Association of ApaI rs7975232 and BsmI rs1544410 in clinical outcomes of COVID-19 patients according to different SARS-CoV-2 variants

DOI record: { "DOI": "10.1038/s41598-023-30859-7", "ISSN": [ "2045-2322" ], "URL": "http://dx.doi.org/10.1038/s41598-023-30859-7", "abstract": "<jats:title>Abstract</jats:title><jats:p>A growing body of research has shown how important vitamin D is in the prognosis of coronavirus disease 19 (COVID-19). The vitamin D receptor is necessary for vitamin D to perform its effects, and its polymorphisms can help in this regard. Therefore, we aimed to evaluate whether the association of <jats:italic>ApaI</jats:italic> rs7975232 and <jats:italic>BsmI</jats:italic> rs1544410 polymorphisms in different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants were influential in the outcomes of COVID-19. The polymerase chain reaction-restriction fragment length polymorphism method was utilized to determine the different genotypes of <jats:italic>ApaI</jats:italic> rs7975232 and <jats:italic>BsmI</jats:italic> rs1544410 in 1734 and 1450 patients who had recovered and deceased, respectively. Our finding revealed that the <jats:italic>ApaI</jats:italic> rs7975232 AA genotype in the Delta and Omicron BA.5 and the CA genotype in the Delta and Alpha variants were associated with higher mortality rate. Also, the <jats:italic>BsmI</jats:italic> rs1544410 GG genotype in the Delta and Omicron BA.5 and the GA genotype in the Delta and Alpha variants were related to a higher mortality rate. The A-G haplotype was linked with COVID-19 mortality in both the Alpha and Delta variants. The A-A haplotype for the Omicron BA.5 variants was statistically significant. In conclusion, our research revealed a connection between SARS-CoV-2 variants and the impacts of <jats:italic>ApaI</jats:italic> rs7975232 and <jats:italic>BsmI</jats:italic> rs1544410 polymorphisms. However, more research is still needed to substantiate our findings.</jats:p>", "alternative-id": [ "30859" ], "article-number": "3612", "assertion": [ { "group": { "label": "Article History", "name": "ArticleHistory" }, "label": "Received", "name": "received", "order": 1, "value": "8 December 2022" }, { "group": { "label": "Article History", "name": "ArticleHistory" }, "label": "Accepted", "name": "accepted", "order": 2, "value": "2 March 2023" }, { "group": { "label": "Article History", "name": "ArticleHistory" }, "label": "First Online", "name": "first_online", "order": 3, "value": "3 March 2023" }, { "group": { "label": "Competing interests", "name": "EthicsHeading" }, "name": "Ethics", "order": 1, "value": "The authors declare no competing interests." } ], "author": [ { "affiliation": [], "family": "Al-Gharrawi", "given": "Ayad Naji Radha", "sequence": "first" }, { "affiliation": [], "family": "Anvari", "given": "Enayat", "sequence": "additional" }, { "affiliation": [], "family": "Fateh", "given": "Abolfazl", "sequence": "additional" } ], "container-title": "Scientific Reports", "container-title-short": "Sci Rep", "content-domain": { "crossmark-restriction": false, "domain": [ "link.springer.com" ] }, "created": { "date-parts": [ [ 2023, 3, 3 ] ], "date-time": "2023-03-03T14:03:05Z", "timestamp": 1677852185000 }, "deposited": { "date-parts": [ [ 2023, 3, 3 ] ], "date-time": "2023-03-03T14:07:48Z", "timestamp": 1677852468000 }, "indexed": { "date-parts": [ [ 2023, 3, 4 ] ], "date-time": "2023-03-04T05:42:47Z", "timestamp": 1677908567220 }, "is-referenced-by-count": 0, "issue": "1", "issued": { "date-parts": [ [ 2023, 3, 3 ] ] }, "journal-issue": { "issue": "1", "published-online": { "date-parts": [ [ 2023, 12 ] ] } }, "language": "en", "license": [ { "URL": "https://creativecommons.org/licenses/by/4.0", "content-version": "tdm", "delay-in-days": 0, "start": { "date-parts": [ [ 2023, 3, 3 ] ], "date-time": "2023-03-03T00:00:00Z", "timestamp": 1677801600000 } }, { "URL": "https://creativecommons.org/licenses/by/4.0", "content-version": "vor", "delay-in-days": 0, "start": { "date-parts": [ [ 2023, 3, 3 ] ], "date-time": "2023-03-03T00:00:00Z", "timestamp": 1677801600000 } } ], "link": [ { "URL": "https://www.nature.com/articles/s41598-023-30859-7.pdf", "content-type": "application/pdf", "content-version": "vor", "intended-application": "text-mining" }, { "URL": "https://www.nature.com/articles/s41598-023-30859-7", "content-type": "text/html", "content-version": "vor", "intended-application": "text-mining" }, { "URL": "https://www.nature.com/articles/s41598-023-30859-7.pdf", "content-type": "application/pdf", "content-version": "vor", "intended-application": "similarity-checking" } ], "member": "297", "original-title": [], "prefix": "10.1038", "published": { "date-parts": [ [ 2023, 3, 3 ] ] }, "published-online": { "date-parts": [ [ 2023, 3, 3 ] ] }, "publisher": "Springer Science and Business Media LLC", "reference": [ { "author": "SR Varikasuvu", "first-page": "111356", "journal-title": "Expert Rev. Anti-infect. Ther.", "key": "30859_CR1", "unstructured": "Varikasuvu, S. R. et al. COVID-19 and vitamin D (Co-VIVID study): A systematic review and meta-analysis of randomized controlled trials. Expert Rev. Anti-infect. Ther. 92, 111356 (2022).", "volume": "92", "year": "2022" }, { "DOI": "10.37201/req/158.2021", "author": "A García-Lledó", "doi-asserted-by": "publisher", "first-page": "115", "journal-title": "Rev. Esp. Quimioter.", "key": "30859_CR2", "unstructured": "García-Lledó, A. et al. Pharmacological treatment of COVID-19: an opinion paper. Rev. Esp. Quimioter. 35, 115 (2022).", "volume": "35", "year": "2022" }, { "DOI": "10.1139/cjpp-2014-0352", "author": "RR Watkins", "doi-asserted-by": "publisher", "first-page": "363", "journal-title": "Can. J. Physiol. Pharmacol.", "key": "30859_CR3", "unstructured": "Watkins, R. R., Lemonovich, T. L. & Salata, R. A. An update on the association of vitamin D deficiency with common infectious diseases. Can. J. Physiol. Pharmacol. 93, 363–368 (2015).", "volume": "93", "year": "2015" }, { "DOI": "10.1016/j.nut.2021.111356", "author": "DTM Brito", "doi-asserted-by": "publisher", "journal-title": "Nutrition", "key": "30859_CR4", "unstructured": "Brito, D. T. M., Ribeiro, L. H. C., da Cunha Daltro, C. H. & de Barros Silva, R. The possible benefits of vitamin D in COVID-19. Nutrition 91, 111356 (2021).", "volume": "91", "year": "2021" }, { "DOI": "10.3390/nu9070651", "author": "PHF Gois", "doi-asserted-by": "publisher", "first-page": "651", "journal-title": "Nutrients", "key": "30859_CR5", "unstructured": "Gois, P. H. F., Ferreira, D., Olenski, S. & Seguro, A. C. Vitamin D and infectious diseases: simple bystander or contributing factor?. Nutrients 9, 651 (2017).", "volume": "9", "year": "2017" }, { "DOI": "10.3390/nu13051714", "author": "H AlSafar", "doi-asserted-by": "publisher", "first-page": "1714", "journal-title": "Nutrients", "key": "30859_CR6", "unstructured": "AlSafar, H. et al. COVID-19 disease severity and death in relation to vitamin D status among SARS-CoV-2-positive UAE residents. Nutrients 13, 1714 (2021).", "volume": "13", "year": "2021" }, { "DOI": "10.1002/rmv.2119", "author": "A Malek Mahdavi", "doi-asserted-by": "publisher", "journal-title": "Rev. Med. Virol.", "key": "30859_CR7", "unstructured": "Malek Mahdavi, A. A brief review of interplay between vitamin D and angiotensin-converting enzyme 2: Implications for a potential treatment for COVID-19. Rev. Med. Virol. 30, e2119 (2020).", "volume": "30", "year": "2020" }, { "DOI": "10.4274/jpr.galenos.2021.45762", "author": "N Zeidan", "doi-asserted-by": "crossref", "first-page": "1", "journal-title": "Pediatr. Res.", "key": "30859_CR8", "unstructured": "Zeidan, N. et al. Vitamin D deficiency and vitamin D receptor FokI polymorphism as risk factors for COVID-19. Pediatr. Res. 9, 1–8 (2022).", "volume": "9", "year": "2022" }, { "DOI": "10.1002/eji.200636043", "author": "E van Etten", "doi-asserted-by": "publisher", "first-page": "395", "journal-title": "Eur. J. Immunol.", "key": "30859_CR9", "unstructured": "van Etten, E. et al. The vitamin D receptor gene FokI polymorphism: functional impact on the immune system. Eur. J. Immunol. 37, 395–405 (2007).", "volume": "37", "year": "2007" }, { "DOI": "10.1002/jmv.22179", "author": "T Kresfelder", "doi-asserted-by": "publisher", "first-page": "1834", "journal-title": "J. Med. Virol.", "key": "30859_CR10", "unstructured": "Kresfelder, T., Janssen, R., Bont, L. & Venter, M. Confirmation of an association between single nucleotide polymorphisms in the VDR gene with respiratory syncytial virus related disease in South African children. J. Med. Virol. 83, 1834–1840 (2011).", "volume": "83", "year": "2011" }, { "DOI": "10.1086/527488", "author": "DE Roth", "doi-asserted-by": "publisher", "first-page": "676", "journal-title": "J. Infect. Dis.", "key": "30859_CR11", "unstructured": "Roth, D. E., Jones, A. B., Prosser, C., Robinson, J. L. & Vohra, S. Vitamin D receptor polymorphisms and the risk of acute lower respiratory tract infection in early childhood. J. Infect. Dis. 197, 676–680 (2008).", "volume": "197", "year": "2008" }, { "DOI": "10.3390/genes13122346", "author": "WHM Albu-Mohammed", "doi-asserted-by": "publisher", "first-page": "2346", "journal-title": "Genes", "key": "30859_CR12", "unstructured": "Albu-Mohammed, W. H. M., Anvari, E. & Fateh, A. Evaluating the role of BglI rs739837 and TaqI rs731236 polymorphisms in Vitamin D receptor with SARS-CoV-2 variants mortality rate. Genes 13, 2346 (2022).", "volume": "13", "year": "2022" }, { "DOI": "10.1016/j.gene.2017.12.027", "author": "Q He", "doi-asserted-by": "publisher", "first-page": "105", "journal-title": "Gene", "key": "30859_CR13", "unstructured": "He, Q. et al. Association between vitamin D receptor polymorphisms and hepatitis B virus infection susceptibility: A meta-analysis study. Gene 645, 105–112 (2018).", "volume": "645", "year": "2018" }, { "DOI": "10.1186/s12881-019-0903-y", "author": "NX Hoan", "doi-asserted-by": "publisher", "first-page": "1", "journal-title": "BMC Med. Genet.", "key": "30859_CR14", "unstructured": "Hoan, N. X. et al. Vitamin D receptor ApaI polymorphism associated with progression of liver disease in Vietnamese patients chronically infected with hepatitis B virus. BMC Med. Genet. 20, 1–12 (2019).", "volume": "20", "year": "2019" }, { "DOI": "10.1016/j.meegid.2021.105098", "author": "R Abdollahzadeh", "doi-asserted-by": "publisher", "journal-title": "Infect. Genet. Evol.", "key": "30859_CR15", "unstructured": "Abdollahzadeh, R. et al. Association of Vitamin D receptor gene polymorphisms and clinical/severe outcomes of COVID-19 patients. Infect. Genet. Evol. 96, 105098 (2021).", "volume": "96", "year": "2021" }, { "DOI": "10.3390/nu7064240", "author": "CL Greiller", "doi-asserted-by": "publisher", "first-page": "4240", "journal-title": "Nutrients", "key": "30859_CR16", "unstructured": "Greiller, C. L. & Martineau, A. R. Modulation of the immune response to respiratory viruses by vitamin D. Nutrients 7, 4240–4270 (2015).", "volume": "7", "year": "2015" }, { "DOI": "10.1016/j.cell.2020.02.052", "author": "M Hoffmann", "doi-asserted-by": "publisher", "first-page": "271", "journal-title": "Cell", "key": "30859_CR17", "unstructured": "Hoffmann, M. et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 181, 271–280 (2020).", "volume": "181", "year": "2020" }, { "DOI": "10.1074/jbc.M705495200", "author": "W Yuan", "doi-asserted-by": "publisher", "first-page": "29821", "journal-title": "J. Biol. Chem.", "key": "30859_CR18", "unstructured": "Yuan, W. et al. 1, 25-dihydroxyvitamin D3 suppresses renin gene transcription by blocking the activity of the cyclic AMP response element in the renin gene promoter. J. Biol. Chem. 282, 29821–29830 (2007).", "volume": "282", "year": "2007" }, { "DOI": "10.1080/07391102.2021.1964601", "author": "Y Song", "doi-asserted-by": "publisher", "first-page": "11594", "journal-title": "J. Biomol. Struct. Dyn.", "key": "30859_CR19", "unstructured": "Song, Y. et al. Vitamin D3 and its hydroxyderivatives as promising drugs against COVID-19: A computational study. J. Biomol. Struct. Dyn. 40, 11594–11610 (2022).", "volume": "40", "year": "2022" }, { "DOI": "10.1152/ajpendo.00174.2021", "author": "S Qayyum", "doi-asserted-by": "publisher", "first-page": "246", "journal-title": "Am. J. Physiol.-Endocrinol. Metab.", "key": "30859_CR20", "unstructured": "Qayyum, S. et al. Vitamin D and lumisterol novel metabolites can inhibit SARS-CoV-2 replication machinery enzymes. Am. J. Physiol.-Endocrinol. Metab. 321, 246–251 (2021).", "volume": "321", "year": "2021" }, { "DOI": "10.3390/nu14224779", "author": "S Qayyum", "doi-asserted-by": "publisher", "first-page": "4779", "journal-title": "Nutrients", "key": "30859_CR21", "unstructured": "Qayyum, S., Slominski, R. M., Raman, C. & Slominski, A. T. Novel CYP11A1-derived vitamin D and lumisterol biometabolites for the management of COVID-19. Nutrients 14, 4779 (2022).", "volume": "14", "year": "2022" }, { "DOI": "10.1111/exd.14170", "author": "RM Slominski", "doi-asserted-by": "publisher", "first-page": "885", "journal-title": "Exp. Dermatol.", "key": "30859_CR22", "unstructured": "Slominski, R. M. et al. COVID-19 and Vitamin D: A lesson from the skin. Exp. Dermatol. 29, 885–890 (2020).", "volume": "29", "year": "2020" }, { "DOI": "10.1016/j.dsx.2017.03.047", "author": "HA Hasan", "doi-asserted-by": "publisher", "first-page": "S531", "journal-title": "Diabetes Metab. Syndr.", "key": "30859_CR23", "unstructured": "Hasan, H. A., Raed, O. A., Muda, W. A. M. B. W., Mohamed, H. J. B. J. & Samsudin, A. R. Association of Vitamin D receptor gene polymorphisms with metabolic syndrome and its components among adult Arabs from the United Arab Emirates. Diabetes Metab. Syndr. 11, S531–S537 (2017).", "volume": "11", "year": "2017" }, { "DOI": "10.1111/cen.14664", "author": "T Apaydin", "doi-asserted-by": "publisher", "first-page": "819", "journal-title": "Clin. Endocrinol.", "key": "30859_CR24", "unstructured": "Apaydin, T. et al. Effects of vitamin D receptor gene polymorphisms on the prognosis of COVID-19. Clin. Endocrinol. 96, 819–830 (2022).", "volume": "96", "year": "2022" }, { "author": "L Karcioğlu", "first-page": "60", "journal-title": "Anatolian Clin. J. Med. Sci.", "key": "30859_CR25", "unstructured": "Karcioğlu, L. Correlation of the variations in prevalence of coronavirus disease 2019 and vitamin D receptor gene polymorphisms in cohorts from 26 countries. Anatolian Clin. J. Med. Sci. 27, 60–70 (2022).", "volume": "27", "year": "2022" }, { "DOI": "10.3390/jcdd9010027", "author": "G Cimmino", "doi-asserted-by": "publisher", "first-page": "27", "journal-title": "J. Cardiovasc. Dev. Dis.", "key": "30859_CR26", "unstructured": "Cimmino, G. et al. Vitamin D Inhibits IL-6 pro-atherothrombotic effects in human endothelial cells: A potential mechanism for protection against COVID-19 infection?. J. Cardiovasc. Dev. Dis. 9, 27 (2022).", "volume": "9", "year": "2022" }, { "DOI": "10.1097/INF.0b013e31829e4d06", "author": "A Moodley", "doi-asserted-by": "publisher", "first-page": "1230", "journal-title": "Pediatr. Infect. Dis. J.", "key": "30859_CR27", "unstructured": "Moodley, A., Qin, M., Singh, K. K. & Spector, S. A. Vitamin D related host genetic variants alter HIV disease progression in children. Pediatr. Infect. Dis. J. 32, 1230–1236 (2013).", "volume": "32", "year": "2013" }, { "DOI": "10.1007/s10875-008-9234-z", "author": "K Alagarasu", "doi-asserted-by": "publisher", "first-page": "196", "journal-title": "J. Clin. Immunol.", "key": "30859_CR28", "unstructured": "Alagarasu, K., Selvaraj, P., Swaminathan, S., Narendran, G. & Narayanan, P. 5′ regulatory and 3′ untranslated region polymorphisms of vitamin D receptor gene in South Indian HIV and HIV–TB patients. J. Clin. Immunol. 29, 196–204 (2009).", "volume": "29", "year": "2009" }, { "DOI": "10.1086/525043", "author": "M Sánchez de laTorre", "doi-asserted-by": "publisher", "first-page": "405", "journal-title": "J. Infect. Dis.", "key": "30859_CR29", "unstructured": "Sánchez de laTorre, M. et al. Vitamin D receptor gene haplotypes and susceptibility to HIV-1 infection in injection drug users. J. Infect. Dis. 197, 405–410 (2008).", "volume": "197", "year": "2008" }, { "DOI": "10.1016/j.gene.2004.05.014", "author": "AG Uitterlinden", "doi-asserted-by": "publisher", "first-page": "143", "journal-title": "Gene", "key": "30859_CR30", "unstructured": "Uitterlinden, A. G., Fang, Y., Van Meurs, J. B., Pols, H. A. & Van Leeuwen, J. P. Genetics and biology of vitamin D receptor polymorphisms. Gene 338, 143–156 (2004).", "volume": "338", "year": "2004" }, { "DOI": "10.1038/nrg3051", "author": "ZE Sauna", "doi-asserted-by": "publisher", "first-page": "683", "journal-title": "Nat. Rev. Genet.", "key": "30859_CR31", "unstructured": "Sauna, Z. E. & Kimchi-Sarfaty, C. Understanding the contribution of synonymous mutations to human disease. Nat. Rev. Genet. 12, 683–691 (2011).", "volume": "12", "year": "2011" } ], "reference-count": 31, "references-count": 31, "relation": {}, "resource": { "primary": { "URL": "https://www.nature.com/articles/s41598-023-30859-7" } }, "score": 1, "short-title": [], "source": "Crossref", "subject": [ "Multidisciplinary" ], "subtitle": [], "title": "Association of ApaI rs7975232 and BsmI rs1544410 in clinical outcomes of COVID-19 patients according to different SARS-CoV-2 variants", "type": "journal-article", "update-policy": "http://dx.doi.org/10.1007/springer_crossmark_policy", "volume": "13" }