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The role of inflammatory gene polymorphisms in severe COVID-19: a review

Yip et al., Virology Journal, doi:10.1186/s12985-024-02597-3
Dec 2024  
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Review of the role of inflammatory gene polymorphisms in severe COVID-19. Authors explore how genetic variations in key inflammatory genes contribute to variability in immune responses and disease severity. Polymorphisms in cytokine genes such as IL-6, IL-8, and TNF-α influence cytokine production and downstream signaling pathways, leading to heightened inflammation and tissue damage. The review also examines variations in interferon pathway genes, NF-κB, cytokine receptors, and the vitamin D receptor, which impact susceptibility and clinical outcomes. Furthermore, atypical factors, including SAMHD1, NTRK1, APP, and LZTFL1, are implicated in severe and long COVID-19 cases.
Yip et al., 20 Dec 2024, peer-reviewed, 8 authors. Contact: sazaly@um.edu.my, nurhafizazainal@um.edu.my.
This PaperMiscellaneousAll
The role of inflammatory gene polymorphisms in severe COVID-19: a review
Jia Qi Yip, Adrian Oo, Yan Ling Ng, Kim Ling Chin, Kim-Kee Tan, Justin Jang Hann Chu, Sazaly Abubakar, Nurhafiza Zainal
Virology Journal, doi:10.1186/s12985-024-02597-3
The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, has profoundly impacted global healthcare systems and spurred extensive research efforts over the past three years. One critical aspect of the disease is the intricate interplay between the virus and the host immune response, particularly the role of inflammatory gene expression in severe COVID-19. While numerous previous studies have explored the role of genetic polymorphisms in COVID-19, research specifically focusing on inflammatory genes and their associations with disease severity remains limited. This review explores the relationship between severe COVID-19 outcomes and genetic polymorphisms within key inflammatory genes. By investigating the impact of genetic variations on immune responses, which include cytokine production and downstream signalling pathways, we aim to provide a comprehensive overview of how genetic polymorphisms contribute to the variability in disease presentation. Through an in-depth analysis of existing literature, we shed light on potential therapeutic targets and personalized approaches that may enhance our understanding of disease pathogenesis and treatment strategies.
Author contributions JQY, AO, and YLN were involved in the initial draft writing. NZ and KLC provided critical revisions to the manuscript. KKT, JJHC, and SAB edited and reviewed the manuscript. All authors have read and agreed to the published version of the manuscript. Funding We extend our sincere gratitude to the Ministry of Science, Technology and Innovation for the MOSTI-Funding (MOSTI004-2021SRF) awarded to Dr. Nurhafiza Zainal, which made this study possible through their generous support. We also appreciate the support from the Higher Institution Centre of Excellence (HICoE) Program (Project MO002-2019). Availability of data and materials Data sharing is not applicable to this article as no datasets were generated or analysed during the current study. Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Competing interests The authors declare that they have no competing interests. Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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' 'Viruses. 2023;15(5):1197.', 'journal-title': 'Viruses'}, { 'issue': '7', 'key': '2597_CR143', 'doi-asserted-by': 'publisher', 'first-page': '2878', 'DOI': '10.1038/s41380-022-01831-0', 'volume': '28', 'author': 'EA Albornoz', 'year': '2023', 'unstructured': 'Albornoz EA, Amarilla AA, Modhiran N, Parker S, Li XX, Wijesundara DK, ' 'et al. SARS-CoV-2 drives NLRP3 inflammasome activation in human ' 'microglia through spike protein. Mol Psychiatry. 2023;28(7):2878–93.', 'journal-title': 'Mol Psychiatry'}, { 'issue': '1', 'key': '2597_CR144', 'doi-asserted-by': 'publisher', 'first-page': '4664', 'DOI': '10.1038/s41467-021-25015-6', 'volume': '12', 'author': 'P Pan', 'year': '2021', 'unstructured': 'Pan P, Shen M, Yu Z, Ge W, Chen K, Tian M, et al. SARS-CoV-2 N protein ' 'promotes NLRP3 inflammasome activation to induce hyperinflammation. Nat ' 'Commun. 2021;12(1):4664.', 'journal-title': 'Nat Commun'}, { 'issue': '10–11', 'key': '2597_CR145', 'doi-asserted-by': 'publisher', 'first-page': '1933', 'DOI': '10.1007/s00011-022-01670-3', 'volume': '72', 'author': 'VNC Leal', 'year': '2023', 'unstructured': 'Leal VNC, Paulino LM, Cambui RAG, Zupelli TG, Yamada SM, Oliveira LAT, ' 'et al. A common variant close to the “tripwire” linker region of NLRP1 ' 'contributes to severe COVID-19. Inflamm Res. 2023;72(10–11):1933–40.', 'journal-title': 'Inflamm Res'}, { 'issue': '1', 'key': '2597_CR146', 'doi-asserted-by': 'publisher', 'first-page': '121', 'DOI': '10.3390/diagnostics13010121', 'volume': '13', 'author': 'S Salamaikina', 'year': '2022', 'unstructured': 'Salamaikina S, Karnaushkina M, Korchagin V, Litvinova M, Mironov K, ' 'Akimkin V. TLRs gene polymorphisms associated with pneumonia before and ' 'during COVID-19 pandemic. Diagnostics (Basel). 2022;13(1):121.', 'journal-title': 'Diagnostics (Basel)'}, { 'issue': '2', 'key': '2597_CR147', 'doi-asserted-by': 'publisher', 'first-page': 'e06187', 'DOI': '10.1016/j.heliyon.2021.e06187', 'volume': '7', 'author': 'K Shirato', 'year': '2021', 'unstructured': 'Shirato K, Kizaki T. SARS-CoV-2 spike protein S1 subunit induces ' 'pro-inflammatory responses via toll-like receptor 4 signaling in murine ' 'and human macrophages. Heliyon. 2021;7(2):e06187.', 'journal-title': 'Heliyon'}, { 'key': '2597_CR148', 'doi-asserted-by': 'publisher', 'first-page': '8874339', 'DOI': '10.1155/2021/8874339', 'volume': '2021', 'author': 'MM Aboudounya', 'year': '2021', 'unstructured': 'Aboudounya MM, Heads RJ. COVID-19 and toll-like receptor 4 (TLR4): ' 'SARS-CoV-2 may bind and activate TLR4 to increase ACE2 expression, ' 'facilitating entry and causing hyperinflammation. Mediators Inflamm. ' '2021;2021:8874339.', 'journal-title': 'Mediators Inflamm'}, { 'key': '2597_CR149', 'first-page': '14', 'volume': '28', 'author': 'M Aribi', 'year': '2023', 'unstructured': 'Aribi M, Mennechet FJD, Touil-Boukoffa C. Editorial: the role of vitamin ' 'D as an immunomodulator. Front Immunol. 2023;28:14.', 'journal-title': 'Front Immunol'}, { 'issue': '7', 'key': '2597_CR150', 'doi-asserted-by': 'publisher', 'first-page': '2097', 'DOI': '10.3390/nu12072097', 'volume': '12', 'author': 'N Charoenngam', 'year': '2020', 'unstructured': 'Charoenngam N, Holick MF. Immunologic effects of vitamin D on human ' 'health and disease. Nutrients. 2020;12(7):2097.', 'journal-title': 'Nutrients'}, { 'issue': '9', 'key': '2597_CR151', 'doi-asserted-by': 'publisher', 'first-page': '5458', 'DOI': '10.4049/jimmunol.0803217', 'volume': '183', 'author': 'LE Jeffery', 'year': '2009', 'unstructured': 'Jeffery LE, Burke F, Mura M, Zheng Y, Qureshi OS, Hewison M, et al. ' '1,25-Dihydroxyvitamin D3 and IL-2 combine to inhibit T cell production ' 'of inflammatory cytokines and promote development of regulatory T cells ' 'expressing CTLA-4 and FoxP3. J Immunol. 2009;183(9):5458–67.', 'journal-title': 'J Immunol'}, { 'issue': '7', 'key': '2597_CR152', 'doi-asserted-by': 'publisher', 'first-page': 'e102141', 'DOI': '10.1371/journal.pone.0102141', 'volume': '9', 'author': 'NM Al-Daghri', 'year': '2014', 'unstructured': 'Al-Daghri NM, Guerini FR, Al-Attas OS, Alokail MS, Alkharfy KM, Draz HM, ' 'et al. Vitamin D receptor gene polymorphisms are associated with obesity ' 'and inflammosome activity. PLoS ONE. 2014;9(7):e102141.', 'journal-title': 'PLoS ONE'}, { 'issue': '6', 'key': '2597_CR153', 'doi-asserted-by': 'publisher', 'first-page': '819', 'DOI': '10.1111/cen.14664', 'volume': '96', 'author': 'T Apaydin', 'year': '2022', 'unstructured': 'Apaydin T, Polat H, Dincer Yazan C, Ilgin C, Elbasan O, Dashdamirova S, ' 'et al. Effects of vitamin D receptor gene polymorphisms on the prognosis ' 'of COVID-19. Clin Endocrinol (Oxf). 2022;96(6):819–30.', 'journal-title': 'Clin Endocrinol (Oxf)'}, { 'issue': '5', 'key': '2597_CR154', 'doi-asserted-by': 'publisher', 'first-page': '1383', 'DOI': '10.1038/s41390-022-02275-6', 'volume': '93', 'author': 'NMS Zeidan', 'year': '2023', 'unstructured': 'Zeidan NMS, El LHMA, Selim DM, Razek SA, Abd-Elrehim GAB, Nashat M, et ' 'al. Vitamin D deficiency and vitamin D receptor FokI polymorphism as ' 'risk factors for COVID-19. Pediatr Res. 2023;93(5):1383–90.', 'journal-title': 'Pediatr Res'}, { 'issue': '1', 'key': '2597_CR155', 'doi-asserted-by': 'publisher', 'first-page': '10170', 'DOI': '10.1038/s41598-024-57424-0', 'volume': '14', 'author': 'N Mohammadifard', 'year': '2024', 'unstructured': 'Mohammadifard N, Sadeghian L, Hassannejad R, Khosravi E, Gharipour M, ' 'Karimi S, et al. Comparing vitamin D receptor gene polymorphisms in ' 'rs11568820, rs7970314, rs4334089 between COVID-19 patients with mild and ' 'severe symptoms: a case control study. Sci Rep. 2024;14(1):10170.', 'journal-title': 'Sci Rep'}, { 'issue': '16', 'key': '2597_CR156', 'doi-asserted-by': 'publisher', 'first-page': 'E3798', 'DOI': '10.1073/pnas.1801213115', 'volume': '115', 'author': 'S Chen', 'year': '2018', 'unstructured': 'Chen S, Bonifati S, Qin Z, St Gelais C, Kodigepalli KM, Barrett BS, et ' 'al. SAMHD1 suppresses innate immune responses to viral infections and ' 'inflammatory stimuli by inhibiting the NF-κB and interferon pathways. ' 'Proc Natl Acad Sci USA. 2018;115(16):E3798–807.', 'journal-title': 'Proc Natl Acad Sci USA'}, { 'issue': '9', 'key': '2597_CR157', 'doi-asserted-by': 'publisher', 'first-page': '7888', 'DOI': '10.3390/ijms24097888', 'volume': '24', 'author': 'B Xu', 'year': '2023', 'unstructured': 'Xu B, Sui Q, Hu H, Hu X, Zhou X, Qian C, et al. SAMHD1 attenuates acute ' 'inflammation by maintaining mitochondrial function in macrophages via ' 'interaction with VDAC1. Int J Mol Sci. 2023;24(9):7888.', 'journal-title': 'Int J Mol Sci'}, { 'key': '2597_CR158', 'doi-asserted-by': 'publisher', 'first-page': '562913', 'DOI': '10.3389/fneur.2020.562913', 'volume': '11', 'author': 'A Khan', 'year': '2020', 'unstructured': 'Khan A, Sergi C. SAMHD1 as the potential link between SARS-CoV-2 ' 'infection and neurological complications. Front Neurol. 2020;11:562913.', 'journal-title': 'Front Neurol'}, { 'issue': '1', 'key': '2597_CR159', 'doi-asserted-by': 'publisher', 'first-page': '15141', 'DOI': '10.1038/s41598-023-42127-9', 'volume': '13', 'author': 'G Taheri', 'year': '2023', 'unstructured': 'Taheri G, Habibi M. Identification of essential genes associated with ' 'SARS-CoV-2 infection as potential drug target candidates with machine ' 'learning algorithms. Sci Rep. 2023;13(1):15141.', 'journal-title': 'Sci Rep'}, { 'issue': '2', 'key': '2597_CR160', 'doi-asserted-by': 'publisher', 'first-page': '108', 'DOI': '10.1089/nat.2022.0055', 'volume': '33', 'author': 'JC Zhao', 'year': '2023', 'unstructured': 'Zhao JC, Saleh A, Crooke ST. SIDT2 inhibits phosphorothioate antisense ' 'oligonucleotide activity by regulating cellular localization of ' 'lysosomes. Nucleic Acid Ther. 2023;33(2):108–16.', 'journal-title': 'Nucleic Acid Ther'}, { 'issue': '1', 'key': '2597_CR161', 'doi-asserted-by': 'publisher', 'first-page': '1133', 'DOI': '10.1038/s42003-022-04073-6', 'volume': '5', 'author': 'A Onoja', 'year': '2022', 'unstructured': 'Onoja A, Picchiotti N, Fallerini C, Baldassarri M, Fava F, GEN-COVID ' 'Multicenter Study, et al. An explainable model of host genetic ' 'interactions linked to COVID-19 severity. 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' '2022;89(2):411–4.', 'journal-title': 'J Alzheimers Dis'}, { 'issue': '157', 'key': '2597_CR164', 'doi-asserted-by': 'publisher', 'first-page': '105598', 'DOI': '10.1016/j.ejps.2020.105598', 'volume': '1', 'author': 'T Zhang', 'year': '2021', 'unstructured': 'Zhang T, Yu J, Wang G, Zhang R. Amyloid precursor protein binds with ' 'TNFRSF21 to induce neural inflammation in Alzheimer’s Disease. Eur J ' 'Pharm Sci. 2021;1(157):105598.', 'journal-title': 'Eur J Pharm Sci'}, { 'issue': '1', 'key': '2597_CR165', 'doi-asserted-by': 'publisher', 'first-page': '396', 'DOI': '10.1038/s41398-023-02692-z', 'volume': '13', 'author': 'J Chen', 'year': '2023', 'unstructured': 'Chen J, Chen J, Lei Z, Zhang F, Zeng LH, Wu X, et al. Amyloid precursor ' 'protein facilitates SARS-CoV-2 virus entry into cells and enhances ' 'amyloid-β-associated pathology in APP/PS1 mouse model of Alzheimer’s ' 'disease. 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Sci Rep. 2024;14(1):8497.', 'journal-title': 'Sci Rep'}, { 'issue': '1', 'key': '2597_CR168', 'doi-asserted-by': 'publisher', 'first-page': '738', 'DOI': '10.1186/s12885-019-5951-3', 'volume': '19', 'author': 'H Wang', 'year': '2019', 'unstructured': 'Wang H, Tan Z, Hu H, Liu H, Wu T, Zheng C, et al. microRNA-21 promotes ' 'breast cancer proliferation and metastasis by targeting LZTFL1. BMC ' 'Cancer. 2019;19(1):738.', 'journal-title': 'BMC Cancer'}, { 'key': '2597_CR169', 'doi-asserted-by': 'publisher', 'first-page': '16', 'DOI': '10.1016/j.molimm.2024.01.010', 'volume': '167', 'author': 'G Song', 'year': '2024', 'unstructured': 'Song G, Sun M, Zhang Y, Zhang B, Peng M, Bao B. Anti-inflammation of ' 'LZTFL1 knockdown in OVA-induced asthmatic mice: Through ERK/GATA3 ' 'signaling pathway. Mol Immunol. 2024;167:16–24.', 'journal-title': 'Mol Immunol'}, { 'issue': '3', 'key': '2597_CR170', 'doi-asserted-by': 'publisher', 'first-page': '1081', 'DOI': '10.4049/jimmunol.1500719', 'volume': '196', 'author': 'H Jiang', 'year': '2016', 'unstructured': 'Jiang H, Promchan K, Lin BR, Lockett S, Chen D, Marshall H, et al. ' 'LZTFL1 upregulated by all-trans retinoic acid during CD4+ T cell ' 'activation enhances IL-5 production. J Immunol. 2016;196(3):1081–90.', 'journal-title': 'J Immunol'}, { 'issue': '7970', 'key': '2597_CR171', 'doi-asserted-by': 'publisher', 'first-page': '445', 'DOI': '10.1038/d41586-023-02269-2', 'volume': '619', 'author': 'H Ledford', 'year': '2023', 'unstructured': 'Ledford H. Gene linked to long COVID found in analysis of thousands of ' 'patients. Nature. 2023;619(7970):445–445.', 'journal-title': 'Nature'}, { 'issue': '1', 'key': '2597_CR172', 'doi-asserted-by': 'publisher', 'first-page': '408', 'DOI': '10.3390/ijms25010408', 'volume': '25', 'author': 'A Constantinescu-Bercu', 'year': '2023', 'unstructured': 'Constantinescu-Bercu A, Lobiuc A, Căliman-Sturdza OA, Oiţă RC, Iavorschi ' 'M, Pavăl NE, et al. Long COVID: molecular mechanisms and detection ' 'techniques. Int J Mol Sci. 2023;25(1):408.', 'journal-title': 'Int J Mol Sci'}, { 'key': '2597_CR173', 'doi-asserted-by': 'crossref', 'unstructured': 'Lammi V, Nakanishi T, Jones SE, Andrews SJ, Karjalainen J, Cortés B, et ' 'al. Genome-wide Association Study of Long COVID. 2023', 'DOI': '10.1016/j.sleep.2023.11.695'}, { 'issue': '5', 'key': '2597_CR174', 'doi-asserted-by': 'publisher', 'first-page': '167', 'DOI': '10.1007/s10142-024-01451-7', 'volume': '24', 'author': 'MK Gupta', 'year': '2024', 'unstructured': 'Gupta MK, Gouda G, Vadde R. Deciphering the role of FOXP4 in long COVID: ' 'exploring genetic associations, evolutionary conservation, and drug ' 'identification through bioinformatics analysis. Funct Integr Genomics. ' '2024;24(5):167.', 'journal-title': 'Funct Integr Genomics'}, { 'issue': '2', 'key': '2597_CR175', 'doi-asserted-by': 'publisher', 'first-page': '2239952', 'DOI': '10.1080/22221751.2023.2239952', 'volume': '12', 'author': 'W Udomsinprasert', 'year': '2023', 'unstructured': 'Udomsinprasert W, Nontawong N, Saengsiwaritt W, Panthan B, Jiaranai P, ' 'Thongchompoo N, et al. Host genetic polymorphisms involved in long-term ' 'symptoms of COVID-19. 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' '2024;15(1):4031.', 'journal-title': 'Nat Commun'}, { 'issue': '16', 'key': '2597_CR181', 'doi-asserted-by': 'publisher', 'first-page': '1522', 'DOI': '10.1056/NEJMoa2020283', 'volume': '383', 'author': 'D Ellinghaus', 'year': '2020', 'unstructured': 'Severe Covid-19 GWAS Group, Ellinghaus D, Degenhardt F, Bujanda L, Buti ' 'M, Albillos A, et al. Genomewide association study of severe covid-19 ' 'with respiratory failure. N Engl J Med. 2020;383(16):1522–34.', 'journal-title': 'N Engl J Med'}, { 'issue': '1', 'key': '2597_CR182', 'doi-asserted-by': 'publisher', 'first-page': '47', 'DOI': '10.2174/1389202916666141223220551', 'volume': '16', 'author': 'J Castiblanco', 'year': '2015', 'unstructured': 'Castiblanco J, Anaya JM. Genetics and vaccines in the era of ' 'personalized medicine. 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