | Facultad de Ciencias Básicas y Biomédicas | spa |
| dc.rights | Attribution-NonCommercial-NoDerivatives 4.0 Internacional | eng |
| dc.rights.accessrights | info:eu-repo/semantics/restrictedAccess | eng |
| dc.rights.uri | http://creativecommons.org/licenses/by-nc-nd/4.0/ | |
| dc.subject | Evolución | spa |
| dc.subject | Filogenética | spa |
| dc.subject | Variabilidad | spa |
| dc.subject | Genoma | spa |
| dc.subject | Mutabilidad | spa |
| dc.subject | Evolution | spa |
| dc.subject | Phylogenetics | eng |
| dc.subject | Variability | eng |
| dc.subject | Genome | eng |
| dc.subject | Mutability | eng |
| dc.title | Análisis molecular y filogenético de SARS-CoV-2 presente en Colombia | spa |
| dc.type.driver | info:eu-repo/semantics/masterThesis | eng |
| dc.type.spa | Trabajo de grado máster | spa |
| dcterms.references | Sifuentes-Rodríguez E, Palacios-Reyes D. Covid-19: The outbreak caused by a new coronavirus. Bol Med Hosp Infant Mex. 2020;77(2):47–53. | eng |
| dcterms.references | Pillay S, Giandhari J, Tegally H, Wilkinson E, Chimukangara B, Lessells R, et al. Whole genome sequencing of sars-cov-2: Adapting illumina protocols for quick and accurate outbreak investigation during a pandemic. Genes (Basel). 2020;11(8):1–13. | eng |
| dcterms.references | OMS. ABC de las Variantes Causantes del COVID-19 – Pregrados y Posgrados en Bogotá [Internet]. Orientaciones para la vigilancia de las variantes del SARS-CoV-2. 2021 [cited 04 November 2021]. Available at: https://www.konradlorenz.edu.co/noticias/abc-de-las-variantes-causantes-del-covid-19/ | spa |
| dcterms.references | Revised U.S. Surveillance Case Definition for Severe Acute Respiratory Syndrome (SARS) and Update on SARS Cases—United States and Worldwide, December 2003. JAMA [Internet]. 2004 [cited 11 Oktober 2021];291(2):173. Available at: https://www.cdc.gov/mmwr/preview/mmwrhtml/mm5249a2.htm | eng |
| dcterms.references | Reina J, Reina N. El coronavirus causante del síndrome respiratorio de Oriente Medio. Med Clin (Barc) [Internet]. 2015 [cited 11 Oktober 2021];145(12):529–31. Available at: https://www.who.int/es/news-room/fact-sheets/detail/middle-east-respiratory-syndrome-coronavirus-(mers-cov) | spa |
| dcterms.references | Nuevo coronavirus 2019 [Internet]. Organizacion Mundial de la Salud. 20202 [cited 17 Augustus 2021]. bl 5–8. Available at: https://www.who.int/es/emergencies/diseases/novel-coronavirus-2019?gclid=Cj0KCQjwwY-LBhD6ARIsACvT72P3W38IU_B1qpsbO8kQbHYewpeWkITELinZM48XKuYSexLXjMTvuncaApCiEALw_wcB | spa |
| dcterms.references | Sars-cov- E. Orientaciones para la vigilancia de las variantes del. 2021;(1):1–22. | spa |
| dcterms.references | Martínez-Flores D, Zepeda-Cervantes J, Cruz-Reséndiz A, Aguirre-Sampieri S, Sampieri A, Vaca L. SARS-CoV-2 Vaccines Based on the Spike Glycoprotein and Implications of New Viral Variants. Front Immunol. 12 Julie 2021;0:2774. | eng |
| dcterms.references | Lokman SM, Rasheduzzaman M, Salauddin A, Barua R, Tanzina AY, Rumi MH, et al. Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach. Infect Genet Evol [Internet]. 2020;84(May):104389. Available at: https://doi.org/10.1016/j.meegid.2020.104389 | eng |
| dcterms.references | Pachetti M, Marini B, Benedetti F, Giudici F, Mauro E, Storici P, et al. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med [Internet]. 2020;18(1):1–9. Available at: https://doi.org/10.1186/s12967-020-02344-6 | eng |
| dcterms.references | Kasibhatla SM, Kinikar M, Limaye S, Kale MM, Kulkarni-Kale U. Understanding evolution of SARS-CoV-2: A perspective from analysis of genetic diversity of RdRp gene. J Med Virol [Internet]. 2020;92(10):1932–7. Available at: http://dx.doi.org/10.1002/jmv.25909 | eng |
| dcterms.references | Woo PCY, Huang Y, Lau SKP, Yuen KY. Coronavirus genomics and bioinformatics analysis. Viruses. 2010;2(8):1805–20. | eng |
| dcterms.references | Duffy S. Why are RNA virus mutation rates so damn high? PLoS Biol. 2018;16(8):1–6. | eng |
| dcterms.references | Chitranshi N, Gupta VK, Rajput R, Godinez A, Pushpitha K, Shen T, et al. Evolving geographic diversity in SARS-CoV2 and in silico analysis of replicating enzyme 3CLprotargeting repurposed drug candidates. J Transl Med [Internet]. 2020;18(1):1–15. Available at: https://doi.org/10.1186/s12967-020-02448-z | eng |
| dcterms.references | Prompetchara E, Ketloy C, Palaga T. Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic. Asian Pacific J Allergy Immunol. 2020;38(1):1–9. | eng |
| dcterms.references | Rothan HA, Byrareddy SN. The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak. J Autoimmun [Internet]. 2020;109(February):102433. Available at: https://doi.org/10.1016/j.jaut.2020.102433 | eng |
| dcterms.references | Pastrian-Soto G. Bases Genéticas y Moleculares del COVID-19 (SARS-CoV-2). Mecanismos de Patogénesis y de Respuesta Inmune. Int J Odontostomatol. 2020;14(3):331–7. | spa |
| dcterms.references | FERNÁNDEZ JOSÉ M. Nuevo mapa genetico del SARS-CoV-2 [Internet]. 2020 [cited 10 Februarie 2022]. Available at: https://www.mendeley.com/reference-manager/library/recently-read/ | spa |
| dcterms.references | Fernando Benavides-Rosero M. COVID-19 y la pandemia global causada por un nuevo coronavirus COVID-19 and the global pandemic caused by a new coronavirus. [cited 26 Oktober 2021]; Available at: https://doi.org/10.22267/rus.202203.203 | eng |
| dcterms.references | Hassan SS, Aljabali AAA, Panda PK, Ghosh S, Attrish D, Choudhury PP, et al. A unique view of SARS-CoV-2 through the lens of ORF8 protein. Comput Biol Med [Internet]. 01 Junie 2021 [cited 25 Oktober 2021];133:104380. Available at: /pmc/articles/PMC8049180/ | eng |
| dcterms.references | Hassan SS, Choudhury PP, Roy B. Rare mutations in the accessory proteins ORF6, ORF7b, and ORF10 of the SARS-CoV-2 genomes. Meta Gene [Internet]. 01 Junie 2021 [cited 25 Oktober 2021];28:100873. Available at: /pmc/articles/PMC7890336/ | eng |
| dcterms.references | Li X, Hou P, Ma W, Wang X, Wang H, Yu Z, et al. SARS-CoV-2 ORF10 suppresses the antiviral innate immune response by degrading MAVS through mitophagy. Cell Mol Immunol 2021 191 [Internet]. 29 November 2021 [cited 11 Februarie 2022];19(1):67–78. Available at: https://www.nature.com/articles/s41423-021-00807-4 | eng |
| dcterms.references | Zhou Z, Huang C, Zhou Z, Huang Z, Su L, Kang S, et al. Structural insight reveals SARS-CoV-2 ORF7a as an immunomodulating factor for human CD14+ monocytes. iScience [Internet]. 19 Maart 2021 [cited 25 Oktober 2021];24(3). Available at: /pmc/articles/PMC7879101/ | eng |
| dcterms.references | Hassan SS, Attrish D, Ghosh S, Choudhury PP, Roy B. Pathogenic perspective of missense mutations of ORF3a protein of SARS-CoV-2. Virus Res. 15 Julie 2021;300:198441. | eng |
| dcterms.references | Pybus OG, Rambaut A. Evolutionary analysis of the dynamics of viral infectious disease. Nat Rev Genet. 2009;10(8):540–50. | eng |
| dcterms.references | Tang X, Wu C, Li X, Song Y, Yao X, Wu X, et al. On the origin and continuing evolution of SARS-CoV-2. Natl Sci Rev. 2020;7(6):1012–23. | eng |
| dcterms.references | Boni MF, Lemey P, Jiang X, Lam TTY, Perry BW, Castoe TA, et al. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat Microbiol [Internet]. 2020; Available at: http://dx.doi.org/10.1038/s41564-020-0771-4 | eng |
| dcterms.references | Wang C, Liu Z, Chen Z, Huang X, Xu M, He T, et al. The establishment of reference sequence for SARS-CoV-2 and variation analysis. J Med Virol. 2020;92(6):667–74. | eng |
| dcterms.references | van Dorp L, Acman M, Richard D, Shaw LP, Ford CE, Ormond L, et al. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. Infect Genet Evol [Internet]. 2020;83(May):104351. Available at: https://doi.org/10.1016/j.meegid.2020.104351 | eng |
| dcterms.references | Islam MR, Hoque MN, Rahman MS, Alam ASMRU, Akther M, Puspo JA, et al. Genome-wide analysis of SARS-CoV-2 virus strains circulating worldwide implicates heterogeneity. Sci Rep [Internet]. 2020;10(1):1–9. Available at: https://doi.org/10.1038/s41598-020-70812-6 | eng |
| dcterms.references | Hou W. Characterization of codon usage pattern in hepatitis C virus subtype 6xa. Clin Lab. 2020;66(8):1649–51. | eng |
| dcterms.references | Gomez-Carballa A, Bello X, Pardo-Seco J, Martinon-Torres F, Salas A. Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders. Genome Res [Internet]. 2020; Available at: http://www.ncbi.nlm.nih.gov/pubmed/32878977 | eng |
| dcterms.references | Nidhan K Biswas PPM. No Title. Anal RNA Seq 3636 SARS-CoV-2 Collect from 55 Ctries Reveal Sel sweep one virus type. 2020;151(5):450–8. | eng |
| dcterms.references | Jones LR, Manrique JM. Quantitative phylogenomic evidence reveals a spatially structured SARS-CoV-2 diversity. Virology [Internet]. 2020;550(August):70–7. Available at: https://doi.org/10.1016/j.virol.2020.08.010 | eng |
| dcterms.references | Khan MI, Khan ZA, Baig MH, Ahmad I, Farouk AEA, Song YG, et al. Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. PLoS One [Internet]. 2020;15(9):e0238344. Available at: http://dx.doi.org/10.1371/journal.pone.0238344 | eng |
| dcterms.references | Organización Mundial de la Salud (OMS). Seguimiento de las variantes del SARS-CoV-2 [Internet]. Organización Mundial de la Salud (OMS). 2021 [cited 22 Januarie 2021]. bl 1–4. Available at: https://www.who.int/es/activities/tracking-SARS-CoV-2-variants | spa |
| dcterms.references | BBC News Mundo. Coronavirus: qué se sabe de la variante de “doble mutación” encontrada en India [Internet]. BBC NEWS. 2021 [cited 22 Oktober 2021]. Available at: https://www.bbc.com/mundo/noticias-55662073 | spa |
| dcterms.references | Cuál es el origen de la variante Delta [Internet]. 2020 [cited 22 Oktober 2021]. Available at: https://www.abc.es/sociedad/abci-origen-variante-delta-nsv-202107081236_noticia.html?ref=https%3A%2F%2Fwww.abc.es%2Fsociedad%2Fabci-origen-variante-delta-nsv-202107081236_noticia.html | spa |
| dcterms.references | Aytekin E. Estas son las variantes de la COVID-19 que plantean dificultades en la lucha mundial contra la pandemia [Internet]. ANADOLU AGENCY. 2021 [cited 23 Oktober 2021]. Available at: https://www.aa.com.tr/es/mundo/estas-son-las-variantes-de-la-covid-19-que-plantean-dificultades-en-la-lucha-mundial-contra-la-pandemia/2284715 | spa |
| dcterms.references | West AP, Barnes CO, Yang Z, Bjorkman PJ. SARS-CoV-2 lineage B.1.526 emerging in the New York region detected by software utility created to query the spike mutational landscape. bioRxiv [Internet]. 23 Februarie 2021 [cited 23 Oktober 2021];2021.02.14.431043. Available at: https://www.biorxiv.org/content/10.1101/2021.02.14.431043v2 | eng |
| dcterms.references | Centro Integral de Informacion Biotecnologica NCBI. Recursos del SARS-CoV-2 - NCBI [Internet]. 1988 [cited 26 Oktober 2021]. Available at: https://www.ncbi.nlm.nih.gov/sars-cov-2/ | eng |
| dcterms.references | Recurso de análisis y base de datos de patógenos de virus (ViPR) - Coronaviridae - Herramientas de búsqueda de ViPR [Internet]. [cited 14 Oktober 2021]. Available at: https://www.viprbrc.org/brc/search_landing.spg?decorator=corona_ncov | spa |
| dcterms.references | Rozewicki J, Li S, Amada KM, Standley DM, Katoh K. MAFFT-DASH: Integrated protein sequence and structural alignment. Nucleic Acids Res. 01 Julie 2019;47(W1):W5–10. | eng |
| dcterms.references | CIPRES Science Gateway | Hogar [Internet]. "Creando el CIPRES Science Gateway para inferencia de grandes filogenia trees. 2010 [cited 13 Oktober 2021]. Available at: https://www.phylo.org/portal2/home.action | eng |
| dcterms.references | Sucar LE. Introduction to bayesian networks and influence diagrams. Decis Theory Model Appl Artif Intell Concepts Solut. 2011;9–32. | eng |
| dcterms.references | S C, F L. Bayesian phylogeny analysis via stochastic approximation Monte Carlo. Mol Phylogenet Evol [Internet]. November 2009 [cited 13 Oktober 2021];53(2):394–403. Available at: https://pubmed.ncbi.nlm.nih.gov/19589389/ | eng |
| dcterms.references | NCBI Virus [Internet]. [cited 15 Oktober 2021]. Available at: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=SARS-CoV-2, taxid:2697049 | eng |
| dcterms.references | Mena EL, Donahue CJ, Vaites LP, Li J, Rona G, O’Leary C, et al. ORF10–Cullin-2–ZYG11B complex is not required for SARS-CoV-2 infection. Proc Natl Acad Sci [Internet]. 27 April 2021 [cited 25 Oktober 2021];118(17). Available at: https://www.pnas.org/content/118/17/e2023157118 | eng |
| dcterms.references | Addetia A, Xie H, Roychoudhury P, Shrestha L, Loprieno M, Huang M-L, et al. Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates. medRxiv [Internet]. 09 Junie 2020 [cited 26 Oktober 2021];2020.06.08.20125856. Available at: https://www.medrxiv.org/content/10.1101/2020.06.08.20125856v1 | eng |
| dcterms.references | Masters PS. Coronavirus genomic RNA packaging [Internet]. Vol 537, Virology. 2019 [cited 26 Oktober 2021]. bl 198–207. Available at: https://DOI: 10.1016/j.virol.2019.08.031. | eng |
| oaire.version | info:eu-repo/semantics/acceptedVersion | eng |
| sb.programa | Maestría en Genética | spa |
| sb.sede | Sede Barranquilla | spa |