Genetic association study of the rs10774671 variant of the OAS1 gene with the severity of COVID-19 in an Ecuadorian population.
Estudio de asociación genética de la variante rs10774671 del gen OAS1 con la severidad de COVID-19 en una población ecuatoriana.
Keywords:
complex trait, COVID-19, genetic association study, genetic variant, Hardy-Weinberg equilibrium, innate immune processes
Abstract
COVID-19 exhibits a wide range of phenotypic manifestations, from asymptomatic to severe phenotypes with fatal complications. The existence of risk factors cannot entirely explain the variance in the phenotypic variability of COVID-19. Genome-wide association analyses have identified target human genes related to virus transmission and the clinical phenotype observed in COVID-19 patients. Genetic variants on the OAS1 gene have been associated with innate immune processes (entry phase and viral replication in host cells). The A or G alleles of rs10774671 in OAS1 encode isoforms with different antiviral activities. One hundred COVID-19 patients were genotyped for the rs10774671 using RFLP-PCR (severe form, n = 43; asymptomatic-mild, n =57). The susceptibility of the two groups to the severe phenotype of COVID-19 was compared. The allele frequency for A was 0.8. The genotypic frequencies for AA and GG homozygotes were 0.62 and 0.02, respectively. A Hardy-Weinberg equilibrium deviation was found in both groups. No statistically significant as- sociations were found in genetic models adjusted for sex (for the additive model OR = 1.18, 95% CI = (0.53-2.61), p = 0.69). A relatively recent mix of different ethnic groups and sample size may influence these findings.
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References
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Shahid Z, Kalayanamitra R, McClafferty B, Kepko D, Ramgobin D, Patel R, Aggarwal CS, Vunnam R, Sahu N, Bhatt D, Jones K, Golamari R, Jain R. COVID-19 and older adults: what we know. J Am Geriatr Soc 2020; 68(5): 926–929. https://doi:10.1111/jgs.16472
Godri Pollitt KJ, Peccia J, Ko AI, Kaminski N, Dela Cruz CS, Nebert DW, Reichardt JKV, Thompson DC, Vasiliou V. COVID-19 vulnerability: the potential impact of genetic susceptibility and airborne transmission. Hum Genomics 2020; 14(1): 17. https://doi:10.1186/s40246-020-00267-3.
Pairo-Castineira E, Clohisey S, Klaric L, Bretherick AD, Rawlik K, Pasko D, Walker S, Parkinson N, Fourman MH, Russell CD, Furniss J, Richmond A, Gountouna E, Wrobel N, Harrison D, Wang B, Wu Y, Meynert A, Griffiths F, Oosthuyzen W, Kousathanas A, Moutsianas L, Yang Z, Zhai R, Zheng C, Grimes G, Beale R, Millar J, Shih B, Keating S, Zechner M, Haley C, Porteous DJ, Hayward C, Yang J, Knight J, Summers C, Shankar-Hari M, Klenerman P, Turtle L, Ho A, Moore SC, Hinds C, Horby P, Nichol A, Maslove D, Ling L, McAuley D, Montgomery H, Walsh T, Pereira AC, Renieri A; GenOMICC Investigators; ISARIC4C Investigators; COVID-19 Human Genetics Initiative; 23andMe Investigators; BRACOVID Investigators; Gen-COVID Investigators; Shen X, Ponting CP, Fawkes A, Tenesa A, Caulfield M, Scott R, Rowan K, Murphy L, Openshaw PJM, Semple MG, Law A, Vitart V, Wilson JF, Baillie JK. Genetic mechanisms of critical illness in COVID-19. Nature 2021; 591(7848): 92–98. https://doi:10.1038/s41586-020-03065-y
Bonnevie-Nielsen V, Field LL, Lu S, Zheng DJ, Li M, Martensen PM, Nielsen TB, Beck-Nielsen H, Lau YL, Pociot F. Variation in antiviral 2′,5′-oligoadenylate synthetase (2′5′AS) enzyme activity is controlled by a single-nucleotide polymorphism at a splice-acceptor site in the OAS1 Gene. Am J Hum Genet 2005; 76(4): 623-633. https://doi:10.1086/429391.
Kjær KH, Pahus J, Hansen MF, Poulsen JB, Christensen EI, Justesen J, Martensen PM. Mitochondrial localization of the OAS1 p46 isoform associated with a common single nucleotide polymorphism. BMC Cell Biol 2014; 15(1): 33. https:// doi:10.1186/1471-2121-15-33.
Banday AR, Stanifer ML, Florez-Vargas O, Onabajo OO, Papenberg BW, Zahoor MA, Mirabello L, Ring TJ, Lee CH, Albert PS, Andreakos E, Arons E, Barsh G, Biesecker LG, Boyle DL, Brahier MS, Burnett-Hartman A, Carrington M, Chang E, Choe PG, Chisholm RL, Colli LM, Dalgard CL, Dude CM, Edberg J, Erdmann N, Feigelson HS, Fonseca BA, Firestein GS, Gehring AJ, Guo C, Ho M, Holland S, Hutchinson AA, Im H, Irby L, Ison MG, Joseph NT, Kim HB, Kreitman RJ, Korf BR, Lipkin SM, Mahgoub SM, Mohammed I, Paschoalini GL, Pacheco JA, Peluso MJ, Rader DJ, Redden DT, Ritchie MD, Rosenblum B, Ross ME, Anna HPS, Savage SA, Sharma S, Siouti E, Smith AK, Triantafyllia V, Vargas JM, Vargas JD, Verma A, Vij V, Wesemann DR, Yeager M, Yu X, Zhang Y, Boulant S, Chanock SJ, Feld JJ, Prokunina-Olsson L. Genetic regulation of OAS1 nonsense-mediated decay underlies association with COVID-19 hospitalization in patients of European and African ancestries. Nat Genet 2022; 54(8):1103–1116. https://doi:0.1038/s41588-022-01113-z
National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/snp/rs10774671. 2021. Reference SNP (rs) Report.
Nagar SD, Conley AB, Chande AT, Rishishwar L, Sharma S, Mariño-Ramírez L, Aguinaga-Romero G, González-Andrade F, Jordan IK. Genetic ancestry and ethnic identity in Ecuador. HGG Adv 2021; 2(4): 100050. https://doi:10.1016/j.xhgg.2021.100050.
Kovich H. Rural Matters — Coronavirus and the Navajo Nation. N Engl J Med 2020; 383(2): 105-107. https://doi:10.1056/NE- JMp2012114.
Huyser KR, Yang TC, Yellow Horse AJ. Indigenous Peoples, concentrated disadvantage, and income inequality in New Mexico: a ZIP code-level investigation of spatially varying associations between socioeconomic disadvantages and confirmed COVID-19 cases. J Epidemiol Community Health 2021; 75(11): 1044-1049. https://doi:10.1136/jech-2020-215055.
Oda G, Sharma A, Lucero-Obusan C, Schirmer P, Sohoni P, Holodniy M. COVID-19 infections among healthcare personnel in the United States Veterans Health Administration, March to August, 2020. J Occup Environ Med 2021; 63(4):291-295. https://doi:10.1097/JOM.0000000000002109.
Coronavirus Resource Center from Johns Hopkins University. https://coronavirus. jhu.edu/map.html. 2023. COVID-19 Dashboard by the Center for Systems Science and Engineering (CSSE).
Proyecto Rodillo. https://rodillo.org/estadisticas-coronavirus/ecuador/. 2022. Ecuador-Estadísticas del Coronavirus.
Fedetz M, Matesanz F, Caro-Maldonado A, Fernandez O, Tamayo JA, Guerrero M, Delgado C, López-Guerrero JA, Alcina A. OAS1 gene haplotype confers susceptibility to multiple sclerosis. Tissue Antigens 2006; 68(5): 446-9. https://doi:10.1111/ j.1399-0039.2006.00694.x.
Imran M, Manzoor S, Khattak NM, Tariq M, Khalid M, Javed F, Bhatti S. Correlation of OAS1 gene polymorphism at exon 7 splice accepter site with interferon-based therapy of HCV infection in Pakistan. Viral Immunol 2014; 27(3): 105-111. https://doi:10.1089/vim.2013.0107.
Solé X, Guinó E, Valls J, Iniesta R, MorenoV. SNPStats: a web tool for the analysis of association studies. Bioinformatics 2006; 22(15): 1928-1929. https://doi:10.1093/bioinformatics/btl268.
Graffelman J. Exploring Diallelic Genetic Markers: The HardyWeinberg Package. J Stat Softw 2015; 64(3) 1-23. https://doi. org/10.18637/jss.v064.i03.
Graffelman J, Weir BS. Testing for Hardy– Weinberg equilibrium at biallelic genetic markers on the X chromosome. Heredity (Edinb) 2016; 116(6): 558-568. https:// doi:10.1038/hdy.2016.20.
Horita N, Kaneko T. Genetic model selection for a case–control study and a meta-analysis. Meta Gene 2015; 5: 1-8. https:// doi:10.1016/j.mgene.2015.04.003.
Sánchez-González MT, Cienfuegos-Jiménez O, Álvarez-Cuevas S, Pérez-Maya AA, Borrego-Soto G, Marino-Martínez IA. Prevalence of the SNP rs10774671 of the OAS1 gene in Mexico as a possible predisposing factor for RNA virus disease. Int J Mol Epidemiol Genet 2021;12(3): 52–60.
Lim JK, Lisco A, McDermott DH, Huynh L, Ward JM, Johnson B, Johnson H, Pape J, Foster GA, Krysztof D, Follmann D, Stramer SL, Margolis LB, Murphy PM. Genetic variation in OAS1 is a risk factor for initial infection with West Nile Virus in man. PLoS Pathog 2009; 5(2):e1000321. https:// doi:10.1371/journal.ppat.1000321.
Zhao Y, Kang H, Ji Y, Chen X. Evaluate the relationship between polymorphisms of OAS1 gene and susceptibility to chronic hepatitis C with high resolution melting analysis. Clin Exp Med 2013; 13(3): 171-176. https://doi:10.1007/s10238-012-019 3-6.
European Molecular Biology Laboratory-European Bioinformatics Institute [EM- BL -EBI]. rs10774671 (SNP) - Population genetics - Homo_sapiens. 2022.
Guardado-Estrada M, Juarez-Torres E, Medina-Martinez I, Wegier A, Macías A, Gomez G, Cruz-Talonia F, Roman-Bassaure E, Piñero D, Kofman-Alfaro S, Berumen J. A great diversity of Amerindian mitochondrial DNA ancestry is present in the Mexican mestizo population. J Hum Genet 2009; 54(12): 695-705. https:// doi:10.1038/jhg.2009.98.
Zambrano AK, Gaviria A, Cobos-Navarrete S, Gruezo C, Rodríguez-Pollit C, Armendáriz-Castillo I, García-Cárdenas JM, Guerrero S, López-Cortés A, Leone PE, Pérez-Villa A, Guevara-Ramírez P, Yumiceba V, Fiallos G, Vela M, Paz-Y-Miño C. The three-hybrid genetic composition of an Ecuadorian population using AIMs-In-Dels compared with autosomes, mitochondrial DNA and Y chromosome data. Sci Rep 2019; 9(1): 9247. https://doi:10.1038/ s41598-019-45723-w.
Harris K, Nielsen R. The Genetic Cost of Neanderthal Introgression. Genetics 2016; 203(2): 881-891. https://doi:10.1534/genetics.116.186890.
Fu Q, Hajdinjak M, Moldovan OT, Constantin S, Mallick S, Skoglund P, Patterson N, Rohland N, Lazaridis I, Nickel B, Viola B, Prüfer K, Meyer M, Kelso J, Reich D, Pääbo S. An early modern human from Romania with a recent Neanderthal ancestor. Nature 2015; 524(7564): 216-219. https://doi:10.1038/nature14558.
Enard D, Petrov DA. Evidence that RNA viruses drove adaptive introgression between Neanderthals and Modern Humans. Cell 2018; 175(2): 360-371.e13. https:// doi:10.1016/j.cell.2018.08.034.
Published
2024-05-21
How to Cite
Pilataxi , K., Balarezo, T., Chávez, E., Acosta , C., Peña, I. Z., Narváez, K., & Álvarez-Nava, F. (2024). Genetic association study of the rs10774671 variant of the OAS1 gene with the severity of COVID-19 in an Ecuadorian population.: Estudio de asociación genética de la variante rs10774671 del gen OAS1 con la severidad de COVID-19 en una población ecuatoriana. Investigación Clínica, 65(2), 169-178. https://doi.org/10.54817/IC.v65n2a04
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