Strong Correlation between the Case Fatality Rate of COVID-19 and the rs6598045 Single Nucleotide Polymorphism (SNP) of the Interferon-Induced Transmembrane Protein 3 (IFITM3) Gene at the Population-Level
Abstract
:1. Introduction
2. Results
2.1. Information on the Polymorphisms of COVID-19-Related Genes
2.2. Ethnic Differences of Case Fatality Rates among COVID-19 Patients
2.3. Regression Analysis between the Case Fatality Rate of COVID-19 and the Polymorphisms of COVID-19-Related Genes
3. Discussion
4. Materials and Methods
4.1. Data Collection
4.2. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
SNP | Single nucleotide polymorphism |
IFITM3 | Interferon-induced transmembrane protein 3 gene |
COVID-19 | Coronavirus disease 2019 |
SARS-CoV-2 | Severe acute respiratory syndrome coronavirus 2 |
ACE2 | Angiotensin I converting enzyme 2 gene |
TMPRSS2 | Transmembrane protease, serine 2 gene |
IL6 | Interleukin 6 gene |
LZTFL1 | Leucine zipper transcription factor-like protein 1 gene |
WHO | World Health Organization |
COPD | Chronic obstructive pulmonary disease |
GWAS | Genome-wide association study |
MAF | Minor allele frequency |
SLC6A20 | Solute carrier family 6 member 20 gene |
CCR9 | C-C chemokine receptor type 9 gene |
FYCO1 | FYVE and coiled-coil domain autophagy adaptor 1 gene |
CXCR6 | C-X-C chemokine receptor type 6 gene |
XCR1 | X-C Motif Chemokine Receptor 1 gene |
IFNAR2 | Interferon α and β receptor subunit 2 gene |
TYK2 | Tyrosine kinase 2 gene |
CCR2 | Chemokine receptor type 2 gene |
References
- Rothan, H.A.; Byrareddy, S.N. The epidemiology and pathogenesis of coronavirus disease (COVID-19) outbreak. J. Autoimmun. 2020, 109, 102433. [Google Scholar] [CrossRef] [PubMed]
- Contini, C.; Di Nuzzo, M.; Barp, N.; Bonazza, A.; De Giorgio, R.; Tognon, M.; Rubino, S. The novel zoonotic COVID-19 pandemic: An expected global health concern. J. Infect. Dev. Ctries. 2020, 14, 254–264. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Halaji, M.; Farahani, A.; Ranjbar, R.; Heiat, M.; Dehkordi, F.S. Emerging coronaviruses: First SARS, second MERS and third SARS-CoV-2: Epidemiological updates of COVID-19. Le Infez. Med. 2020, 28, 6–17. [Google Scholar]
- Bourgonje, A.R.; Abdulle, A.E.; Timens, W.; Hillebrands, J.L.; Navis, G.J.; Gordijn, S.J.; Bolling, M.C.; Dijkstra, G.; Voors, A.A.; Osterhaus, A.D.; et al. Angiotensin-converting enzyme 2 (ACE2), SARS-CoV-2 and the pathophysiology of coronavirus disease 2019 (COVID-19). J. Pathol. 2020. [Google Scholar] [CrossRef] [PubMed]
- Hoffmann, M.; Kleine-Weber, H.; Schroeder, S.; Kruger, N.; Herrler, T.; Erichsen, S.; Schiergens, T.S.; Herrler, G.; Wu, N.H.; Nitsche, A.; et al. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell 2020, 181, 271–280.e8. [Google Scholar] [CrossRef] [PubMed]
- Asselta, R.; Paraboschi, E.M.; Mantovani, A.; Duga, S. ACE2 and TMPRSS2 variants and expression as candidates to sex and country differences in COVID-19 severity in Italy. Aging (Albany NY) 2020, 12, 10087–10098. [Google Scholar] [CrossRef]
- Lopera Maya, E.A.; van der Graaf, A.; Lanting, P.; van der Geest, M.; Fu, J.; Swertz, M.; Franke, L.; Wijmenga, C.; Deelen, P.; Zhernakova, A.; et al. Lack of Association Between Genetic Variants at ACE2 and TMPRSS2 Genes Involved in SARS-CoV-2 Infection and Human Quantitative Phenotypes. Front. Genet. 2020, 11, 613. [Google Scholar] [CrossRef]
- Zhang, Y.; Qin, L.; Zhao, Y.; Zhang, P.; Xu, B.; Li, K.; Liang, L.; Zhang, C.; Dai, Y.; Feng, Y.; et al. Interferon-Induced Transmembrane Protein 3 Genetic Variant rs12252-C Associated With Disease Severity in Coronavirus Disease 2019. J. Infect. Dis. 2020, 222, 34–37. [Google Scholar] [CrossRef]
- Kirtipal, N.; Bharadwaj, S. Interleukin 6 polymorphisms as an indicator of COVID-19 severity in humans. J. Biomol. Struct. Dyn. 2020, 1–3. [Google Scholar] [CrossRef]
- Ellinghaus, D.; Degenhardt, F.; Bujanda, L.; Buti, M.; Albillos, A.; Invernizzi, P.; Fernandez, J.; Prati, D.; Baselli, G.; Asselta, R.; et al. Genomewide Association Study of Severe Covid-19 with Respiratory Failure. N. Engl. J. Med. 2020, 383, 1522–1534. [Google Scholar] [CrossRef]
- Kim, Y.C.; Jeong, M.J.; Jeong, B.H. Strong association of regulatory single nucleotide polymorphisms (SNPs) of the IFITM3 gene with influenza H1N1 2009 pandemic virus infection. Cell. Mol. Immunol. 2020, 17, 662–664. [Google Scholar] [CrossRef] [PubMed]
- Allen, E.K.; Randolph, A.G.; Bhangale, T.; Dogra, P.; Ohlson, M.; Oshansky, C.M.; Zamora, A.E.; Shannon, J.P.; Finkelstein, D.; Dressen, A.; et al. SNP-mediated disruption of CTCF binding at the IFITM3 promoter is associated with risk of severe influenza in humans. Nat. Med. 2017, 23, 975–983. [Google Scholar] [CrossRef] [PubMed]
- Zhang, Y.H.; Zhao, Y.; Li, N.; Peng, Y.C.; Giannoulatou, E.; Jin, R.H.; Yan, H.P.; Wu, H.; Liu, J.H.; Liu, N.; et al. Interferon-induced transmembrane protein-3 genetic variant rs12252-C is associated with severe influenza in Chinese individuals. Nat. Commun. 2013, 4, 1418. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Bailey, C.C.; Zhong, G.; Huang, I.C.; Farzan, M. IFITM-Family Proteins: The Cell’s First Line of Antiviral Defense. Annu. Rev. Virol. 2014, 1, 261–283. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Zani, A.; Yount, J.S. Antiviral Protection by IFITM3 In Vivo. Curr. Clin. Microbiol. Rep. 2018, 5, 229–237. [Google Scholar] [CrossRef] [Green Version]
- Smith, S.; Weston, S.; Kellam, P.; Marsh, M. IFITM proteins-cellular inhibitors of viral entry. Curr. Opin. Virol. 2014, 4, 71–77. [Google Scholar] [CrossRef]
- Bailey, C.C.; Huang, I.C.; Kam, C.; Farzan, M. Ifitm3 limits the severity of acute influenza in mice. PLoS Pathog. 2012, 8, e1002909. [Google Scholar] [CrossRef] [Green Version]
- John, S.P.; Chin, C.R.; Perreira, J.M.; Feeley, E.M.; Aker, A.M.; Savidis, G.; Smith, S.E.; Elia, A.E.; Everitt, A.R.; Vora, M.; et al. The CD225 domain of IFITM3 is required for both IFITM protein association and inhibition of influenza A virus and dengue virus replication. J. Virol. 2013, 87, 7837–7852. [Google Scholar] [CrossRef] [Green Version]
- Li, K.; Markosyan, R.M.; Zheng, Y.M.; Golfetto, O.; Bungart, B.; Li, M.; Ding, S.; He, Y.; Liang, C.; Lee, J.C.; et al. IFITM proteins restrict viral membrane hemifusion. PLoS Pathog. 2013, 9, e1003124. [Google Scholar] [CrossRef]
- Everitt, A.R.; Clare, S.; Pertel, T.; John, S.P.; Wash, R.S.; Smith, S.E.; Chin, C.R.; Feeley, E.M.; Sims, J.S.; Adams, D.J.; et al. IFITM3 restricts the morbidity and mortality associated with influenza. Nature 2012, 484, 519–523. [Google Scholar] [CrossRef] [Green Version]
- Prabhu, S.S.; Chakraborty, T.T.; Kumar, N.; Banerjee, I. Association between IFITM3 rs12252 polymorphism and influenza susceptibility and severity: A meta-analysis. Gene 2018, 674, 70–79. [Google Scholar] [CrossRef] [PubMed]
- Makvandi-Nejad, S.; Laurenson-Schafer, H.; Wang, L.; Wellington, D.; Zhao, Y.; Jin, B.; Qin, L.; Kite, K.; Moghadam, H.K.; Song, C.; et al. Lack of Truncated IFITM3 Transcripts in Cells Homozygous for the rs12252-C Variant That is Associated With Severe Influenza Infection. J. Infect. Dis. 2018, 217, 257–262. [Google Scholar] [CrossRef] [PubMed]
- Kim, Y.C.; Jeong, B.H. No Correlation of the Disease Severity of Influenza A Virus Infection with the rs12252 Polymorphism of the Interferon-Induced Transmembrane Protein 3 Gene. Intervirology 2017, 60, 69–74. [Google Scholar] [CrossRef] [PubMed]
- David, S.; Correia, V.; Antunes, L.; Faria, R.; Ferrao, J.; Faustino, P.; Nunes, B.; Maltez, F.; Lavinha, J.; Rebelo de Andrade, H. Population genetics of IFITM3 in Portugal and Central Africa reveals a potential modifier of influenza severity. Immunogenetics 2018, 70, 169–177. [Google Scholar] [CrossRef] [PubMed]
- Hartshorn, K.L. Innate Immunity and Influenza A Virus Pathogenesis: Lessons for COVID-19. Front. Cell. Infect. Microbiol. 2020, 10, 563850. [Google Scholar] [CrossRef]
- Abdelrahman, Z.; Li, M.; Wang, X. Comparative Review of SARS-CoV-2, SARS-CoV, MERS-CoV, and Influenza A Respiratory Viruses. Front. Immunol. 2020, 11, 552909. [Google Scholar] [CrossRef]
- Perone, G. The determinants of COVID-19 case fatality rate (CFR) in the Italian regions and provinces: An analysis of environmental, demographic, and healthcare factors. Sci. Total Environ. 2020, 755, 142523. [Google Scholar] [CrossRef]
- Wang, Z.H.T.; Zhu, L.; Sheng, H.; Huang, S.; Hu, J. Active quarantine measures are the primary means to reduce the fatality rate of COVID-19. Bull. World Health Organ. 2020, 1–12. [Google Scholar] [CrossRef]
- Cote, M.L. Study designs in genetic epidemiology. Methods Mol. Biol. 2009, 520, 247–257. [Google Scholar] [CrossRef]
- Schwartz, S. The fallacy of the ecological fallacy: The potential misuse of a concept and the consequences. Am. J. Public Health 1994, 84, 819–824. [Google Scholar] [CrossRef] [Green Version]
- Parsons, P.A.; Bodmer, W.F. The evolution of overdominance: Natural selection and heterozygote advantage. Nature 1961, 190, 7–12. [Google Scholar] [CrossRef] [PubMed]
- Pairo-Castineira, E.; Clohisey, S.; Klaric, L.; Bretherick, A.D.; Rawlik, K.; Pasko, D.; Walker, S.; Parkinson, N.; Fourman, M.H.; Russell, C.D.; et al. Genetic mechanisms of critical illness in Covid-19. Nature 2020. In press. [Google Scholar] [CrossRef] [PubMed]
- Kim, Y.C.; Jeong, B.H. Ethnic variation in risk genotypes based on single nucleotide polymorphisms (SNPs) of the interferon-inducible transmembrane 3 (IFITM3) gene, a susceptibility factor for pandemic 2009 H1N1 influenza A virus. Immunogenetics 2020, 72, 447–453. [Google Scholar] [CrossRef] [PubMed]
Subject Groups | Matching Groups in1000 Genome Project | Case | Death | Case Fatality Rate (%) |
---|---|---|---|---|
African a | African (AFR) | 278,815 | 5785 | 2.07 |
European b | European (EUR) | 2,656,437 | 196,541 | 7.40 |
American c | American (AMR) | 4,933,972 | 241,931 | 4.90 |
East Asian d | East Asian (EAS) | 104,035 | 5620 | 5.40 |
South Asian e | South Asian (SAS) | 336,933 | 5813 | 1.73 |
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. |
© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
Share and Cite
Kim, Y.-C.; Jeong, B.-H. Strong Correlation between the Case Fatality Rate of COVID-19 and the rs6598045 Single Nucleotide Polymorphism (SNP) of the Interferon-Induced Transmembrane Protein 3 (IFITM3) Gene at the Population-Level. Genes 2021, 12, 42. https://doi.org/10.3390/genes12010042
Kim Y-C, Jeong B-H. Strong Correlation between the Case Fatality Rate of COVID-19 and the rs6598045 Single Nucleotide Polymorphism (SNP) of the Interferon-Induced Transmembrane Protein 3 (IFITM3) Gene at the Population-Level. Genes. 2021; 12(1):42. https://doi.org/10.3390/genes12010042
Chicago/Turabian StyleKim, Yong-Chan, and Byung-Hoon Jeong. 2021. "Strong Correlation between the Case Fatality Rate of COVID-19 and the rs6598045 Single Nucleotide Polymorphism (SNP) of the Interferon-Induced Transmembrane Protein 3 (IFITM3) Gene at the Population-Level" Genes 12, no. 1: 42. https://doi.org/10.3390/genes12010042
APA StyleKim, Y.-C., & Jeong, B.-H. (2021). Strong Correlation between the Case Fatality Rate of COVID-19 and the rs6598045 Single Nucleotide Polymorphism (SNP) of the Interferon-Induced Transmembrane Protein 3 (IFITM3) Gene at the Population-Level. Genes, 12(1), 42. https://doi.org/10.3390/genes12010042