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Razavi A, Raei M, Shirato K. Association of IFNAR2 and TYK2 with COVID-19 pathology: current and future. Front Immunol 2024; 15:1462628. [PMID: 39351231 PMCID: PMC11439707 DOI: 10.3389/fimmu.2024.1462628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 09/02/2024] [Indexed: 10/04/2024] Open
Affiliation(s)
- Alireza Razavi
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Research Center for Clinical Virology, Tehran University of Medical Science, Tehran, Iran
| | - Maedeh Raei
- Gastrointestinal Cancer Research Center, Non-Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ken Shirato
- Department of Molecular Predictive Medicine and Sport Science, Kyorin University Faculty of Medicine, Mitaka, Japan
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Kamenarova K, Kachakova-Yordanova D, Baymakova M, Georgiev M, Mihova K, Petkova V, Beltcheva O, Argirova R, Atanasov P, Kunchev M, Andonova R, Zasheva A, Drenska R, Ivanov I, Pantileeva D, Koleva V, Penev A, Lekova-Nikova D, Georgiev D, Pencheva D, Bozhilova R, Ivanova N, Dimova I, Plochev K, Popov G, Popivanov I, Gabrovsky N, Leseva M, Mitev V, Kaneva R. Rare host variants in ciliary expressed genes contribute to COVID-19 severity in Bulgarian patients. Sci Rep 2024; 14:19487. [PMID: 39174791 PMCID: PMC11341789 DOI: 10.1038/s41598-024-70514-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 08/19/2024] [Indexed: 08/24/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a pneumonia with extremely heterogeneous clinical presentation, ranging from asymptomatic to severely ill patients. Previous studies have reported links between the presence of host genetic variants and the outcome of the COVID-19 infection. In our study, we used whole exome sequencing in a cohort of 444 SARS-CoV-2 patients, admitted to hospital in the period October-2020-April-2022, to search for associations between rare pathogenic/potentially pathogenic variants and COVID-19 progression. We used gene prioritization-based analysis in genes that have been reported by host genetic studies. Although we did not identify correlation between the presence of rare pathogenic variants and COVID-19 outcome, in critically ill patients we detected known mutations in a number of genes associated with severe disease related to cardiovascular disease, primary ciliary dyskinesia, cystic fibrosis, DNA damage repair response, coagulation, primary immune disorder, hemoglobin subunit β, and others. Additionally, we report 93 novel pathogenic variants found in severely infected patients who required intubation or died. A network analysis showed main component, consisting of 13 highly interconnected genes related to epithelial cilium. In conclusion, we have detected rare pathogenic host variants that may have influenced the COVID-19 outcome in Bulgarian patients.
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Affiliation(s)
- Kunka Kamenarova
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria.
- Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria.
| | - Darina Kachakova-Yordanova
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
- Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
| | - Magdalena Baymakova
- Department of Infectious Diseases, Military Medical Academy, Sofia, Bulgaria
| | - Martin Georgiev
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
- Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
| | - Kalina Mihova
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
- Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
| | - Veronika Petkova
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
- Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
| | - Olga Beltcheva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
- Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
| | - Radka Argirova
- Acibadem City Clinic, University Multidisciplinary Hospital for Active Treatment "Tokuda", Sofia, Bulgaria
| | - Petar Atanasov
- University Multidisciplinary Hospital for Active Treatment and Emergency Medicine "N.I. Pirogov", Sofia, Bulgaria
| | - Metodi Kunchev
- Department of Virology, Military Medical Academy, Sofia, Bulgaria
| | - Radina Andonova
- Department of Infectious Diseases, Military Medical Academy, Sofia, Bulgaria
| | - Anelia Zasheva
- Department of Infectious Diseases, Military Medical Academy, Sofia, Bulgaria
| | - Rumiana Drenska
- University Multidisciplinary Hospital for Active Treatment and Emergency Medicine "N.I. Pirogov", Sofia, Bulgaria
| | - Ivaylo Ivanov
- University Multidisciplinary Hospital for Active Treatment and Emergency Medicine "N.I. Pirogov", Sofia, Bulgaria
| | - Diana Pantileeva
- University Multidisciplinary Hospital for Active Treatment and Emergency Medicine "N.I. Pirogov", Sofia, Bulgaria
| | - Vesselina Koleva
- Acibadem City Clinic, University Multidisciplinary Hospital for Active Treatment "Tokuda", Sofia, Bulgaria
| | - Anton Penev
- Acibadem City Clinic, University Multidisciplinary Hospital for Active Treatment "Tokuda", Sofia, Bulgaria
| | - Diana Lekova-Nikova
- Acibadem City Clinic, University Multidisciplinary Hospital for Active Treatment "Tokuda", Sofia, Bulgaria
| | - Delyan Georgiev
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
- Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
| | - Daniela Pencheva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
- Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
| | - Radosveta Bozhilova
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
- Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
| | - Nevyana Ivanova
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
- Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
| | - Ivanka Dimova
- Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
| | - Kamen Plochev
- Department of Infectious Diseases, Military Medical Academy, Sofia, Bulgaria
| | - Georgi Popov
- Department of Infectious Diseases, Military Medical Academy, Sofia, Bulgaria
| | - Ivan Popivanov
- Department of Military Medicine, Military Medical Academy, Sofia, Bulgaria
| | - Nikolay Gabrovsky
- University Multidisciplinary Hospital for Active Treatment and Emergency Medicine "N.I. Pirogov", Sofia, Bulgaria
| | - Magdalena Leseva
- University Multidisciplinary Hospital for Active Treatment and Emergency Medicine "N.I. Pirogov", Sofia, Bulgaria
| | - Vanio Mitev
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
- Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
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Angulo-Aguado M, Carrillo-Martinez JC, Contreras-Bravo NC, Morel A, Parra-Abaunza K, Usaquén W, Fonseca-Mendoza DJ, Ortega-Recalde O. Next-generation sequencing of host genetics risk factors associated with COVID-19 severity and long-COVID in Colombian population. Sci Rep 2024; 14:8497. [PMID: 38605121 PMCID: PMC11009356 DOI: 10.1038/s41598-024-57982-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 03/24/2024] [Indexed: 04/13/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) was considered a major public health burden worldwide. Multiple studies have shown that susceptibility to severe infections and the development of long-term symptoms is significantly influenced by viral and host factors. These findings have highlighted the potential of host genetic markers to identify high-risk individuals and develop target interventions to reduce morbimortality. Despite its importance, genetic host factors remain largely understudied in Latin-American populations. Using a case-control design and a custom next-generation sequencing (NGS) panel encompassing 81 genetic variants and 74 genes previously associated with COVID-19 severity and long-COVID, we analyzed 56 individuals with asymptomatic or mild COVID-19 and 56 severe and critical cases. In agreement with previous studies, our results support the association between several clinical variables, including male sex, obesity and common symptoms like cough and dyspnea, and severe COVID-19. Remarkably, thirteen genetic variants showed an association with COVID-19 severity. Among these variants, rs11385942 (p < 0.01; OR = 10.88; 95% CI = 1.36-86.51) located in the LZTFL1 gene, and rs35775079 (p = 0.02; OR = 8.53; 95% CI = 1.05-69.45) located in CCR3 showed the strongest associations. Various respiratory and systemic symptoms, along with the rs8178521 variant (p < 0.01; OR = 2.51; 95% CI = 1.27-4.94) in the IL10RB gene, were significantly associated with the presence of long-COVID. The results of the predictive model comparison showed that the mixed model, which incorporates genetic and non-genetic variables, outperforms clinical and genetic models. To our knowledge, this is the first study in Colombia and Latin-America proposing a predictive model for COVID-19 severity and long-COVID based on genomic analysis. Our study highlights the usefulness of genomic approaches to studying host genetic risk factors in specific populations. The methodology used allowed us to validate several genetic variants previously associated with COVID-19 severity and long-COVID. Finally, the integrated model illustrates the importance of considering genetic factors in precision medicine of infectious diseases.
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Affiliation(s)
- Mariana Angulo-Aguado
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Juan Camilo Carrillo-Martinez
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Nora Constanza Contreras-Bravo
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Adrien Morel
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | | | - William Usaquén
- Populations Genetics and Identification Group, Institute of Genetics, Universidad Nacional de Colombia, Bogotá, D.C, Colombia
| | - Dora Janeth Fonseca-Mendoza
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia
| | - Oscar Ortega-Recalde
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, D.C, Colombia.
- Departamento de Morfología, Facultad de Medicina e Instituto de Genética, Universidad Nacional de Colombia, Bogotá, D.C, Colombia.
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Ren H, Lin Y, Huang L, Xu W, Luo D, Zhang C. Association of genetic polymorphisms with COVID-19 infection and outcomes: An updated meta-analysis based on 62 studies. Heliyon 2024; 10:e23662. [PMID: 38187247 PMCID: PMC10767390 DOI: 10.1016/j.heliyon.2023.e23662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 11/23/2023] [Accepted: 12/09/2023] [Indexed: 01/09/2024] Open
Abstract
Background The relationship between genetic polymorphisms and coronavirus disease 2019 (COVID-19) remains to be inconsistent. This meta-analysis aimed to provide an updated evaluation of the role of genetic polymorphisms in the infection, severity and mortality of COVID-19 based on all available published studies. Methods A systematic search was performed using six databases: PubMed, Embase, Web of Science, Cochrane Library, Chinese National Knowledge Infrastructure (CNKI) and Wanfang. Summary odds ratios (ORs) and corresponding 95 % confidence intervals (CIs) were used to calculate the genotypic comparison. All statistical analyses were conducted in Stata 12.0. Results A total of 62 studies with 19600 cases and 28899 controls was included in this meta-analysis. For COVID-19 infection, ACE Ins/Del polymorphism might be related with significantly decreased risk of COVID-19 infection under dominant, homozygote and allelic models. Meanwhile, the IFITM3 rs12252 and TMPRSS2 rs12329760 polymorphisms were significantly associated with the increased risk of COVID-19 infection under one or more models. Regarding COVID-19 severity, ACE2 rs2074192, ACE2 rs2106809, IFITM3 rs12252 and VDR rs1544410 polymorphisms might be related with significantly increased risk of COVID-19 severity in one or more models. Moreover, the analysis of TMPRSS2 rs2070788 indicated that a variant A allele decreased the risk of COVID-19 severity in recessive model. For COVID-19 mortality, the variant C allele of IFITM3 rs12252 polymorphism might be related with significantly increased risk of COVID-19 mortality under all genetic models. Conclusions This meta-analysis indicated that he infection, severity or mortality of COVID-19 were related to the above genetic polymorphisms, which might provide an important theoretical basis for understanding the clinical feature of COVID-19 disease.
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Affiliation(s)
- Hongyue Ren
- Department of Basic Medicine, Zhangzhou Health Vocational College, Zhangzhou 363000, Fujian Province, China
| | - Yanyan Lin
- Department of Basic Medicine, Zhangzhou Health Vocational College, Zhangzhou 363000, Fujian Province, China
| | - Lifeng Huang
- Department of Basic Medicine, Zhangzhou Health Vocational College, Zhangzhou 363000, Fujian Province, China
| | - Wenxin Xu
- Department of Medical Technology/Collaborative Innovation Center for Translation Medical Testing and Application Technology, Zhangzhou Health Vocational College, Zhangzhou 363000, Fujian Province, China
| | - Deqing Luo
- Department of Orthopaedic Surgery, Dongnan Hospital of Xiamen University, School of Medicine, Xiamen University, Zhangzhou 363000, Fujian Province, China
| | - Chunbin Zhang
- Department of Medical Technology/Collaborative Innovation Center for Translation Medical Testing and Application Technology, Zhangzhou Health Vocational College, Zhangzhou 363000, Fujian Province, China
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Gabdoulkhakova AG, Mingaleeva RN, Romozanova AM, Sagdeeva AR, Filina YV, Rizvanov AA, Miftakhova RR. Immunology of SARS-CoV-2 Infection. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:65-83. [PMID: 38467546 DOI: 10.1134/s0006297924010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 03/13/2024]
Abstract
According to the data from the World Health Organization, about 800 million of the world population had contracted coronavirus infection caused by SARS-CoV-2 by mid-2023. Properties of this virus have allowed it to circulate in the human population for a long time, evolving defense mechanisms against the host immune system. Severity of the disease depends largely on the degree of activation of the systemic immune response, including overstimulation of macrophages and monocytes, cytokine production, and triggering of adaptive T- and B-cell responses, while SARS-CoV-2 evades the immune system actions. In this review, we discuss immune responses triggered in response to the SARS-CoV-2 virus entry into the cell and malfunctions of the immune system that lead to the development of severe disease.
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Affiliation(s)
- Aida G Gabdoulkhakova
- Kazan Federal University, Kazan, 420008, Russia.
- Kazan State Medical Academy - Branch Campus of the Federal State Budgetary Educational Institution of Further Professional Education "Russian Medical Academy of Continuous Professional Education" of the Ministry of Health of the Russian Federation, Kazan, 420012, Russia
| | | | | | | | | | - Albert A Rizvanov
- Kazan Federal University, Kazan, 420008, Russia
- Division of Medical and Biological Sciences, Tatarstan Academy of Sciences, Kazan, 420111, Russia
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Benmansour R, Tagajdid MR, El Hamzaoui H, Fjouji S, Doghmi N, Houba A, Belbacha I, Elkochri S, Aabi R, Elannaz H, Laraqui A, El Mchichi B, Chmitah T, Touil N, Ennibi K, Eljaoudi R, Elmir E, Amine Lahlou I, Oumzil H. TYK2, IFITM3, IFNAR2 and OAS3 single-nucleotide polymorphisms among severe COVID-19 ICU patients in Morocco. Int J Immunopathol Pharmacol 2024; 38:3946320241257241. [PMID: 38760017 PMCID: PMC11102656 DOI: 10.1177/03946320241257241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/24/2024] [Indexed: 05/19/2024] Open
Abstract
OBJECTIVES This study aimed to explore the potential correlation between specific single nucleotide polymorphisms (TYK2, IFITM3, IFNAR2, and OAS3 variants) and the severity of COVID-19 in Moroccan patients. METHODS A genetic analysis was conducted on 109 patients with PCR-confirmed SARS-CoV-2 infection in Morocco. Among these patients, 46% were hospitalized in the intensive care unit, while 59% were not hospitalized. Importantly, all patients lacked known risk factors associated with COVID-19 severity. Genotyping was performed to identify variations in TYK2 rs74956615, IFITM3 rs12252, IFNAR2 rs2236757, and OAS3 rs10735079. Statistical analysis was applied using codominant, dominant and recessive logistic regression models to assess correlations with COVID-19 severity. RESULTS Our findings revealed no significant correlation between TYK2 rs74956615, IFITM3 rs12252, IFNAR2 rs2236757, and OAS3 rs10735079 with COVID-19 severity in Moroccan patients, as indicated in logistic regression models (p > .05). Interestingly, these results may offer insights into the mitigated impact of the COVID-19 pandemic and the reduced severity observed in SARS-CoV-2 infected patients in Morocco. Age, however, exhibited a significant correlation with severity (p < .001), with a trend towards increased likelihood of ICU admission with advancing age. Additionally, In the severe group, a higher proportion of patients were females (54%), indicating a statistically significant correlation with disease severity (p = .04). Nevertheless, female ICU patients aged above 60 years accounted for 37%, compared to 17% for males. CONCLUSION This study underscores the absence of a genetic association between the selected polymorphisms and COVID-19 severity in Moroccan patients. Advanced age emerges as the primary factor influencing the severity of COVID-19 patients without comorbidities. We recommend setting the threshold for advanced age at 60 years as a risk factor for severe forms of COVID-19.
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Affiliation(s)
- R. Benmansour
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - M. R. Tagajdid
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - H. El Hamzaoui
- Emergency Department, University Hospital Ibn Sina, Rabat, And School of Medicine and Pharmacy, University Mohamed V in Rabat, Rabat, Morocco
| | - S. Fjouji
- Department of Anesthesia, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - N. Doghmi
- Department of Anesthesia, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - A. Houba
- Department of Anesthesia, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - I. Belbacha
- Virology Department, Institut National D’Hygiène, Rabat, Morocco
| | - S. Elkochri
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - R. Aabi
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - H. Elannaz
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - A. Laraqui
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - B. El Mchichi
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - T. Chmitah
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - N. Touil
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - K. Ennibi
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - R. Eljaoudi
- Medical Biotechnology Laboratory, School of Medicine and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
| | - E. Elmir
- Virology Department, Institut National D’Hygiène, Rabat, Morocco
| | - I. Amine Lahlou
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - H. Oumzil
- Medical Biotechnology Laboratory, School of Medicine and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
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López-Bielma MF, Falfán-Valencia R, Abarca-Rojano E, Pérez-Rubio G. Participation of Single-Nucleotide Variants in IFNAR1 and IFNAR2 in the Immune Response against SARS-CoV-2 Infection: A Systematic Review. Pathogens 2023; 12:1320. [PMID: 38003785 PMCID: PMC10675296 DOI: 10.3390/pathogens12111320] [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: 09/21/2023] [Revised: 10/22/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Host genetic factors significantly influence susceptibility to SARS-CoV-2 infection and COVID-19 severity. Among these genetic factors are single-nucleotide variants (SNVs). IFNAR2 and IFNAR1 genes have been associated with severe COVID-19 in populations from the United Kingdom, Africa, and Latin America. IFNAR1 and IFNAR2 are subunits forming the type I interferon receptor (IFNAR). SNVs in the IFNAR genes impact protein function, affecting antiviral response and disease phenotypes. This systematic review aimed to describe IFNAR1 and IFNAR2 variants associated with COVID-19 susceptibility and severity. Accordingly, the current review focused on IFNAR1 and IFNAR2 studies published between January 2021 and February 2023, utilizing the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) protocol. The electronic search was conducted in PubMed databases using Boolean operators and inclusion and exclusion criteria. Of the 170 literature pieces, 11 studies were included. We include case reports of rare SNVs, defined by minor allele frequency (MAF) < 1%, and genome-wide associated studies (GWAS). Variants in IFNAR1 and IFNAR2 could potentially be new targets for therapies that limit the infection and the resulting inflammation by SARS-CoV-2 infection.
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Affiliation(s)
- María Fernanda López-Bielma
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico (R.F.-V.)
- Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico (R.F.-V.)
| | - Edgar Abarca-Rojano
- Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Gloria Pérez-Rubio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico (R.F.-V.)
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8
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Martínez-Pomar N, Cunill V, Segura-Guerrero M, Pol-Pol E, Escobar Oblitas D, Pons J, Ayestarán I, Pruneda PC, Losada I, Toledo-Pons N, García Gasalla M, Ferrer Balaguer JM. Hyperinflammatory Immune Response in COVID-19: Host Genetic Factors in Pyrin Inflammasome and Immunity to Virus in a Spanish Population from Majorca Island. Biomedicines 2023; 11:2548. [PMID: 37760989 PMCID: PMC10525993 DOI: 10.3390/biomedicines11092548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The hyperinflammatory response caused by SARS-CoV-2 infection contributes to its severity, and many critically ill patients show features of cytokine storm (CS) syndrome. We investigated, by next-generation sequencing, 24 causative genes of primary immunodeficiencies whose defect predisposes to CS. We studied two cohorts with extreme phenotypes of SARS-CoV-2 infection: critical/severe hyperinflammatory patients (H-P) and asymptomatic patients (AM-risk-P) with a high risk (older age) to severe COVID-19. To explore inborn errors of the immunity, we investigated the presence of pathogenic or rare variants, and to identify COVID-19 severity-associated markers, we compared the allele frequencies of common genetic polymorphisms between our two cohorts. We found: 1 H-P carries the likely pathogenic variant c.887-2 A>C in the IRF7 gene and 5 H-P carries variants in the MEFV gene, whose role in the pathogenicity of the familial Mediterranean fever (FMF) disease is controversial. The common polymorphism analysis showed three potential risk biomarkers for developing the hyperinflammatory response: the homozygous haplotype rs1231123A/A-rs1231122A/A in MEFV gene, the IFNAR2 p.Phe8Ser variant, and the CARMIL2 p.Val181Met variant. The combined analysis showed an increased risk of developing severe COVID-19 in patients that had at least one of our genetic risk markers (odds ratio (OR) = 6.2 (95% CI) (2.430-16.20)).
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Affiliation(s)
- Natalia Martínez-Pomar
- Immunology Department, Hospital Universitari Son Espases, 07120 Palma de Mallorca, Spain; (V.C.); (M.S.-G.); (J.M.F.B.)
- Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma de Mallorca, Spain (I.L.); (N.T.-P.)
| | - Vanesa Cunill
- Immunology Department, Hospital Universitari Son Espases, 07120 Palma de Mallorca, Spain; (V.C.); (M.S.-G.); (J.M.F.B.)
- Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma de Mallorca, Spain (I.L.); (N.T.-P.)
| | - Marina Segura-Guerrero
- Immunology Department, Hospital Universitari Son Espases, 07120 Palma de Mallorca, Spain; (V.C.); (M.S.-G.); (J.M.F.B.)
- Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma de Mallorca, Spain (I.L.); (N.T.-P.)
| | - Elisabet Pol-Pol
- Immunology Department, Hospital Universitari Son Espases, 07120 Palma de Mallorca, Spain; (V.C.); (M.S.-G.); (J.M.F.B.)
- Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma de Mallorca, Spain (I.L.); (N.T.-P.)
| | - Danilo Escobar Oblitas
- Immunology Department, Hospital Universitari Son Espases, 07120 Palma de Mallorca, Spain; (V.C.); (M.S.-G.); (J.M.F.B.)
- Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma de Mallorca, Spain (I.L.); (N.T.-P.)
| | - Jaime Pons
- Immunology Department, Hospital Universitari Son Espases, 07120 Palma de Mallorca, Spain; (V.C.); (M.S.-G.); (J.M.F.B.)
- Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma de Mallorca, Spain (I.L.); (N.T.-P.)
| | - Ignacio Ayestarán
- Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma de Mallorca, Spain (I.L.); (N.T.-P.)
- Intensive Care Unit (ICU), Hospital Universitari Son Espases, 07120 Palma de Mallorca, Spain
| | | | - Inés Losada
- Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma de Mallorca, Spain (I.L.); (N.T.-P.)
- Internal Medicine, Hospital Universitari Son Llàtzer, 07198 Palma de Mallorca, Spain
| | - Nuria Toledo-Pons
- Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma de Mallorca, Spain (I.L.); (N.T.-P.)
- Pneumology Department, Hospital Universitari Son Espases, 07120 Palma de Mallorca, Spain
| | - Mercedes García Gasalla
- Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma de Mallorca, Spain (I.L.); (N.T.-P.)
- Internal Medicine, Hospital Universitari Son Espases, 07120 Palma de Mallorca, Spain
| | - Joana Maria Ferrer Balaguer
- Immunology Department, Hospital Universitari Son Espases, 07120 Palma de Mallorca, Spain; (V.C.); (M.S.-G.); (J.M.F.B.)
- Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma de Mallorca, Spain (I.L.); (N.T.-P.)
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9
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Adimulam T, Arumugam T, Naidoo A, Naidoo K, Ramsuran V. Polymorphisms within the SARS-CoV-2 Human Receptor Genes Associate with Variable Disease Outcomes across Ethnicities. Genes (Basel) 2023; 14:1798. [PMID: 37761938 PMCID: PMC10531089 DOI: 10.3390/genes14091798] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
The contribution of human genes to the variability of disease outcomes has been shown to be important across infectious diseases. Studies have shown mutations within specific human genes are associated with variable COVID-19 outcomes. We focused on the SARS-CoV-2 receptors/co-receptors to identify the role of specific polymorphisms within ACE2, TMPRSS2, NRP1 and CD147. Polymorphisms within ACE2 (rs2285666), TMPRSS2 (rs12329760), CD147 (rs8259) and NRP1 (rs10080) have been shown to associate with COVID-19 severity. Using cryopreserved samples from COVID-19-positive African, European and South Asian individuals within South Africa, we determined genotype frequencies. The genetic variant rs2285666 was associated with COVID-19 severity with an ethnic bias. African individuals with a CC genotype demonstrate more severe COVID-19 outcomes (OR = 7.5; 95% CI 1.164-80.89; p = 0.024) compared with those with a TT genotype. The expressions of ACE2 and SARS-CoV-2 viral load were measured using droplet digital PCR. Our results demonstrate rs2285666 and rs10080 were significantly associated with increased SARS-CoV-2 viral load and worse outcomes in certain ethnicities. This study demonstrates two important findings. Firstly, SARS-CoV-2 viral load is significantly lower in Africans compared with individuals of European and South Asian descent (p = 0.0002 and p < 0.0001). Secondly, SARS-CoV-2 viral load associates with specific SARS-CoV-2 receptor variants. A limited number of studies have examined the receptor/co-receptor genes within Africa. This study investigated genetic variants within the SARS-CoV-2 receptor/co-receptor genes and their association with COVID-19 severity and SARS-CoV-2 viral load across different ethnicities. We provide a genetic basis for differences in COVID-19 severity across ethnic groups in South Africa, further highlighting the importance of further investigation to determine potential therapeutic targets and to guide vaccination strategies that may prioritize specific genotypes.
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Affiliation(s)
- Theolan Adimulam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa; (T.A.); (T.A.)
| | - Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa; (T.A.); (T.A.)
| | - Anushka Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4041, South Africa; (A.N.); (K.N.)
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4041, South Africa; (A.N.); (K.N.)
- South African Medical Research Council (SAMRC), Durban 4013, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa; (T.A.); (T.A.)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4041, South Africa; (A.N.); (K.N.)
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10
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Khadzhieva MB, Gracheva AS, Belopolskaya OB, Kolobkov DS, Kashatnikova DA, Redkin IV, Kuzovlev AN, Grechko AV, Salnikova LE. COVID-19 severity: does the genetic landscape of rare variants matter? Front Genet 2023; 14:1152768. [PMID: 37456666 PMCID: PMC10339319 DOI: 10.3389/fgene.2023.1152768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023] Open
Abstract
Rare variants affecting host defense against pathogens may be involved in COVID-19 severity, but most rare variants are not expected to have a major impact on the course of COVID-19. We hypothesized that the accumulation of weak effects of many rare functional variants throughout the exome may contribute to the overall risk in patients with severe disease. This assumption is consistent with the omnigenic model of the relationship between genetic and phenotypic variation in complex traits, according to which association signals tend to spread across most of the genome through gene regulatory networks from genes outside the major pathways to disease-related genes. We performed whole-exome sequencing and compared the burden of rare variants in 57 patients with severe and 29 patients with mild/moderate COVID-19. At the whole-exome level, we observed an excess of rare, predominantly high-impact (HI) variants in the group with severe COVID-19. Restriction to genes intolerant to HI or damaging missense variants increased enrichment for these classes of variants. Among various sets of genes, an increased signal of rare HI variants was demonstrated predominantly for primary immunodeficiency genes and the entire set of genes associated with immune diseases, as well as for genes associated with respiratory diseases. We advocate taking the ideas of the omnigenic model into account in COVID-19 studies.
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Affiliation(s)
- Maryam B. Khadzhieva
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- The Laboratory of Molecular Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Alesya S. Gracheva
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
- The Department of Population Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Olesya B. Belopolskaya
- The Resource Center “Bio-bank Center”, Research Park of St. Petersburg State University, St. Petersburg, Russia
- The Laboratory of Genogeography, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry S. Kolobkov
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Darya A. Kashatnikova
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ivan V. Redkin
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Artem N. Kuzovlev
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Andrey V. Grechko
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Lyubov E. Salnikova
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- The Laboratory of Molecular Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
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Fakhkhari M, Caidi H, Sadki K. HLA alleles associated with COVID-19 susceptibility and severity in different populations: a systematic review. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2023; 24:10. [PMID: 36710951 PMCID: PMC9867832 DOI: 10.1186/s43042-023-00390-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/15/2023] [Indexed: 01/23/2023] Open
Abstract
Background COVID-19 is a respiratory disease caused by a novel coronavirus called as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Detected for the first time in December 2019 in Wuhan and it has quickly spread all over the world in a couple of months and becoming a world pandemic. Symptoms of the disease and clinical outcomes are very different in infected people. These differences highlight the paramount need to study and understand the human genetic variation that occurring viral infections. Human leukocyte antigen (HLA) is an important component of the viral antigen presentation pathway, and it plays an essential role in conferring differential viral susceptibility and severity of diseases. HLA alleles have been involved in the immune response to viral diseases such as SARS-CoV-2. Main body of the abstract Herein, we sought to evaluate this hypothesis by summarizing the association between HLA class I and class II alleles with COVID-19 susceptibility and/or severity reported in previous studies among different populations (Chinese, Italian, Iranian, Japanese, Spanish, etc.). The findings of all selected articles showed that several alleles have been found associated with COVID-19 susceptibility and severity. Even results across articles have been inconsistent and, in some cases, conflicting, highlighting that the association between the HLA system and the COVID-19 outcome might be ethnic-dependent, there were some alleles in common between some populations such as HLA-DRB1*15 and HLA-A*30:02. Conclusion These contradictory findings warrant further large, and reproducible studies to decipher any possible genetic predisposition underlying susceptibility to SARS-COV-2 and disease progression and host immune response.
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Affiliation(s)
- Meryem Fakhkhari
- Research Laboratory in Oral Biology and Biotechnology, Faculty of Dental Medicine, Mohammed V University in Rabat, Rabat, Morocco
| | - Hayat Caidi
- NARST Surveillance Unit, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Khalid Sadki
- Research Laboratory in Oral Biology and Biotechnology, Faculty of Dental Medicine, Mohammed V University in Rabat, Rabat, Morocco
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12
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Host Genetic Variants Linked to COVID-19 Neurological Complications and Susceptibility in Young Adults-A Preliminary Analysis. J Pers Med 2023; 13:jpm13010123. [PMID: 36675784 PMCID: PMC9860613 DOI: 10.3390/jpm13010123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
To date, multiple efforts have been made to use genome-wide association studies (GWAS) to untangle the genetic basis for SARS-CoV-2 infection susceptibility and severe COVID-19. However, data on the genetic-related effects of SARS-CoV-2 infection on the presence of accompanying and long-term post-COVID-19 neurological symptoms in younger individuals remain absent. We aimed to examine the possible association between SNPs found in a GWAS of COVID-19 outcomes and three phenotypes: SARS-CoV-2 infection, neurological complications during disease progression, and long-term neurological complications in young adults with a mild-to-moderate disease course. University students (N = 336, age 18-25 years, European ancestry) with or without COVID-19 and neurological symptoms in anamnesis comprised the study sample. Logistic regression was performed with COVID-19-related phenotypes as outcomes, and the top 25 SNPs from GWAS meta-analyses and an MR study linking COVID-19 and cognitive deficits were found. We replicated previously reported associations of the FURIN and SLC6A20 gene variants (OR = 2.36, 95% CI 1.31-4.24) and OR = 1.94, 95% CI 1.08-3.49, respectively) and remaining neurological complications (OR = 2.12, 95% CI 1.10-4.35 for SLC6A20), while NR1H2 (OR = 2.99, 95% CI 1.39-6.69) and TMPRSS2 (OR = 2.03, 95% CI 1.19-3.50) SNPs were associated with neurological symptoms accompanying COVID-19. Our findings indicate that genetic variants related to a severe COVID-19 course in adults may contribute to the occurrence of neurological repercussions in individuals at a young age.
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