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Yazdanparast S, Bakhtiyaridovvombaygi M, Mikanik F, Ahmadi R, Ghorbani M, Mansoorian MR, Mansoorian M, Chegni H, Moshari J, Gharehbaghian A. Spotlight on contributory role of host immunogenetic profiling in SARS-CoV-2 infection: Susceptibility, severity, mortality, and vaccine effectiveness. Life Sci 2023:121907. [PMID: 37394094 DOI: 10.1016/j.lfs.2023.121907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/04/2023]
Abstract
BACKGROUND The SARS-CoV-2 virus has spread continuously worldwide, characterized by various clinical symptoms. The immune system responds to SARS-CoV-2 infection by producing Abs and secreting cytokines. Recently, numerous studies have highlighted that immunogenetic factors perform a putative role in COVID-19 pathogenesis and implicate vaccination effectiveness. AIM This review summarizes the relevant articles and evaluates the significance of mutation and polymorphism in immune-related genes regarding susceptibility, severity, mortality, and vaccination effectiveness of COVID-19. Furthermore, the correlation between host immunogenetic and SARS-CoV-2 reinfection is discussed. METHOD A comprehensive search was conducted to identify relevant articles using five databases until January 2023, which resulted in 105 total articles. KEY FINDINGS Taken to gather this review summarized that: (a) there is a plausible correlation between immune-related genes and COVID-19 outcomes, (b) the HLAs, cytokines, chemokines, and other immune-related genes expression profiles can be a prognostic factor in COVID-19-infected patients, and (c) polymorphisms in immune-related genes have been associated with the effectiveness of vaccination. SIGNIFICANCE Regarding the importance of mutation and polymorphisms in immune-related genes in COVID-19 outcomes, modulating candidate genes is expected to help clinical decisions, patient outcomes management, and innovative therapeutic approach development. In addition, the manipulation of host immunogenetics is hypothesized to induce more robust cellular and humoral immune responses, effectively increase the efficacy of vaccines, and subsequently reduce the incidence rates of reinfection-associated COVID-19.
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Affiliation(s)
- Somayeh Yazdanparast
- Student Research Committee, Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Bakhtiyaridovvombaygi
- Student Research Committee, Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Mikanik
- Student Research Committee, Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Reza Ahmadi
- Department of Infectious Diseases, School of Medicine, Infectious Diseases Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Mohammad Ghorbani
- Laboratory Hematology and Transfusion Medicine, Department of Pathology, Faculty Medicine, Gonabad University of Medical Sciences, Gonabad, Iran.
| | | | - Mozhgan Mansoorian
- Nursing Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Hamid Chegni
- Department of Immunology, School of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jalil Moshari
- School of Medicine, Gonabad University of Medical Science, Gonabad, Iran
| | - Ahmad Gharehbaghian
- Department of Hematology and Blood Bank, School of Allied Medical Science, Shahid Beheshti University of Medical Science, Tehran, Iran; Pediatric Congenital Hematologic Disorders Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Gholami M, Sakhaee F, Mirzaei Gheinari F, Sotoodehnejadnematalahi F, Ghazanfari Jajin M, Zamani MS, Ahmadi I, Anvari E, Fateh A. Interferon-Induced Transmembrane Protein 3 rs34481144 C/T Genotype and Clinical Parameters Related to Progression of COVID-19. J Immunol Res 2023; 2023:2345062. [PMID: 37323564 PMCID: PMC10266908 DOI: 10.1155/2023/2345062] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/04/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023] Open
Abstract
Recent research has associated the interferon-induced transmembrane protein 3 gene (IFITM3) with the outcomes of coronavirus disease 2019 (COVID-19), although the findings are contradictory. This study aimed to determine the relationship between IFITM3 gene rs34481144 polymorphism and clinical parameters with COVID-19 mortality. The tetra-primer amplification refractory mutation system-polymerase chain reaction assay was used to analyze IFITM3 rs34481144 polymorphism in 1,149 deceased and 1,342 recovered patients. The clinical parameters were extracted from the patients' medical records. In this study, the frequency of IFITM3 rs34481144 CT genotypes (OR 1.47, 95% CI 1.23-1.76, P < 0.0001) in both sexes was significantly higher in deceased patients than in recovered patients. Moreover, IFITM3 rs34481144 TT genotypes (OR 3.38, 95% CI 1.05-10.87, P < 0.0001) in women were significantly associated with COVID-19 mortality. The multivariable logistic regression model results indicated that mean age (P < 0.001), alkaline phosphatase (P = 0.005), alanine aminotransferase (P < 0.001), low-density lipoprotein (P < 0.001), high-density lipoprotein (P < 0.001), fasting blood glucose (P = 0.010), creatinine (P < 0.001), uric acid (P < 0.001), C-reactive protein (P = 0.004), 25-hydroxyvitamin D (P < 0.001), erythrocyte sedimentation rate (P < 0.001), and real-time PCR Ct values (P < 0.001) were linked with increased COVID-19 death rates. In conclusion, IFITM3 rs34481144 gene polymorphism was linked to the mortality of COVID-19, with the rs34481144-T allele being especially important for mortality. Further studies are needed to confirm the results of this study.
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Affiliation(s)
- Melika Gholami
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Sakhaee
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | | | | | | | | | - Iraj Ahmadi
- Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Enayat Anvari
- Department of Physiology, School of Medicine, Ilam University of Medical Science, Ilam, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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Li Y, Wei L, He L, Sun J, Liu N. Interferon-induced transmembrane protein 3 gene polymorphisms are associated with COVID-19 susceptibility and severity: A meta-analysis. J Infect 2022; 84:825-833. [PMID: 35461906 PMCID: PMC9022375 DOI: 10.1016/j.jinf.2022.04.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/01/2022] [Accepted: 04/15/2022] [Indexed: 01/17/2023]
Abstract
BACKGROUND Recent evidence has linked the interferon-induced transmembrane protein 3 gene (IFITM3) to coronavirus disease 2019 (COVID-19) outcomes, but the results are inconsistent. The purpose of this meta-analysis was to evaluate the association of IFITM3 gene polymorphisms with COVID-19 susceptibility and severity. METHOD A systematic search was performed with PubMed, Web of Science, Cochrane Library, and Embase from the date of inception to 20 December 2021. The results were analyzed with pooled odds ratios (ORs) and 95% confidence intervals (95% CIs). The robustness was performed using the method of sequential removal for each trial. RESULTS Four studies involving 1989 subjects were included, from which 1114 patients were positive for COVID-19. For IFITM3 rs12252, the pooled OR showed that there was a significant association between the genotype frequencies and infection with COVID-19 in any of the gene models, i.e., the allelic model (OR = 1.91, 95% CI, 1.36-2.68), the dominant model (OR = 1.80, 95% CI, 1.27-2.56), the recessive model (OR = 5.67, 95% CI, 1.01-31.77), the heterozygous model (OR = 1.65, 95% CI, 1.16-2.36) and the homozygous model (OR = 5.88, 95% CI, 1.05-32.98). The results stratified by severity showed that there was a significant correlation only between the allelic (OR = 0.69, 95% CI, 0.49-0.97) and recessive (OR = 0.43, 95% CI, 0.20-0.93) models. Our results did not support the associations between the IFITM3 rs34481144 gene polymorphism and COVID-19 susceptibility or severity in any of the gene models. CONCLUSIONS The findings indicated that IFITM3 rs12252 gene polymorphisms were associated with COVID-19 susceptibility and that the rs12252-C variant was particularly critical for severity. Genetic factors should be considered in future vaccine development.
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Affiliation(s)
- Yapeng Li
- Rehabilitation Therapy Center, Luoyang Orthopedic Hospital of Henan Province, Orthopedic Hospital of Henan Province, Luoyang, China
| | - Lanlan Wei
- Inspection and Monitoring Center, Luoyang Center for Disease Control and Prevention, Luoyang, China
| | - Lanye He
- Department of Geratology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiahui Sun
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
| | - Nanyang Liu
- Department of Geratology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China,Corresponding author
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Viral and Host Genetic and Epigenetic Biomarkers Related to SARS-CoV-2 Cell Entry, Infection Rate, and Disease Severity. BIOLOGY 2022; 11:biology11020178. [PMID: 35205046 PMCID: PMC8869311 DOI: 10.3390/biology11020178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/14/2022] [Accepted: 01/14/2022] [Indexed: 12/23/2022]
Abstract
The rapid spread of COVID-19 outbreak lead to a global pandemic declared in March 2020. The common features of corona virus family helped to resolve structural characteristics and entry mechanism of SARS-CoV-2. However, rapid mutagenesis leads to the emergence of new strains that may have different reproduction rates or infectivity and may impact the course and severity of the disease. Host related factors may also play a role in the susceptibility for infection as well as the severity and outcomes of the COVID-19. We have performed a literature and database search to summarize potential viral and host-related genomic and epigenomic biomarkers, such as genetic variability, miRNA, and DNA methylation in the molecular pathway of SARS-CoV-2 entry into the host cell, that may be related to COVID-19 susceptibility and severity. Bioinformatics tools may help to predict the effect of mutations in the spike protein on the binding to the ACE2 receptor and the infectivity of the strain. SARS-CoV-2 may also target several transcription factors and tumour suppressor genes, thus influencing the expression of different host genes and affecting cell signalling. In addition, the virus may interfere with RNA expression in host cells by exploiting endogenous miRNA and its viral RNA. Our analysis showed that numerous human miRNA may form duplexes with different coding and non-coding regions of viral RNA. Polymorphisms in human genes responsible for viral entry and replication, as well as in molecular damage response and inflammatory pathways may also contribute to disease prognosis and outcome. Gene ontology analysis shows that proteins encoded by such polymorphic genes are highly interconnected in regulation of defense response. Thus, virus and host related genetic and epigenetic biomarkers may help to predict the course of the disease and the response to treatment.
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Hubacek JA. Effects of selected inherited factors on susceptibility to SARS-CoV-2 infection and COVID-19 progression. Physiol Res 2021; 70:S125-S134. [PMID: 34913347 DOI: 10.33549/physiolres.934730] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genetic predispositions may influence geographical and interethnic differences in COVID-19 prevalence and mortality in affected populations. Of the many genes implicated in COVID-19 progression, a substantial number have no direct functional link on virus transfer/viability or on the host immune system. To address this knowledge deficit, a large number of in silico studies have recently been published. However, the results of these studies often contradict the findings of studies involving real patients. For example, the ACE2 has been shown to play an important role in regulating coronavirus entry into cells, but none of its variations have been directly associated with COVID-19 susceptibility or severity. Consistently was reported that increased risk of COVID-19 is associated with blood group A and with the APOE4 allele. Among other genes with potential impacts are the genes for CCR5, IL-10, CD14, TMPRSS2 and angiotensin-converting enzyme. Variants within the protein-coding genes OAS1 and LZTFL1 (transferred to the human genome from Neanderthals) are understood to be among the strongest predictors of disease severity. The intensive research efforts have helped to identify the genes and polymorphisms that contribute to SARS-CoV-2 infection and COVID-19 severity.
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Affiliation(s)
- J A Hubacek
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, Prague 4, Czech Republic.
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6
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Deng H, Yan X, Yuan L. Human genetic basis of coronavirus disease 2019. Signal Transduct Target Ther 2021; 6:344. [PMID: 34545062 PMCID: PMC8450706 DOI: 10.1038/s41392-021-00736-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/28/2021] [Accepted: 08/08/2021] [Indexed: 02/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in considerable morbidity and mortality worldwide. COVID-19 incidence, severity, and mortality rates differ greatly between populations, genders, ABO blood groups, human leukocyte antigen (HLA) genotypes, ethnic groups, and geographic backgrounds. This highly heterogeneous SARS-CoV-2 infection is multifactorial. Host genetic factors such as variants in the angiotensin-converting enzyme gene (ACE), the angiotensin-converting enzyme 2 gene (ACE2), the transmembrane protease serine 2 gene (TMPRSS2), along with HLA genotype, and ABO blood group help to explain individual susceptibility, severity, and outcomes of COVID-19. This review is focused on COVID-19 clinical and viral characteristics, pathogenesis, and genetic findings, with particular attention on genetic diversity and variants. The human genetic basis could provide scientific bases for disease prediction and targeted therapy to address the COVID-19 scourge.
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Affiliation(s)
- Hao Deng
- Health Management Center, the Third Xiangya Hospital, Central South University, Changsha, China.
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, China.
- Disease Genome Research Center, Central South University, Changsha, China.
- Department of Neurology, the Third Xiangya Hospital, Central South University, Changsha, China.
| | - Xue Yan
- Health Management Center, the Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, China
- Disease Genome Research Center, Central South University, Changsha, China
| | - Lamei Yuan
- Health Management Center, the Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, China
- Disease Genome Research Center, Central South University, Changsha, China
- Department of Neurology, the Third Xiangya Hospital, Central South University, Changsha, China
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7
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Sodeifian F, Nikfarjam M, Kian N, Mohamed K, Rezaei N. The role of type I interferon in the treatment of COVID-19. J Med Virol 2021; 94:63-81. [PMID: 34468995 PMCID: PMC8662121 DOI: 10.1002/jmv.27317] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 12/17/2022]
Abstract
Although significant research has been done to find effective drugs against coronavirus disease 2019 (COVID‐19) caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), no definite effective drug exists. Thus, research has now shifted towards immunomodulatory agents other than antivirals. In this review, we aim to describe the latest findings on the role of type I interferon (IFN)‐mediated innate antiviral response against SARS‐CoV‐2 and discuss the use of IFNs as a medication for COVID‐19. A growing body of evidence has indicated a promoting active but delayed IFNs response to SARS‐CoV‐2 and Middle East respiratory syndrome coronavirus in infected bronchial epithelial cells. Studies have demonstrated that IFNs' administration before the viral peak and the inflammatory phase of disease could offer a highly protective effect. However, IFNs' treatment during the inflammatory and severe stages of the disease causes immunopathology and long‐lasting harm for patients. Therefore, it is critical to note the best time window for IFNs' administration. Further investigation of the clinical effectiveness of interferon for patients with mild to severe COVID‐19 and its optimal timing and route of administration can be beneficial in finding a safe and effective antiviral therapy for the COVID‐19 disease. 1‐IFNs have many antiviral actions including; the activation of cytotoxic T‐cell responses, the inhibition of the viral mRNA translation, the degradation of the viral RNA, RNA editing and modulating the synthesis of Nitric Oxide. 2‐IFNS are two‐edged immunomodulatory agents; as they can provide a protective effect if administered in the early phases of the disease before the viral peak, whereas a harming effect is observed when administered in the inflammatory phase. 3‐More human trials are needed to find the best time window for administrating type I IFN for patients with various COVID‐19 modalities.
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Affiliation(s)
- Fatemeh Sodeifian
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Science, Tehran, Iran.,USERN SBMU Office, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Science, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Manama, Bahrain
| | - Mahsa Nikfarjam
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Science, Tehran, Iran.,USERN SBMU Office, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Naghmeh Kian
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Science, Tehran, Iran.,USERN SBMU Office, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Kawthar Mohamed
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Manama, Bahrain.,Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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Abstract
Coronavirus disease (COVID-19) is an infectious disease caused by a newly discovered coronavirus, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). There is growing evidence that host genetics play an important role in COVID-19 severity. Based on current knowledge about the human protein machinery for SARS-CoV-2 entry, the host innate immune response, and virus-host interactions, the potential effects of human genetic polymorphisms, which may contribute to clinical differences in SARS-CoV-2 pathogenesis, may help to determine the individual risk for COVID-19 infection and outcome.
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Affiliation(s)
- Joris R Delanghe
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.
| | - Marijn M Speeckaert
- Department of Nephrology, Ghent University Hospital, Ghent, Belgium; Research Foundation-Flanders (FWO), Brussels, Belgium
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Nemudryi A, Nemudraia A, Wiegand T, Nichols J, Snyder DT, Hedges JF, Cicha C, Lee H, Vanderwood KK, Bimczok D, Jutila MA, Wiedenheft B. SARS-CoV-2 genomic surveillance identifies naturally occurring truncation of ORF7a that limits immune suppression. Cell Rep 2021; 35:109197. [PMID: 34043946 PMCID: PMC8118641 DOI: 10.1016/j.celrep.2021.109197] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/04/2021] [Accepted: 05/10/2021] [Indexed: 12/15/2022] Open
Abstract
Over 950,000 whole-genome sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been determined for viruses isolated from around the world. These sequences are critical for understanding the spread and evolution of SARS-CoV-2. Using global phylogenomics, we show that mutations frequently occur in the C-terminal end of ORF7a. We isolate one of these mutant viruses from a patient sample and use viral challenge experiments to link this isolate (ORF7aΔ115) to a growth defect. ORF7a is implicated in immune modulation, and we show that the C-terminal truncation negates anti-immune activities of the protein, which results in elevated type I interferon response to the viral infection. Collectively, this work indicates that ORF7a mutations occur frequently, and that these changes affect viral mechanisms responsible for suppressing the immune response.
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Affiliation(s)
- Artem Nemudryi
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Anna Nemudraia
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Tanner Wiegand
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Joseph Nichols
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Deann T Snyder
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Jodi F Hedges
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Calvin Cicha
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Helen Lee
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | | | - Diane Bimczok
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Mark A Jutila
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA.
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10
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Nemudryi A, Nemudraia A, Wiegand T, Nichols J, Snyder DT, Hedges JF, Cicha C, Lee H, Vanderwood KK, Bimczok D, Jutila M, Wiedenheft B. SARS-CoV-2 genomic surveillance identifies naturally occurring truncations of ORF7a that limit immune suppression. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.02.22.21252253. [PMID: 33655280 PMCID: PMC7924305 DOI: 10.1101/2021.02.22.21252253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Over 200,000 whole genome sequences of SARS-CoV-2 have been determined for viruses isolated from around the world. These sequences have been critical for understanding the spread and evolution of SARS-CoV-2. Using global phylogenomics, we show that mutations frequently occur in the C-terminal end of ORF7a. We have isolated one of these mutant viruses from a patient sample and used viral challenge experiments to demonstrate that Δ115 mutation results in a growth defect. ORF7a has been implicated in immune modulation, and we show that the C-terminal truncation results in distinct changes in interferon stimulated gene expression. Collectively, this work indicates that ORF7a mutations occur frequently and that these changes affect viral mechanisms responsible for suppressing the immune response.
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Affiliation(s)
- Artem Nemudryi
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
- Twitter: @artemnemudryi
- Lead contact
| | - Anna Nemudraia
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Tanner Wiegand
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Joseph Nichols
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Deann T Snyder
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Jodi F Hedges
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Calvin Cicha
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Helen Lee
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | | | - Diane Bimczok
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Mark Jutila
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
- Twitter: @WiedenheftLab
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11
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Nikoloudis D, Kountouras D, Hiona A. The frequency of combined IFITM3 haplotype involving the reference alleles of both rs12252 and rs34481144 is in line with COVID-19 standardized mortality ratio of ethnic groups in England. PeerJ 2020; 8:e10402. [PMID: 33240681 PMCID: PMC7666821 DOI: 10.7717/peerj.10402] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/30/2020] [Indexed: 12/20/2022] Open
Abstract
Evidence was brought forward in England and the USA that Black, Asian, Latino and Minority Ethnic people exhibit higher mortality risk from COVID-19 than White people. While socioeconomic factors were suggested to contribute to this trend, they arguably do not explain the range of the differences observed, allowing for possible genetic implications. Almost concurrently, the analysis of a cohort in Chinese COVID-19 patients proposed an association between the severity of the disease and the presence of the minor allele of rs12252 of the Interferon-induced transmembrane protein 3 (IFITM3) gene. This SNP, together with rs34481144, are the two most studied polymorphisms of IFITM3 and have been associated in the past with increased severity in Influenza, Dengue, Ebola, and HIV viruses. IFITM3 is an immune effector protein that is pivotal for the restriction of viral replication, but also for the regulation of cytokine production. Following up on these two developments in the ongoing SARS-CoV-2 pandemic, the present study investigates a possible association between the differences in mortality of ethnic groups in England and the combined haplotypes of rs12252 and rs34481144. The respective allele frequencies were collected for 26 populations from the 1000 Genomes Project and subgroups were pooled wherever possible to create correspondences with ethnic groups in England. A significant correlation (r = 0.9687, p = 0.0003) and a striking agreement was observed between the reported Standardized Mortality Ratios and the frequency of the combined haplotype of both reference alleles, suggesting that the combination of the reference alleles of the specific SNPs may be implicated in more severe outcomes of COVID-19. This study calls for further focus on the role of IFITM3 variants in the mechanism of cellular invasion of SARS-CoV-2, their impact in COVID-19 severity and their possible implications in vaccination efficacy.
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Affiliation(s)
- Dimitris Nikoloudis
- Center for Preventive Medicine & Longevity, Bioiatriki Healthcare Group, Athens, Attiki, Greece
| | - Dimitrios Kountouras
- Center for Preventive Medicine & Longevity, Bioiatriki Healthcare Group, Athens, Attiki, Greece
| | - Asimina Hiona
- Center for Preventive Medicine & Longevity, Bioiatriki Healthcare Group, Athens, Attiki, Greece
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