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Cao C, Mehmood A, Li D. Molecular dynamic simulation reveals spider antimicrobial peptide Latarcin-1 and human eosinophil cationic protein as peptide inhibitors of SARS-CoV-2 variants. J Biomol Struct Dyn 2024; 42:5858-5868. [PMID: 37938133 DOI: 10.1080/07391102.2023.2274514] [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: 12/06/2022] [Accepted: 06/17/2023] [Indexed: 11/09/2023]
Abstract
COVID-19 has rapidly proliferated around 180 countries, and new cases are reported frequently. No peptide medication has been developed that can reliably block SARS-CoV-2 infection. The investigation focuses on the crucial host receptors angiotensin-converting enzyme 2 (ACE2) , which can bind receptor-binding domain (RBD) on the SARS-CoV-2 spike protein (S). To investigate the inhibitory effects of human Eosinophil Cationic Protein (hECP) and Latarcin-1 (L1)on SARS-CoV-2 infection, we have selected them as research subjects. Further, we ran extensive molecular dynamics simulations to bring the docked peptide-ACE2 complex into its equilibrium state. The outcomes were then evaluated with g_MMPBSA and interaction analysis. We have also considered the Delta and Omicron variants to examine these peptides' inhibitory effects. The experimental findings revealed an enhanced capability of L1 and hECP as SARS-CoV-2 inhibitors, occupying hot spots and numerous key residues in ACE2. These include ASP30, ASP38, GLU35 and GLU75, which significantly inhibit the binding of RBD and ACE2 and are effective against two common variants in a similar manner. In addition, this study can serve as a springboard for future research on SARS-CoV-2 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Cheng Cao
- Institute of Biothermal Science and Technology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, P.R. China
- AI Research Center, Peng Cheng Laboratory, Shenzhen, Guangdong, P.R. China
| | - Aamir Mehmood
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Daixi Li
- Institute of Biothermal Science and Technology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, P.R. China
- AI Research Center, Peng Cheng Laboratory, Shenzhen, Guangdong, P.R. China
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2
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Kim GJ, Elnaggar JH, Varnado M, Feehan AK, Tauzier D, Rose R, Lamers SL, Sevalia M, Nicholas N, Gravois E, Fort D, Crabtree JS, Miele L. A bioinformatic analysis of T-cell epitope diversity in SARS-CoV-2 variants: association with COVID-19 clinical severity in the United States population. Front Immunol 2024; 15:1357731. [PMID: 38784379 PMCID: PMC11112498 DOI: 10.3389/fimmu.2024.1357731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/05/2024] [Indexed: 05/25/2024] Open
Abstract
Long-term immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires the identification of T-cell epitopes affecting host immunogenicity. In this computational study, we explored the CD8+ epitope diversity estimated in 27 of the most common HLA-A and HLA-B alleles, representing most of the United States population. Analysis of 16 SARS-CoV-2 variants [B.1, Alpha (B.1.1.7), five Delta (AY.100, AY.25, AY.3, AY.3.1, AY.44), and nine Omicron (BA.1, BA.1.1, BA.2, BA.4, BA.5, BQ.1, BQ.1.1, XBB.1, XBB.1.5)] in analyzed MHC class I alleles revealed that SARS-CoV-2 CD8+ epitope conservation was estimated at 87.6%-96.5% in spike (S), 92.5%-99.6% in membrane (M), and 94.6%-99% in nucleocapsid (N). As the virus mutated, an increasing proportion of S epitopes experienced reduced predicted binding affinity: 70% of Omicron BQ.1-XBB.1.5 S epitopes experienced decreased predicted binding, as compared with ~3% and ~15% in the earlier strains Delta AY.100-AY.44 and Omicron BA.1-BA.5, respectively. Additionally, we identified several novel candidate HLA alleles that may be more susceptible to severe disease, notably HLA-A*32:01, HLA-A*26:01, and HLA-B*53:01, and relatively protected from disease, such as HLA-A*31:01, HLA-B*40:01, HLA-B*44:03, and HLA-B*57:01. Our findings support the hypothesis that viral genetic variation affecting CD8 T-cell epitope immunogenicity contributes to determining the clinical severity of acute COVID-19. Achieving long-term COVID-19 immunity will require an understanding of the relationship between T cells, SARS-CoV-2 variants, and host MHC class I genetics. This project is one of the first to explore the SARS-CoV-2 CD8+ epitope diversity that putatively impacts much of the United States population.
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Affiliation(s)
- Grace J. Kim
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Jacob H. Elnaggar
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
- Department of Microbiology, Immunology, and Parasitology, Lousiana State University Health Sciences Center (LSUHSC), New Orleans, LA, United States
| | - Mallory Varnado
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Amy K. Feehan
- Research and Development, Oschner Medical Center, New Orleans, LA, United States
| | - Darlene Tauzier
- Department of Pathology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Rebecca Rose
- Research and Development, BioInfoExperts, LLC, Thibodaux, LA, United States
| | - Susanna L. Lamers
- Research and Development, BioInfoExperts, LLC, Thibodaux, LA, United States
| | - Maya Sevalia
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Najah Nicholas
- School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Elizabeth Gravois
- Department of Pathology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Daniel Fort
- Research and Development, Oschner Medical Center, New Orleans, LA, United States
| | - Judy S. Crabtree
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Lucio Miele
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
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Hai NTT, Nhung VP, Tam NTT, Ngoc TTB, Thuong MTH, Dai HV, Duong NT, Hai NV, Ton ND, Thach PN, Ha NH. HLA alleles associated with susceptibility and severity of the COVID-19 in Vietnamese. Hum Immunol 2024; 85:110796. [PMID: 38580537 DOI: 10.1016/j.humimm.2024.110796] [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: 06/15/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/07/2024]
Abstract
The diversity of clinical manifestations in COVID-19 has been observed not only among individuals but also among various populations in globally. HLA molecules play a central role in physiology, protective immunity, and deleterious, disease-related autoimmune reactivity or overreaction. This study exploited the association between HLA frequencies and SARS-CoV-2 susceptibility and disease severity among the Vietnamese cohort (159 patients and 52 controls). A significant difference in frequency of both HLA class I and II in mild, moderate, and severe/fatal COVID-19 patients and negative exposure individuals - the controls were observed. Regarding SARS-CoV-2 sensitivity, HLA-A*03:01, 30:01, HLA-DQA1*01:02, DRB1*15:01, and DRB5*02:02 presented higher frequency in the control group compared with infected patients but DRB1 09:01 frequency was higher in infected patients. Regarding COVID-19 severity, HLA-F*01:01, 01:03 and DPA1*01:03 and 02:01, DPB1*04:01, DQA1*01:02, and DQB1*05:02 alleles were detected with higher frequency in severe patients but DOB*01:01, DRB1*05:01 and 09:01 had a significantly higher frequency in the mild group than remaining groups. Surprisingly, HLA-DQA1*01:02 and DRB1*09:01 alleles were identified with both inversely potential roles in protective function and severe risk. The obtained data herein will contribute to explore on the role of host genetic background in the pathology of COVID-19 disease.
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Affiliation(s)
- Nguyen Thi Thanh Hai
- National Hospital for Tropical Diseases, Kim Chung, Dong Anh, Hanoi 10000, Viet Nam; Department of Biochemistry, Hanoi Medical University, 1 Ton That Tung, Dong Da, Hanoi 10000, Viet Nam
| | - Vu Phuong Nhung
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10000, Viet Nam
| | - Nguyen Thi Thanh Tam
- Department of Biochemistry, Hanoi Medical University, 1 Ton That Tung, Dong Da, Hanoi 10000, Viet Nam
| | - Tran Thi Bich Ngoc
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10000, Viet Nam
| | - Ma Thi Huyen Thuong
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10000, Viet Nam
| | - Ha Van Dai
- National Hospital for Tropical Diseases, Kim Chung, Dong Anh, Hanoi 10000, Viet Nam
| | - Nguyen Thuy Duong
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10000, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Viet Nam
| | - Nong Van Hai
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10000, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Viet Nam
| | - Nguyen Dang Ton
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10000, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Viet Nam
| | - Pham Ngoc Thach
- National Hospital for Tropical Diseases, Kim Chung, Dong Anh, Hanoi 10000, Viet Nam
| | - Nguyen Hai Ha
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 10000, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Viet Nam.
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López-Bielma MF, Falfán-Valencia R, Fierro-Piña A, Abarca-Rojano E, Córdoba-Lanus E, Fricke-Galindo I, Romero-Villaseñor P, Buendía-Roldán I, Chávez-Galán L, Jaime-Capetillo ME, Pérez-Rubio G. Genetic variants in ATP2B2 as risk factors for mortality in patients unrelated but not associated with families with severe COVID-19. Heliyon 2024; 10:e29493. [PMID: 38628728 PMCID: PMC11019202 DOI: 10.1016/j.heliyon.2024.e29493] [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: 01/08/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
Introduction The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus Disease 2019 (COVID-19). The disease has a wide range of clinical manifestations, from asymptomatic to severe. Ancestral contribution, sex, immune response, and genetic factors influence the presentation of the disease. The objective of the present study was to validate these genetic variants in patients with severe COVID-19 who died and in survivor patients. Methods: Single nucleotide variants (SNVs) in six genes: ATPase plasma membrane Ca2+ transporting 2 (ATP2B2), transmembrane serine protease 2 (TMPRSS2), dedicator of cytokinesis 2 (DOCK2), (interferon alpha and beta receptor subunit 2) IFNAR2, tumor necrosis factor receptor superfamily, member 1A (TNFRSF1A), and tumor necrosis factor receptor superfamily, member 1B (TNFRSF1B), were explored in two groups: the first consisted of severe COVID-19-related patients (familial cases from 58 families, n = 130), and the second group of unrelated severe COVID-19 patients (n = 1045). In each study group, death was evaluated as the outcome. Results In non-related patients with severe COVID-19, carriers of GG genotype (rs2289274) in the ATP2B2 gene showed a high-risk probability of non-surviving (OR = 1.43). Survival analysis to 75 days indicates that carriers of GG have a higher risk than GA or AA genotypes (p = 0.0059). The haplotype GG (rs2289273-rs2289274) in ATP2B2 was found to be associated with a high risk of death in severe non-related COVID-19 patients. No significant associations were found between severe COVID-19-related patients and SNVs in ATP2B2, TMPRSS2, DOCK2, IFNAR2, TNFRSF1A, or TNFRSF1B. Conclusions Unrelated patients with severe COVID-19 that carry the GG genotype (rs2289274) in ATP2B2 showed a high death risk. Survival analysis to 75 days indicates that carriers of GG have a higher risk of non-survival compared to GA or AA genotypes.
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Affiliation(s)
- María Fernanda López-Bielma
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
- Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - Aurelio Fierro-Piña
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - Edgar Abarca-Rojano
- Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico
| | - Elizabeth Córdoba-Lanus
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, 38296, San Cristóbal de La Laguna, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Ingrid Fricke-Galindo
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - Priscila Romero-Villaseñor
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - Ivette Buendía-Roldán
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - Leslie Chávez-Galán
- Laboratory of Integrative Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - María Esther Jaime-Capetillo
- Clinical Laboratory Service, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, 14080, Mexico
| | - Gloria Pérez-Rubio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
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5
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Naidoo L, Arumugam T, Ramsuran V. Narrative Review Explaining the Role of HLA-A, -B, and -C Molecules in COVID-19 Disease in and around Africa. Infect Dis Rep 2024; 16:380-406. [PMID: 38667755 PMCID: PMC11049896 DOI: 10.3390/idr16020029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) has left a devasting effect on various regions globally. Africa has exceptionally high rates of other infectious diseases, such as tuberculosis (TB), human immunodeficiency virus (HIV), and malaria, and was not impacted by COVID-19 to the extent of other continents Globally, COVID-19 has caused approximately 7 million deaths and 700 million infections thus far. COVID-19 disease severity and susceptibility vary among individuals and populations, which could be attributed to various factors, including the viral strain, host genetics, environment, lifespan, and co-existing conditions. Host genetics play a substantial part in COVID-19 disease severity among individuals. Human leukocyte antigen (HLA) was previously been shown to be very important across host immune responses against viruses. HLA has been a widely studied gene region for various disease associations that have been identified. HLA proteins present peptides to the cytotoxic lymphocytes, which causes an immune response to kill infected cells. The HLA molecule serves as the central region for infectious disease association; therefore, we expect HLA disease association with COVID-19. Therefore, in this narrative review, we look at the HLA gene region, particularly, HLA class I, to understand its role in COVID-19 disease.
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Affiliation(s)
- Lisa Naidoo
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa; (L.N.); (T.A.)
| | - Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa; (L.N.); (T.A.)
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa; (L.N.); (T.A.)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban 4041, South Africa
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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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Torki E, Hoseininasab F, Moradi M, Sami R, Sullman MJM, Fouladseresht H. The demographic, laboratory and genetic factors associated with long Covid-19 syndrome: a case-control study. Clin Exp Med 2024; 24:1. [PMID: 38231284 PMCID: PMC10794331 DOI: 10.1007/s10238-023-01256-1] [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: 10/19/2023] [Accepted: 12/15/2023] [Indexed: 01/18/2024]
Abstract
Long Covid-19 syndrome (LCS) manifests with a wide range of clinical symptoms, yet the factors associated with LCS remain poorly understood. The current study aimed to investigate the relationships that demographic characteristics, clinical history, laboratory indicators, and the frequency of HLA-I alleles have with the likelihood of developing LCS. We extracted the demographic characteristics and clinical histories from the medical records of 88 LCS cases (LCS+ group) and 96 individuals without LCS (LCS- group). Furthermore, we evaluated the clinical symptoms, serum levels of interleukin (IL)-6 and tumor necrosis factor-α, laboratory parameters, and the frequencies of HLA-I alleles. Following this we used multiple logistic regression to investigate the association these variables had with LCS. Subjects in the LCS+ group were more likely to have experienced severe Covid-19 symptoms and had higher body mass index (BMI), white blood cell, lymphocyte counts, C-reactive protein (CRP), and IL-6 levels than those in the LCS- group (for all: P < 0.05). Moreover, the frequencies of the HLA-A*11, -B*14, -B*38, -B*50, and -C*07 alleles were higher in the LCS+ group (for all: P < 0.05). After adjusting for the most important variables, the likelihood of suffering from LCS was significantly associated with BMI, CRP, IL-6, the HLA-A*11, and -C*07 alleles, as well as a positive history of severe Covid-19 (for all: P < 0.05). Our study showed that a history of severe Covid-19 during the acute phase of the disease, the HLA-A*11, and -C*07 alleles, higher BMI, as well as elevated serum CRP and IL-6 levels, were all associated with an increased likelihood of LCS.
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Affiliation(s)
- Ensiye Torki
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fahimeh Hoseininasab
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Marjan Moradi
- Department of Genetics, School of Science, Shahrekord University, Shahrekord, Iran
| | - Ramin Sami
- Department of Internal Medicine, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mark J M Sullman
- Department of Life and Health Sciences, University of Nicosia, Nicosia, Cyprus
- Department of Social Sciences, University of Nicosia, Nicosia, Cyprus
| | - Hamed Fouladseresht
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
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8
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Bandinelli F, Martinelli-Consumi B, Manetti M, Vallecoccia MS. Sex Bias in Diagnostic Delay: Are Axial Spondyloarthritis and Ankylosing Spondylitis Still Phantom Diseases in Women? A Systematic Review and Meta-Analysis. J Pers Med 2024; 14:91. [PMID: 38248792 PMCID: PMC10817445 DOI: 10.3390/jpm14010091] [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: 12/24/2023] [Revised: 01/01/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
Diagnostic delay (DD) is associated with poor radiological and quality of life outcomes in axial spondyloarthritis (ax-SpA) and ankylosing spondylitis (AS). The female (F) population is often misdiagnosed, as classification criteria were previously studied mostly in males (M). We conducted a systematic review to investigate (i) the difference in DD between the sexes, the impact of HLA*B27 and clinical and social factors (work and education) on this gap, and (ii) the possible influence of the year of publication (before and after the 2009 ASAS classification criteria), geographical region (Europe and Israel vs. extra-European countries), sample sources (mono-center vs. multi-center studies), and world bank (WB) economic class on DD in both sexes. We searched, in PubMed and Embase, studies that reported the mean or median DD or the statistical difference in DD between sexes, adding a manual search. Starting from 399 publications, we selected 26 studies (17 from PubMed and Embase, 9 from manual search) that were successively evaluated with the modified Newcastle-Ottawa Scale (m-NOS). The mean DD of 16 high-quality (m-NOS > 4/8) studies, pooled with random-effects meta-analysis, produces results higher in F (1.48, 95% CI 0.83-2.14, p < 0.0001) but with significant results at the second analysis only in articles published before the 2009 ASAS classification criteria (0.95, 95% CI 0.05-1.85, p < 0.0001) and in extra-European countries (3.16, 95% CI 2.11-4.22, p < 0.05). With limited evidence, some studies suggest that DD in F might be positively influenced by HLA*B27 positivity, peripheral involvement, and social factors.
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Affiliation(s)
- Francesca Bandinelli
- Rheumatology Department, Usl Tuscany Center, San Giovanni di Dio Hospital, 50143 Florence, Italy;
| | | | - Mirko Manetti
- Section of Anatomy and Histology, Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy;
| | - Maria Sole Vallecoccia
- Department of Emergency and Critical Care, Santa Maria Nuova Hospital, 50122 Florence, Italy;
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9
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Maiti AK. Therapeutic Challenges in COVID-19. Curr Mol Med 2024; 24:14-25. [PMID: 36567277 DOI: 10.2174/1566524023666221222162641] [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: 09/02/2022] [Revised: 10/18/2022] [Accepted: 11/10/2022] [Indexed: 12/27/2022]
Abstract
SARS-CoV2 is a novel respiratory coronavirus and, understanding its molecular mechanism is a prerequisite to developing effective treatment for COVID-19. This RNA genome-carrying virus has a protein coat with spikes (S) that attaches to the ACE2 receptor at the cell surface of human cells. Several repurposed drugs are used to treat COVID-19 patients that are proven to be largely unsuccessful or have limited success in reducing mortalities. Several vaccines are in use to reduce the viral load to prevent developing symptoms. Major challenges to their efficacy include the inability of antibody molecules to enter cells but remain effective in the bloodstream to kill the virus. The efficacy of vaccines also depends on their neutralizing ability to constantly evolve new virus strains due to novel mutations and evolutionary survival dynamics. Taken together, SARS-CoV2 antibody vaccines may not be very effective and other approaches based on genetic, genomic, and protein interactome could be fruitful to identify therapeutic targets to reduce disease-related mortalities.
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Affiliation(s)
- Amit K Maiti
- Department of Genetics and Genomics, Mydnavar, 28475 Greenfield Rd, Southfield MI 48076, USA
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10
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Kusumoto T, Chubachi S, Namkoong H, Tanaka H, Lee H, Otake S, Nakagawara K, Fukushima T, Morita A, Watase M, Asakura T, Masaki K, Kamata H, Ishii M, Hasegawa N, Harada N, Ueda T, Ueda S, Ishiguro T, Arimura K, Saito F, Yoshiyama T, Nakano Y, Mutoh Y, Suzuki Y, Edahiro R, Murakami K, Sato Y, Okada Y, Koike R, Kitagawa Y, Tokunaga K, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K. Characteristics of patients with COVID-19 who have deteriorating chest X-ray findings within 48 h: a retrospective cohort study. Sci Rep 2023; 13:22054. [PMID: 38086863 PMCID: PMC10716517 DOI: 10.1038/s41598-023-49340-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023] Open
Abstract
The severity of chest X-ray (CXR) findings is a prognostic factor in patients with coronavirus disease 2019 (COVID-19). We investigated the clinical and genetic characteristics and prognosis of patients with worsening CXR findings during early hospitalization. We retrospectively included 1656 consecutive Japanese patients with COVID-19 recruited through the Japan COVID-19 Task Force. Rapid deterioration of CXR findings was defined as increased pulmonary infiltrates in ≥ 50% of the lung fields within 48 h of admission. Rapid deterioration of CXR findings was an independent risk factor for death, most severe illness, tracheal intubation, and intensive care unit admission. The presence of consolidation on CXR, comorbid cardiovascular and chronic obstructive pulmonary diseases, high body temperature, and increased serum aspartate aminotransferase, potassium, and C-reactive protein levels were independent risk factors for rapid deterioration of CXR findings. Risk variant at the ABO locus (rs529565-C) was associated with rapid deterioration of CXR findings in all patients. This study revealed the clinical features, genetic features, and risk factors associated with rapid deterioration of CXR findings, a poor prognostic factor in patients with COVID-19.
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Affiliation(s)
- Tatsuya Kusumoto
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Shotaro Chubachi
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
| | - Ho Namkoong
- Department of Infectious Diseases, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
| | - Hiromu Tanaka
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Ho Lee
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Shiro Otake
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Kensuke Nakagawara
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Takahiro Fukushima
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Atsuho Morita
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Mayuko Watase
- Department of Respiratory Medicine, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Takanori Asakura
- Department of Pulmonary Medicine, Saitama City Hospital, Saitama, Japan
| | - Katsunori Masaki
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hirofumi Kamata
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Makoto Ishii
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Naoki Hasegawa
- Department of Infectious Diseases, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Norihiro Harada
- Department of Respiratory Medicine, Juntendo University Faculty of Medicine and Graduate School of Medicine, Tokyo, Japan
| | - Tetsuya Ueda
- Department of Respiratory Medicine, Osaka Saiseikai Nakatsu Hospital, Osaka, Japan
| | - Soichiro Ueda
- Department of Internal Medicine, Japan Community Health Care Organization (JCHO), Saitama Medical Center, Saitama, Japan
| | - Takashi Ishiguro
- Department of Respiratory Medicine, Saitama Cardiovascular and Respiratory Center, Kumagaya, Japan
| | - Ken Arimura
- Department of Respiratory Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Fukuki Saito
- Department of Emergency and Critical Care Medicine, Kansai Medical University General Medical Center, Moriguchi, Japan
| | - Takashi Yoshiyama
- Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Yasushi Nakano
- Department of Internal Medicine, Kawasaki Municipal Ida Hospital, Kawasaki, Japan
| | - Yoshikazu Mutoh
- Department of Infectious Diseases, Tosei General Hospital, Seto, Japan
| | - Yusuke Suzuki
- Department of Respiratory Medicine, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Ryuya Edahiro
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Koji Murakami
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yasunori Sato
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- The Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Ryuji Koike
- Medical Innovation Promotion Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine, Tokyo, Japan
| | - Akinori Kimura
- Institute of Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
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11
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Wang R, Sun Y, Kuang BH, Yan X, Lei J, Lin YX, Tian J, Li Y, Xie X, Chen T, Zhang H, Zeng YX, Zhao J, Feng L. HLA-Bw4 in association with KIR3DL1 favors natural killer cell-mediated protection against severe COVID-19. Emerg Microbes Infect 2023; 12:2185467. [PMID: 36849422 PMCID: PMC10013568 DOI: 10.1080/22221751.2023.2185467] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Replicating SARS-CoV-2 has been shown to degrade HLA class I on target cells to evade the cytotoxic T-cell (CTL) response. HLA-I downregulation can be sensed by NK cells to unleash killer cell immunoglobulin-like receptor (KIR)-mediated self-inhibition by the cognate HLA-I ligands. Here, we investigated the impact of HLA and KIR genotypes and HLA-KIR combinations on COVID-19 outcome. We found that the peptide affinities of HLA alleles were not correlated with COVID-19 severity. The predicted poor binders for SARS-CoV-2 peptides belong to HLA-B subtypes that encode KIR ligands, including Bw4 and C1 (introduced by B*46:01), which have a small F pocket and cannot accommodate SARS-CoV-2 CTL epitopes. However, HLA-Bw4 weak binders were beneficial for COVID-19 outcome, and individuals lacking the HLA-Bw4 motif were at higher risk for serious illness from COVID-19. The presence of the HLA-Bw4 and KIR3DL1 combination had a 58.8% lower risk of developing severe COVID-19 (OR = 0.412, 95% CI = 0.187-0.904, p = 0.02). This suggests that HLA-Bw4 alleles that impair their ability to load SARS-CoV-2 peptides will become targets for NK-mediated destruction. Thus, we proposed that the synergistic responsiveness of CTLs and NK cells can efficiently control SARS-CoV-2 infection and replication, and NK-cell-mediated anti-SARS-CoV-2 immune responses being mostly involved in severe infection when the level of ORF8 is high enough to degrade HLA-I. The HLA-Bw4/KIR3DL1 genotype may be particularly important for East Asians undergoing COVID-19 who are enriched in HLA-Bw4-inhibitory KIR interactions and carry a high frequency of HLA-Bw4 alleles that bind poorly to coronavirus peptides.
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Affiliation(s)
- Ruihua Wang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Ying Sun
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Bo-Hua Kuang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Xiao Yan
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China.,Department of Biochemistry, School of Medicine, Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Jinju Lei
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, People's Republic of China
| | - Yu-Xin Lin
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Jinxiu Tian
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Yating Li
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Xiaoduo Xie
- Department of Biochemistry, School of Medicine, Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Tao Chen
- State Key Laboratory of Respiratory Disease at People's Hospital of Yangjiang, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Hui Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yi-Xin Zeng
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease at People's Hospital of Yangjiang, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Lin Feng
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
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12
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Ceylan AC, Çavdarlı B, Ceylan GG, Topçu V, Satılmış SBA, Bektaş ŞG, Kalem AK, Kayaaslan B, Eser F, Kalkan EA, İnan O, Hasanoğlu İ, Yüksel S, Ateş İ, İzdeş S, Güner R, Gündüz CNS. Impact of Inflammation-Related Genes on COVID-19: Prospective Study at Turkish Cohort. TOHOKU J EXP MED 2023; 261:179-185. [PMID: 37635061 DOI: 10.1620/tjem.2023.j071] [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] [Indexed: 08/29/2023]
Abstract
The pandemic coronavirus disease 2019 (COVID-19) has caused a high mortality rate and poses a significant threat to the population. The disease may progress with mild symptoms or may cause the need for intensive care, depending on many factors. In this study, it was aimed to determine if there is a tendency due to genetic factors in COVID-19 patients. Ninety-four of 188 patients with mild clinical and 94 with severe clinical symptoms were included in the study. The targeted panel including coagulopathy (F2, F5), viral invasion (ACE2), and inflammation (CXCL8, IFNAR2, IFNL4, IL10, IL2, IL6, IRF7, TLR3, TLR7, TNF) related genes was performed sequenced by the next generation sequencing (NGS). The variants found were classified and univariate analyses were performed to select candidate variables for logistic model. Risk factors and variants were compared. It was revealed that the presence of 2 or more risk factors caused the disease to progress severely (p < 0.001). Heterozygous IRF7:c.1357-23dup variant had a 2.5 times higher risk for mild disease compared to severe disease. Other variants were found to be more significant in mild disease. Since polymorphic variants were not evaluated in the literature, the findings of our study could not be compared with the literature. However, as variants that may be effective in the severity of infections may differ according to ethnicity. This study has the feature of being a guide for subsequent studies to be carried out especially in Turkish population. Clinical course of the COVID-19 is likely to depend on a variety of risk factors, including age, sex, clinical status, immunology and genetic factors.
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Affiliation(s)
- Ahmet Cevdet Ceylan
- Department of Medical Genetics, Faculty of Medicine, Ankara Yıldırım Beyazıt University
- Department of Medical Genetics, Ankara City Hospital
| | | | - Gülay Güleç Ceylan
- Department of Medical Genetics, Faculty of Medicine, Ankara Yıldırım Beyazıt University
- Department of Medical Genetics, Ankara City Hospital
| | - Vehap Topçu
- Department of Medical Genetics, Ankara City Hospital
| | | | | | - Ayşe K Kalem
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara Yıldırım Beyazıt University
- Department of Infectious Diseases and Clinical Microbiology, Ankara City Hospital
| | - Bircan Kayaaslan
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara Yıldırım Beyazıt University
- Department of Infectious Diseases and Clinical Microbiology, Ankara City Hospital
| | - Fatma Eser
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara Yıldırım Beyazıt University
- Department of Infectious Diseases and Clinical Microbiology, Ankara City Hospital
| | | | - Osman İnan
- Department of Internal Medicine, Ankara City Hospital
| | - İmran Hasanoğlu
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara Yıldırım Beyazıt University
- Department of Infectious Diseases and Clinical Microbiology, Ankara City Hospital
| | - Selcen Yüksel
- Department of Biostatistics, Ankara Yıldırım Beyazıt University
| | - İhsan Ateş
- Department of Internal Medicine, Ankara City Hospital, Health Science University
| | - Seval İzdeş
- Department of Anesthesiology and Reanimation-Critical Care, Ankara City Hospital
- Department of Anesthesiology and Reanimation-Critical Care, Faculty of Medicine, Ankara Yıldırım Beyazıt University
| | - Rahmet Güner
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Ankara Yıldırım Beyazıt University
- Department of Infectious Diseases and Clinical Microbiology, Ankara City Hospital
| | - C Nur Semerci Gündüz
- Department of Medical Genetics, Faculty of Medicine, Ankara Yıldırım Beyazıt University
- Department of Medical Genetics, Ankara City Hospital
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13
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Boquett JA, Vianna FSL, Fagundes NJR, Schroeder L, Barbian M, Zagonel-Oliveira M, Andreis TF, Pôrto LCMS, Chies JAB, Schuler-Faccini L, Ashton-Prolla P, Rosset C. HLA haplotypes and differential regional mortality caused by COVID-19 in Brazil: an ecological study based on a large bone marrow donor bank dataset. AN ACAD BRAS CIENC 2023; 95:e20220801. [PMID: 37851747 DOI: 10.1590/0001-3765202320220801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/19/2022] [Indexed: 10/20/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) mortality rates varied among the states of Brazil during the course of the pandemics. The human leukocyte antigen (HLA) is a critical component of the antigen presentation pathway. Individuals with different HLA genotypes may trigger different immune responses against pathogens, which could culminate in different COVID-19 responses. HLA genotypes are variable, especially in the highly admixed Brazilian population. In this ecological study, we aimed to investigate the correlation between HLA haplotypes and the different regional distribution of COVID-19 mortality in Brazil. HLA data was obtained from 4,148,713 individuals registered in The Brazilian Voluntary Bone Marrow Donors Registry. COVID-19 data was retrieved from epidemiological bulletins issued by State Health Secretariats via Brazil's Ministry of Health from February/2020 to July/2022. We found a positive significant correlation between the HLA-A*01~B*08~DRB1*03 haplotype and COVID-19 mortality rates when we analyzed data from 26 states and the Federal District. This result indicates that the HLA-A*01~B*08~DRB1*03 haplotype may represent an additional risk factor for dying due to COVID-19. This haplotype should be further studied in other populations for a better understanding of the variation in COVID-19 outcomes across the world.
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Affiliation(s)
- Juliano André Boquett
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Saúde da Criança e do Adolescente, Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Rua Ramiro Barcelos, 2400, Santa Cecília, 90035-002 Porto Alegre, RS, Brazil
| | - Fernanda S L Vianna
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Rua Ramiro Barcelos, 2350, Santa Cecília, 90035-903 Porto Alegre, RS, Brazil
| | - Nelson J R Fagundes
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Lucas Schroeder
- Programa de Pós-Graduação em Computação Aplicada, Universidade do Vale do Rio dos Sinos, Laboratório de Visualização Avançada (VIZLab), Avenida Unisinos, 950, Cristo Rei, 93022-750 São Leopoldo, RS, Brazil
| | - Marcia Barbian
- Universidade Federal do Rio Grande do Sul, Departamento de Estatística, Instituto de Matemática e Estatística, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Marcelo Zagonel-Oliveira
- Programa de Pós-Graduação em Computação Aplicada, Universidade do Vale do Rio dos Sinos, Laboratório de Visualização Avançada (VIZLab), Avenida Unisinos, 950, Cristo Rei, 93022-750 São Leopoldo, RS, Brazil
| | - Tiago F Andreis
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Rua Ramiro Barcelos, 2350, Santa Cecília, 90035-903 Porto Alegre, RS, Brazil
| | - Luis Cristóvão M S Pôrto
- Universidade Estadual do Rio de Janeiro, Laboratório de Histocompatibilidade e Criopreservação, Rua São Francisco Xavier, 524, Maracanã, 20550-013 Rio de Janeiro, RJ, Brazil
| | - José Artur B Chies
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
| | - Lavinia Schuler-Faccini
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Saúde da Criança e do Adolescente, Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Rua Ramiro Barcelos, 2400, Santa Cecília, 90035-002 Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Rua Ramiro Barcelos, 2350, Santa Cecília, 90035-903 Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (iNaGeMP), Rua Ramiro Barcelos, 2350, Santa Cecília, 90035-903 Porto Alegre, RS, Brazil
| | - Patricia Ashton-Prolla
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Avenida Bento Gonçalves, 9500, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Rua Ramiro Barcelos, 2350, Santa Cecília, 90035-903 Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Rua Ramiro Barcelos, 2350, Santa Cecília, 90035-903 Porto Alegre, RS, Brazil
| | - Clévia Rosset
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Rua Ramiro Barcelos, 2350, Santa Cecília, 90035-903 Porto Alegre, RS, Brazil
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14
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Chen R, Fulton KM, Tran A, Duque D, Kovalchik K, Caron E, Twine SM, Li J. Integrated Immunopeptidomics and Proteomics Study of SARS-CoV-2-Infected Calu-3 Cells Reveals Dynamic Changes in Allele-specific HLA Abundance and Antigen Presentation. Mol Cell Proteomics 2023; 22:100645. [PMID: 37709257 PMCID: PMC10580047 DOI: 10.1016/j.mcpro.2023.100645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 08/29/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023] Open
Abstract
We present an integrated immunopeptidomics and proteomics study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection to comprehensively decipher the changes in host cells in response to viral infection. Immunopeptidomics analysis identified viral antigens presented by host cells through both class I and class II MHC system for recognition by the adaptive immune system. The host proteome changes were characterized by quantitative proteomics and glycoproteomics and from these data, the activation of toll-like receptor 3-interferon pathway was identified. Glycosylation analysis of human leukocyte antigen (HLA) proteins from the elution and flow-through of immunoprecipitation revealed that SARS-CoV-2 infection changed the glycosylation pattern of certain HLA alleles with different HLA alleles, showing distinct dynamic changes in relative abundance. The difference in the glycosylation and abundance of HLA alleles changed the number of strong binding antigens each allele presented, suggesting the impact of SARS-CoV-2 infection on antigen presentation is allele-specific. These results could be further exploited to explain the imbalanced response from innate and adaptive immune system in coronavirus disease 2019 cases, which would be helpful for the development of therapeutics and vaccine for coronavirus disease 2019 and preparation for future pandemic.
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Affiliation(s)
- Rui Chen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada.
| | - Kelly M Fulton
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Anh Tran
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Diana Duque
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Kevin Kovalchik
- CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Etienne Caron
- CHU Sainte-Justine Research Center, Montreal, Quebec, Canada; Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, Quebec, Canada
| | - Susan M Twine
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Jianjun Li
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada.
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15
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Fedeli U, Casotto V, Barbiellini Amidei C, Vianello A, Guarnieri G. COPD-Related Mortality before and after Mass COVID-19 Vaccination in Northern Italy. Vaccines (Basel) 2023; 11:1392. [PMID: 37631960 PMCID: PMC10459975 DOI: 10.3390/vaccines11081392] [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: 07/12/2023] [Revised: 08/08/2023] [Accepted: 08/18/2023] [Indexed: 08/28/2023] Open
Abstract
BACKGROUND/OBJECTIVE Little is known about the impact of the COVID-19 pandemic on mortality from COPD at the population level. The objective was to investigate COPD-related mortality throughout different epidemic waves in Italy before and after the vaccination campaign, which started in late December 2020 and initially targeted the population aged ≥80 years. METHODS Death certificates of residents in Veneto (Northeastern Italy) aged ≥40 years between 2008 and 2021 were analyzed. Age-standardized morality rates were computed for death certificates with any mention of COPD. Generalized estimating equation (GEE) models were fitted to estimate the expected mortality during the pandemic. The results were stratified by age groups of 40-79 and ≥80 years, main comorbidities, and place of death. RESULTS COPD was mentioned in 3478 death certificates in 2020 (+14% compared to the 2018-2019 average) and in 3133 in 2021 (+3%). Age-standardized mortality rates increased in all age and sex groups in 2020; in 2021, mortality returned to pre-pandemic levels among the elderly but not in the population aged 40-79 years (+6%). GEE models confirmed this differential trend by age. COPD-related mortality peaks were observed, especially in the first pandemic waves, with COVID-19 identified as the underlying cause of death in a relevant proportion (up to 35% in November 2020-January 2021). Mortality with comorbid diabetes and hypertensive diseases slightly increased during the pandemic. CONCLUSION COPD-related mortality increased at the beginning of the pandemic, due to deaths from COVID-19. The start of the vaccination campaign was associated with an important decline in COPD-related mortality, especially among the elderly, who first benefited from COVID-19 vaccines. The study findings show the role of mass vaccination in reducing COPD-related deaths during the later phases of the pandemic.
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Affiliation(s)
- Ugo Fedeli
- Epidemiological Department, Azienda Zero-Veneto Region, 35131 Padua, Italy; (U.F.); (V.C.); (C.B.A.)
| | - Veronica Casotto
- Epidemiological Department, Azienda Zero-Veneto Region, 35131 Padua, Italy; (U.F.); (V.C.); (C.B.A.)
| | | | - Andrea Vianello
- Department of Cardiac-Thoracic-Vascular Sciences and Public Health, Respiratory Pathophysiology Division, University of Padova, 35126 Padua, Italy;
| | - Gabriella Guarnieri
- Department of Cardiac-Thoracic-Vascular Sciences and Public Health, Respiratory Pathophysiology Division, University of Padova, 35126 Padua, Italy;
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Udomsinprasert W, Nontawong N, Saengsiwaritt W, Panthan B, Jiaranai P, Thongchompoo N, Santon S, Runcharoen C, Sensorn I, Jittikoon J, Chaikledkaew U, Chantratita W. Host genetic polymorphisms involved in long-term symptoms of COVID-19. Emerg Microbes Infect 2023:2239952. [PMID: 37497655 PMCID: PMC10392286 DOI: 10.1080/22221751.2023.2239952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Host genetic polymorphisms are recognized as a critical determinant of diversity in clinical symptoms of Coronavirus disease 2019 (COVID-19). Accordingly, this study aimed to determine possible associations between single nucleotide polymorphisms (SNPs) in 37 candidate genes and clinical consequences of COVID-19 - especially long-term symptoms, Long COVID. A total of 260 COVID-19 patients, divided into mild (n=239) and severe (n=21) and further categorized based on the presence of Long COVID (no, n=211; yes, n=49), were recruited. Genotyping of selected polymorphisms in 37 genes responsible for viral entry, immune response, and inflammation was performed using MassARRAY system. Out of 37 SNPs, 9 including leucine zipper transcription factor like-1 (LZTFL1) rs10490770 C allele, LZTFL1 rs11385942 dupA allele, nicotinamide adenine dinucleotide synthetase-1 (NADSYN1) rs12785878 TT genotype, plexin A-4 (PLXNA4) rs1424597 AA genotype, LZTFL1 rs17713054 A allele, interleukin-10 (IL10) rs1800896 TC genotype and C allele, angiotensin converting enzyme-2 (ACE2) rs2285666 T allele, and plasmanylethanolamine desaturase-1 (PEDS1) rs6020298 GG genotype and G allele were significantly associated with an increased risk of developing Long COVID, whereas interleukin-10 receptor subunit beta (IL10RB) rs8178562 GG genotype was significantly associated with a reduced risk of Long COVID. Kaplan-Meier curve displayed that polymorphisms in the above genes were significantly associated with cumulative rate of Long COVID occurrence. Polymorphisms in LZTFL1 rs10490770, LZTFL1 rs11385942, LZTFL1 rs17713054, NADSYN1 rs12785878, PLXNA4 rs1424597, IL10 rs1800896, ACE2 rs2285666, PEDS1 rs6020298, and IL10RB rs8178562 appear to be genetic factors involved in development of Long COVID.
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Affiliation(s)
- Wanvisa Udomsinprasert
- Department of Biochemistry, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | | | | | - Bhakbhoom Panthan
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Poramate Jiaranai
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Nartthawee Thongchompoo
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Siwalee Santon
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Chakkaphan Runcharoen
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Insee Sensorn
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Jiraphun Jittikoon
- Department of Biochemistry, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Usa Chaikledkaew
- Social and Administrative Pharmacy Division, Department of Pharmacy, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Mahidol University Health Technology Assessment (MUHTA) Graduate Program, Mahidol University, Bangkok 10400, Thailand
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
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Wilson GN. A Clinical Qualification Protocol Highlights Overlapping Genomic Influences and Neuro-Autonomic Mechanisms in Ehlers-Danlos and Long COVID-19 Syndromes. Curr Issues Mol Biol 2023; 45:6003-6023. [PMID: 37504295 PMCID: PMC10378515 DOI: 10.3390/cimb45070379] [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: 06/05/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/29/2023] Open
Abstract
A substantial fraction of the 15% with double-jointedness or hypermobility have the traditionally ascertained joint-skeletal, cutaneous, and cardiovascular symptoms of connective tissue dysplasia and its particular manifestation as Ehlers-Danlos syndrome (EDS). The holistic ascertainment of 120 findings in 1261 EDS patients added neuro-autonomic symptoms like headaches, muscle weakness, brain fog, chronic fatigue, dyspnea, and bowel irregularity to those of arthralgia and skin laxity, 15 of these symptoms shared with those of post-infectious SARS-CoV-2 (long COVID-19). Underlying articulo-autonomic mechanisms guided a clinical qualification protocol that qualified DNA variants in 317 genes as having diagnostic utility for EDS, six of them identical (F2-LIFR-NLRP3-STAT1-T1CAM1-TNFRSF13B) and eighteen similar to those modifying COVID-19 severity/EDS, including ADAMTS13/ADAMTS2-C3/C1R-IKBKG/IKBKAP-PIK3C3/PIK3R1-POLD4/POLG-TMPRSS2/TMPRSS6-WNT3/WNT10A. Also, contributing to EDS and COVID-19 severity were forty and three genes, respectively, impacting mitochondrial functions as well as parts of an overlapping gene network, or entome, that are hypothesized to mediate the cognitive-behavioral, neuro-autonomic, and immune-inflammatory alterations of connective tissue in these conditions. The further characterization of long COVID-19 natural history and genetic predisposition will be necessary before these parallels to EDS can be carefully delineated and translated into therapies.
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Affiliation(s)
- Golder N Wilson
- Department of Pediatrics, Texas Tech University Health Sciences Center, Lubbock, and KinderGenome Genetics Private Practice, 5347 W Mockingbird, Dallas, TX 75209, USA
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18
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Velastegui E, Vera E, Vanden Berghe W, Muñoz MS, Orellana-Manzano A. "HLA-C: evolution, epigenetics, and pathological implications in the major histocompatibility complex". Front Genet 2023; 14:1206034. [PMID: 37465164 PMCID: PMC10350511 DOI: 10.3389/fgene.2023.1206034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023] Open
Abstract
HLA-C, a gene located within the major histocompatibility complex, has emerged as a prominent target in biomedical research due to its involvement in various diseases, including cancer and autoimmune disorders; even though its recent addition to the MHC, the interaction between HLA-C and KIR is crucial for immune responses, particularly in viral infections. This review provides an overview of the structure, origin, function, and pathological implications of HLA-C in the major histocompatibility complex. In the last decade, we systematically reviewed original publications from Pubmed, ScienceDirect, Scopus, and Google Scholar. Our findings reveal that genetic variations in HLA-C can determine susceptibility or resistance to certain diseases. However, the first four exons of HLA-C are particularly susceptible to epigenetic modifications, which can lead to gene silencing and alterations in immune function. These alterations can manifest in diseases such as alopecia areata and psoriasis and can also impact susceptibility to cancer and the effectiveness of cancer treatments. By comprehending the intricate interplay between genetic and epigenetic factors that regulate HLA-C expression, researchers may develop novel strategies for preventing and treating diseases associated with HLA-C dysregulation.
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Affiliation(s)
- Erick Velastegui
- Escuela Politécnica Nacional, Departamento de Ciencias de los Alimentos y Biotecnología, Facultad de Ingeniería Química y Agroindustria, Quito, Ecuador
| | - Edwin Vera
- Escuela Politécnica Nacional, Departamento de Ciencias de los Alimentos y Biotecnología, Facultad de Ingeniería Química y Agroindustria, Quito, Ecuador
| | - Wim Vanden Berghe
- Epigenetic Signaling Lab, Faculty Biomedical Sciences, PPES, University of Antwerp, Antwerp, Belgium
| | - Mindy S. Muñoz
- Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Andrea Orellana-Manzano
- Escuela Superior Politécnica del Litoral, Laboratorio para investigaciones biomédicas, Facultad de Ciencias de la Vida (FCV), Guayaquil, Ecuador
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19
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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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20
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Bnina AB, El Bahri Y, Cheybi A, Lazrek NB, Chouchane S, Omezzine A, Naija W, Bouatay A. Association between Human Leukocyte Antigen (HLA) DQB1*06 and HLA DQB1*03 and adverse outcomes in a group of critically ill patients with COVID-19 in Tunisia: a cross-sectional study. Pan Afr Med J 2023; 45:109. [PMID: 37719057 PMCID: PMC10504440 DOI: 10.11604/pamj.2023.45.109.39956] [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: 04/05/2023] [Accepted: 06/08/2023] [Indexed: 09/19/2023] Open
Abstract
Introduction Human Leukocyte Antigen (HLA) system is a highly polymorphic genetic system associated with the prognosis of several infectious diseases. The aim of this study is to investigate the association of HLA polymorphism with the outcome of coronavirus disease 2019 (COVID-19) in Tunisian critically ill patients. Methods this retrospective cross-sectional study included 42 consecutive patients hospitalized in intensive care unit (ICU) for COVID-19 in March 2021. Genotyping of HLA loci was performed by LABType™ sequence-specific oligonucleotide (SSO) typing kits (One lambda Inc, USA). Statistical analyses were performed using Statistical Package for Social Sciences (SPSS®) version 23.0. A p-value <0.05 was considered significant. Multivariable regression analysis was performed for the association between HLA polymorphism with adverse outcomes with adjustment for potential confounders such as age, sex, co-morbidities and blood type. Results patients included in our study had a mean age of 64.5 ± 11.5 (34-83) years and were mainly men (64.3%; (n=27)). The most common cardiovascular risk factors were obesity (61.9%; (n=26)) and hypertension (26.2%; (n=11)). Thirty-two patients died (76.2%). Eleven patients (26.2%) required intubation during hospitalization. We found that HLA DQB1*06 allele was significantly associated with protection against mortality aOR: 0.066, 95% CI 0.005-0.821; p = 0.035. HLA DQB1*03 allele was significantly associated with protection against intubation aOR: 0.151, 95% CI 0.023-0.976; p = 0.047. Conclusion it was found that there are 2 protective HLA alleles against COVID-19 severity and mortality in critically ill patients. This could allow focusing on people genetically predisposed to develop severe forms of COVID-19.
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Affiliation(s)
- Amène Ben Bnina
- Hematology Laboratory, Sahloul Teaching Hospital, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Yasmine El Bahri
- Hematology Laboratory, Sahloul Teaching Hospital, Sousse, Tunisia
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
| | - Amény Cheybi
- Hematology Laboratory, Sahloul Teaching Hospital, Sousse, Tunisia
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
| | - Nada Ben Lazrek
- Hematology Laboratory, Sahloul Teaching Hospital, Sousse, Tunisia
| | - Syrine Chouchane
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
- Department of Anesthesia and Intensive Care, Sahloul Teaching Hospital, Sousse, Tunisia
| | - Asma Omezzine
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Biochemistry Laboratory, Sahloul Teaching Hospital, Sousse, Tunisia
| | - Walid Naija
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
- Department of Anesthesia and Intensive Care, Sahloul Teaching Hospital, Sousse, Tunisia
| | - Amina Bouatay
- Hematology Laboratory, Sahloul Teaching Hospital, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
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21
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Nabi AHMN, Ebihara A, Shekhar HU. Impacts of SARS-CoV-2 on diabetes mellitus: A pre and post pandemic evaluation. World J Virol 2023; 12:151-171. [PMID: 37396707 PMCID: PMC10311579 DOI: 10.5501/wjv.v12.i3.151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/24/2023] [Accepted: 04/13/2023] [Indexed: 06/21/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by the novel beta coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) crippled the whole world and has resulted in large number of morbidity and mortality. The origin of the SARS-CoV-2 is still disputed. The risk of infection with SARS-CoV-2 is dependent on several risk factors as observed in many studies. The severity of the disease depends on many factors including the viral strain, host immunogenetics, environmental factors, host genetics, host nutritional status and presence of comorbidities like hypertension, diabetes, Chronic Obstructive Pulmonary Disease, cardiovascular disease, renal impairment. Diabetes is a metabolic disorder mainly characterized by hyperglycemia. Diabetic individuals are intrinsically prone to infections. SARS-CoV-2 infection in patients with diabetes result in β-cell damage and cytokine storm. Damage to the cells impairs the equilibrium of glucose, leading to hyperglycemia. The ensuing cytokine storm causes insulin resistance, especially in the muscles and liver, which also causes a hyperglycemic state. All of these increase the severity of COVID-19. Genetics also play pivotal role in disease pathogenesis. This review article focuses from the probable sources of coronaviruses and SARS-CoV-2 to its impacts on individuals with diabetes and host genetics in pre- and post-pandemic era.
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Affiliation(s)
- A H M Nurun Nabi
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Akio Ebihara
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Hossain Uddin Shekhar
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
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22
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Brand M, Keşmir C. Evolution of SARS-CoV-2-specific CD4 + T cell epitopes. Immunogenetics 2023; 75:283-293. [PMID: 36719467 PMCID: PMC9887569 DOI: 10.1007/s00251-023-01295-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 02/01/2023]
Abstract
Vaccination clearly decreases coronavirus disease 2019 (COVID-19) mortality; however, they also impose selection pressure on the virus, which promotes the evolution of immune escape variants. For example, despite the high vaccination level in especially Western countries, the Omicron variant caused millions of breakthrough infections, suggesting that the highly mutated spike protein in the Omicron variant can escape antibody immunity much more efficiently than the other variants of concern (VOCs). In this study, we investigated the resistance/susceptibility of T helper cell responses that are necessary for generating efficient long-lasting antibody immunity, in several VOCs. By predicting T helper cell epitopes on the spike protein for most common HLA-DRB1 alleles worldwide, we found that although most of high frequency HLA-DRB1 alleles have several potential T helper cell epitopes, few alleles like HLA-DRB1 13:01 and 11:01 are not predicted to have any significant T helper cell responses after vaccination. Using these predictions, a population based on realistic human leukocyte antigen-II (HLA-II) frequencies were simulated to visualize the T helper cell immunity on the population level. While a small fraction of this population had alarmingly little predicted CD4 T cell epitopes, the majority had several epitopes that should be enough to generate efficient B cell responses. Moreover, we show that VOC spike mutations hardly affect T helper epitopes and mainly occur in other residues of the spike protein. These results suggest that lack of long-lasting antibody responses is not likely due to loss of T helper cell epitopes in new VOCs.
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Affiliation(s)
- Marina Brand
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - Can Keşmir
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, Netherlands.
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23
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Suarez-Pajes E, Tosco-Herrera E, Ramirez-Falcon M, Gonzalez-Barbuzano S, Hernandez-Beeftink T, Guillen-Guio B, Villar J, Flores C. Genetic Determinants of the Acute Respiratory Distress Syndrome. J Clin Med 2023; 12:3713. [PMID: 37297908 PMCID: PMC10253474 DOI: 10.3390/jcm12113713] [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: 04/17/2023] [Revised: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a life-threatening lung condition that arises from multiple causes, including sepsis, pneumonia, trauma, and severe coronavirus disease 2019 (COVID-19). Given the heterogeneity of causes and the lack of specific therapeutic options, it is crucial to understand the genetic and molecular mechanisms that underlie this condition. The identification of genetic risks and pharmacogenetic loci, which are involved in determining drug responses, could help enhance early patient diagnosis, assist in risk stratification of patients, and reveal novel targets for pharmacological interventions, including possibilities for drug repositioning. Here, we highlight the basis and importance of the most common genetic approaches to understanding the pathogenesis of ARDS and its critical triggers. We summarize the findings of screening common genetic variation via genome-wide association studies and analyses based on other approaches, such as polygenic risk scores, multi-trait analyses, or Mendelian randomization studies. We also provide an overview of results from rare genetic variation studies using Next-Generation Sequencing techniques and their links with inborn errors of immunity. Lastly, we discuss the genetic overlap between severe COVID-19 and ARDS by other causes.
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Affiliation(s)
- Eva Suarez-Pajes
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Eva Tosco-Herrera
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Melody Ramirez-Falcon
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Silvia Gonzalez-Barbuzano
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Tamara Hernandez-Beeftink
- Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester LE1 7RH, UK
| | - Beatriz Guillen-Guio
- Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester LE1 7RH, UK
| | - Jesús Villar
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Research Unit, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
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24
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Wang M, Yu F, Chang W, Zhang Y, Zhang L, Li P. Inflammasomes: a rising star on the horizon of COVID-19 pathophysiology. Front Immunol 2023; 14:1185233. [PMID: 37251383 PMCID: PMC10213254 DOI: 10.3389/fimmu.2023.1185233] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/02/2023] [Indexed: 05/31/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a contagious respiratory virus that is the cause of the coronavirus disease 2019 (COVID-19) pandemic which has posed a serious threat to public health. COVID-19 is characterized by a wide spectrum of clinical manifestations, ranging from asymptomatic infection to mild cold-like symptoms, severe pneumonia or even death. Inflammasomes are supramolecular signaling platforms that assemble in response to danger or microbial signals. Upon activation, inflammasomes mediate innate immune defense by favoring the release of proinflammatory cytokines and triggering pyroptotic cell death. Nevertheless, abnormalities in inflammasome functioning can result in a variety of human diseases such as autoimmune disorders and cancer. A growing body of evidence has showed that SARS-CoV-2 infection can induce inflammasome assembly. Dysregulated inflammasome activation and consequent cytokine burst have been associated with COVID-19 severity, alluding to the implication of inflammasomes in COVID-19 pathophysiology. Accordingly, an improved understanding of inflammasome-mediated inflammatory cascades in COVID-19 is essential to uncover the immunological mechanisms of COVID-19 pathology and identify effective therapeutic approaches for this devastating disease. In this review, we summarize the most recent findings on the interplay between SARS-CoV-2 and inflammasomes and the contribution of activated inflammasomes to COVID-19 progression. We dissect the mechanisms involving the inflammasome machinery in COVID-19 immunopathogenesis. In addition, we provide an overview of inflammasome-targeted therapies or antagonists that have potential clinical utility in COVID-19 treatment.
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Affiliation(s)
- Man Wang
- *Correspondence: Man Wang, ; Peifeng Li,
| | | | | | | | | | - Peifeng Li
- *Correspondence: Man Wang, ; Peifeng Li,
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25
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Mashayekhi P, Omrani MD, Yassin Z, Dehghanifard A, Ashouri L, Aghabozorg Afjeh SS, Shabanzadeh Z. Influence of HLA-A, -B, -DR Polymorphisms on the Severity of COVID-19: A Case-Control Study in the Iranian Population. ARCHIVES OF IRANIAN MEDICINE 2023; 26:261-266. [PMID: 38301089 PMCID: PMC10685865 DOI: 10.34172/aim.2023.40] [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: 11/05/2022] [Accepted: 03/12/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND As an emerging pandemic disease, COVID-19 encompasses a spectrum of clinical diagnoses, from the common cold to severe respiratory syndrome. Considering the shreds of evidence demonstrating the relationship between human leukocyte antigen (HLA) allele diversity and infectious disease susceptibility, this study was conducted to determine the association of HLA alleles with COVID-19 severity in Iranian subjects. METHODS In this case-control study, a total of 200 unrelated individuals (consisting of 100 people with severe COVID-19 and an average age of 55.54 as the case group, and 100 patients with mild COVID-19 with an average age of 48.97 as the control group) were recruited, and HLA typing (Locus A, B, and DR) was performed using the Olerup sequence-specific oligonucleotide (SSO) HLA-typing kit. RESULTS Our results showed that HLA-A*11 and HLA-DRB1*14 alleles were more frequently observed in severe COVID-19 cases, while HLA-B*52 was more common in mild cases, which was in agreement with some previous studies. CONCLUSION Our results confirmed the evidence for the association of HLA alleles with COVID-19 outcomes. We found that HLA-A*11 and HLA-DRB1*14 alleles may be susceptibility factors for severe COVID-19, while HLA-B*52 may be a protective factor. These findings provide new insight into the pathogenesis of COVID-19 and help patient management.
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Affiliation(s)
- Parisa Mashayekhi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mir Davood Omrani
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zeynab Yassin
- Antimicrobial resistance Research Center, Institute Of Immunology And Infectious Disease, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Dehghanifard
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Leila Ashouri
- Antimicrobial resistance Research Center, Institute Of Immunology And Infectious Disease, Iran University of Medical Sciences, Tehran, Iran
| | | | - Zahra Shabanzadeh
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Scaramuzzo G, Nucera F, Asmundo A, Messina R, Mari M, Montanaro F, Johansen MD, Monaco F, Fadda G, Tuccari G, Hansbro NG, Hansbro PM, Hansel TT, Adcock IM, David A, Kirkham P, Caramori G, Volta CA, Spadaro S. Cellular and molecular features of COVID-19 associated ARDS: therapeutic relevance. J Inflamm (Lond) 2023; 20:11. [PMID: 36941580 PMCID: PMC10027286 DOI: 10.1186/s12950-023-00333-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/08/2023] [Indexed: 03/23/2023] Open
Abstract
The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection can be asymptomatic or cause a disease (COVID-19) characterized by different levels of severity. The main cause of severe COVID-19 and death is represented by acute (or acute on chronic) respiratory failure and acute respiratory distress syndrome (ARDS), often requiring hospital admission and ventilator support.The molecular pathogenesis of COVID-19-related ARDS (by now termed c-ARDS) is still poorly understood. In this review we will discuss the genetic susceptibility to COVID-19, the pathogenesis and the local and systemic biomarkers correlated with c-ARDS and the therapeutic options that target the cell signalling pathways of c-ARDS.
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Affiliation(s)
- Gaetano Scaramuzzo
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Department of Emergency, Section of Intensive Care and Anesthesia, Azienda Ospedaliera-Universitaria Sant'Anna, Ferrara, Italy
| | - Francesco Nucera
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Alessio Asmundo
- Medicina Legale, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Roberto Messina
- Intensive Care Unit, Dipartimento di Patologia Umana e dell'Età Evolutiva Gaetano Barresi, Università di Messina, Messina, Italy
| | - Matilde Mari
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Department of Emergency, Section of Intensive Care and Anesthesia, Azienda Ospedaliera-Universitaria Sant'Anna, Ferrara, Italy
| | - Federica Montanaro
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Department of Emergency, Section of Intensive Care and Anesthesia, Azienda Ospedaliera-Universitaria Sant'Anna, Ferrara, Italy
| | - Matt D Johansen
- Centre for Inflammation, School of Life Sciences, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia
| | - Francesco Monaco
- Chirurgia Toracica, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Guido Fadda
- Section of Pathological Anatomy, Department of Human Pathology of Adult and Developmental Age "Gaetano Barresi", University of Messina, Messina, Italy
| | - Giovanni Tuccari
- Section of Pathological Anatomy, Department of Human Pathology of Adult and Developmental Age "Gaetano Barresi", University of Messina, Messina, Italy
| | - Nicole G Hansbro
- Centre for Inflammation, School of Life Sciences, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia
| | - Philip M Hansbro
- Centre for Inflammation, School of Life Sciences, Faculty of Science, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia
| | - Trevor T Hansel
- Medical Research Council and Asthma, UK Centre in Allergic Mechanisms of Asthma, London, UK
| | - Ian M Adcock
- Airway Disease Section, National Heart and Lung Institute, Imperial College London, London, UK
| | - Antonio David
- Intensive Care Unit, Dipartimento di Patologia Umana e dell'Età Evolutiva Gaetano Barresi, Università di Messina, Messina, Italy
| | - Paul Kirkham
- Department of Biomedical Sciences, Faculty of Sciences and Engineering, University of Wolverhampton, West Midlands, Wolverhampton, UK
| | - Gaetano Caramori
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy.
| | - Carlo Alberto Volta
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Department of Emergency, Section of Intensive Care and Anesthesia, Azienda Ospedaliera-Universitaria Sant'Anna, Ferrara, Italy
| | - Savino Spadaro
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Department of Emergency, Section of Intensive Care and Anesthesia, Azienda Ospedaliera-Universitaria Sant'Anna, Ferrara, Italy
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Alsaedi SB, Mineta K, Gao X, Gojobori T. Computational network analysis of host genetic risk variants of severe COVID-19. Hum Genomics 2023; 17:17. [PMID: 36859360 PMCID: PMC9977643 DOI: 10.1186/s40246-023-00454-y] [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: 11/24/2022] [Accepted: 01/28/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Genome-wide association studies have identified numerous human host genetic risk variants that play a substantial role in the host immune response to SARS-CoV-2. Although these genetic risk variants significantly increase the severity of COVID-19, their influence on body systems is poorly understood. Therefore, we aim to interpret the biological mechanisms and pathways associated with the genetic risk factors and immune responses in severe COVID-19. We perform a deep analysis of previously identified risk variants and infer the hidden interactions between their molecular networks through disease mapping and the similarity of the molecular functions between constructed networks. RESULTS We designed a four-stage computational workflow for systematic genetic analysis of the risk variants. We integrated the molecular profiles of the risk factors with associated diseases, then constructed protein-protein interaction networks. We identified 24 protein-protein interaction networks with 939 interactions derived from 109 filtered risk variants in 60 risk genes and 56 proteins. The majority of molecular functions, interactions and pathways are involved in immune responses; several interactions and pathways are related to the metabolic and cardiovascular systems, which could lead to multi-organ complications and dysfunction. CONCLUSIONS This study highlights the importance of analyzing molecular interactions and pathways to understand the heterogeneous susceptibility of the host immune response to SARS-CoV-2. We propose new insights into pathogenicity analysis of infections by including genetic risk information as essential factors to predict future complications during and after infection. This approach may assist more precise clinical decisions and accurate treatment plans to reduce COVID-19 complications.
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Affiliation(s)
- Sakhaa B. Alsaedi
- grid.45672.320000 0001 1926 5090Division of Computer, Electrical and Mathematical Sciences and Engineering, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Saudi Arabia ,grid.412892.40000 0004 1754 9358College of Computer Science and Engineering (CCSE), Taibah University, Medina, Saudi Arabia
| | - Katsuhiko Mineta
- grid.45672.320000 0001 1926 5090Division of Computer, Electrical and Mathematical Sciences and Engineering, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Saudi Arabia ,grid.5290.e0000 0004 1936 9975AND Research Organization for Nano and Life Innovation, Waseda University, Tokyo, 162-0041 Japan
| | - Xin Gao
- grid.45672.320000 0001 1926 5090Division of Computer, Electrical and Mathematical Sciences and Engineering, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Saudi Arabia
| | - Takashi Gojobori
- Division of Computer, Electrical and Mathematical Sciences and Engineering, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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Kakodkar P, Dokouhaki P, Wu F, Shavadia J, Nair R, Webster D, Sawyer T, Huan T, Mostafa A. The role of the HLA allelic repertoire on the clinical severity of COVID-19 in Canadians, living in the Saskatchewan province. Hum Immunol 2023; 84:163-171. [PMID: 36707385 PMCID: PMC9852320 DOI: 10.1016/j.humimm.2023.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/11/2023] [Accepted: 01/11/2023] [Indexed: 01/22/2023]
Abstract
AIMS The HLA system has been implicated as an underlying determinant for modulating the immune response to SARS-CoV-2. In this study, we aimed to determine the association of patients' HLA genetic profiles with the disease severity of COVID-19 infection. METHODS Prospective study was conducted on COVID-19 patients (n = 40) admitted to hospitals in Saskatoon, Canada, between March and December 2020. Next-generation sequencing was performed on the patient samples to obtain high-resolution HLA typing profiles. The statistical association between HLA allelic frequency and disease severity was examined. The disease severity was categorized based on the length of hospital stay and intensive care needs or demise during the hospital stay. RESULTS HLA allelic frequencies of the high and low-severity cohorts were normalized against corresponding background allelic frequencies. In the high-severity cohort, A*02:06 (11.8-fold), B*51:01 (2.4-fold), B*15:01(3.1-fold), C*01:02 (3.3-fold), DRB1*08:02 (31.2-fold), DQ*06:09 (11-fold), and DPB1*04:02(4-fold) were significantly overrepresented (p < 0.05) making these deleterious alleles. In the low-severity cohort, A*24:02 (2.8-fold), B*35:01 (2.8-fold), DRB1*04:07 (5.3-fold), and DRB1*08:11 (22-fold) were found to be significantly overrepresented (p < 0.05) making these protective alleles. These above alleles interact with NK cell antiviral activity via the killer immunoglobulin-like receptors (KIR). The high-severity cohort had a higher predilection for HLA alleles associated with KIR subgroups; Bw4-80I (1.1-fold), and C1 (1.6-fold) which promotes NK cell inhibition, while the low-severity cohort had a higher predilection for Bw4-80T (1.6-fold), and C2 (1.6-fold) which promote NK cell activation. CONCLUSION In this study, the HLA allelic repository with the distribution of deleterious and protective alleles was found to correlate with the severity of the clinical course in COVID-19. Moreover, the interaction of specific HLA alleles with the KIR-associated subfamily modulates the NK cell-mediated surveillance of SARS-CoV-2. Both deleterious HLA alleles and inhibitory KIR appear prominently in the severe COVID-19 group focusing on the importance of NK cells in the convalescence of COVID-19.
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Affiliation(s)
- Pramath Kakodkar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan College of Medicine, Canada.
| | - Pouneh Dokouhaki
- Department of Pathology and Laboratory Medicine, University of Saskatchewan College of Medicine, Canada.
| | - Fang Wu
- Department of Pathology and Laboratory Medicine, University of Saskatchewan College of Medicine, Canada.
| | - Jay Shavadia
- Division of Cardiology, Department of Medicine, University of Saskatchewan, Canada.
| | - Revathi Nair
- College of Medicine, University of Saskatchewan, Canada.
| | - Destinie Webster
- Department of Pathology and Laboratory Medicine, University of Saskatchewan College of Medicine, Canada.
| | - Terry Sawyer
- Department of Pathology and Laboratory Medicine, University of Saskatchewan College of Medicine, Canada.
| | - Tao Huan
- Department of Chemistry, University of British Columbia, Canada.
| | - Ahmed Mostafa
- Department of Pathology and Laboratory Medicine, University of Saskatchewan College of Medicine, Canada.
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Yaghoobi A, Lord JS, Rezaiezadeh JS, Yekaninejad MS, Amini M, Izadi P. TMPRSS2 polymorphism (rs12329760) and the severity of the COVID-19 in Iranian population. PLoS One 2023; 18:e0281750. [PMID: 36795725 PMCID: PMC9934348 DOI: 10.1371/journal.pone.0281750] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/31/2023] [Indexed: 02/17/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been responsible for the recent pandemic since early 2020. Due to the wide range of clinical symptoms of this disease, from asymptomatic to severe and critical forms, it seems that genetic differences among patients, along with other factors (such as gender, age, and underlying diseases), can explain part of the variation in disease symptoms. The TMPRSS2 enzyme plays a vital role in the early stages of the interaction of the SARS-CoV-2 with the host cells by facilitating viral entry. There is a polymorphism in the TMPRSS2 gene, called rs12329760(C to T) as a missense variant, which causes the replacement of valine to methionine in the TMPRSS2 protein at position 160. The present study investigated the association between the TMPRSS2 genotype and the severity of the Coronavirus disease 2019 (COVID-19) in Iranian patients. The TMPRSS2 genotype of 251 COVID-19 patients (151 patients with asymptomatic to mild and 100 patients with severe to critical symptoms) was detected on genomic DNA extracted from patients' peripheral blood via the ARMS-PCR method. Our results showed a significant association between the minor T allele and the severity of the COVID-19 (P-value = 0.043) under the dominant and additive inheritance model. In conclusion, the results of this study showed that the T allele of the rs12329760 in the TMPRSS2 gene is a risk allele for severe form of COVID-19 in Iranian patients in contrast to most previous studies on this variant in European ancestry populations which suggested this variant as a protective allele. Our results reiterate to the ethnic-specific risk alleles and hidden unknown complexity behind the host genetic susceptibility. However, further studies are needed to address the complex mechanisms behind the interaction of the TMPRSS2 protein and the SARS-CoV-2 and the role of rs12329760 polymorphism in determining the disease severity.
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Affiliation(s)
- Arash Yaghoobi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Javad Safdari Lord
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Javad Soltani Rezaiezadeh
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mir Saeed Yekaninejad
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Amini
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Pantea Izadi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- * E-mail:
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30
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Lin F, Lin X, Fu B, Xiong Y, Zaky MY, Wu H. Functional studies of HLA and its role in SARS-CoV-2: Stimulating T cell response and vaccine development. Life Sci 2023; 315:121374. [PMID: 36621539 PMCID: PMC9815883 DOI: 10.1016/j.lfs.2023.121374] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
In the biological immune process, the major histocompatibility complex (MHC) plays an indispensable role in the expression of HLA molecules in the human body when viral infection activates the T-cell response to remove the virus. Since the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in 2019, how to address and prevent SARS-CoV-2 has become a common problem facing all mankind. The T-cell immune response activated by MHC peptides is a way to construct a defense line and reduce the transmission and harm of the virus. Presentation of SARS-CoV-2 antigen is associated with different types of HLA phenotypes, and different HLA phenotypes induce different immune responses. The prediction of SARS-CoV-2 mutation information and the design of vaccines based on HLAs can effectively activate autoimmunity and cope with virus mutations, which can provide some references for the prevention and treatment of SARS-CoV-2.
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Affiliation(s)
- Feng Lin
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Xiaoyuan Lin
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China.
| | - Beibei Fu
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Yan Xiong
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China
| | - Mohamed Y Zaky
- Molecular Physiology Division, Zoology Department, Faculty of Science, Beni-Suef University, P.O. Box 62521, Beni-Suef, Egypt; Department of Oncology and Department of Biomedical and Clinical Science, Faculty of Medicine, Linköping University, Sweden
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Shapingba, Chongqing, China.
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The Search of Association of HLA Class I and Class II Alleles with COVID-19 Mortality in the Russian Cohort. Int J Mol Sci 2023; 24:ijms24043068. [PMID: 36834479 PMCID: PMC9960097 DOI: 10.3390/ijms24043068] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/18/2023] [Accepted: 01/24/2023] [Indexed: 02/08/2023] Open
Abstract
HLA genes play a pivotal role in the immune response via presenting the pathogen peptides on the cell surface in a host organism. Here, we studied the association of HLA allele variants of class I (loci A, B, C) and class II (loci DRB1, DQB1, DPB1) genes with the outcome of COVID-19 infection. We performed high-resolution sequencing of class HLA I and class II genes based on the sample population of 157 patients who died from COVID-19 and 76 patients who survived despite severe symptoms. The results were further compared with HLA genotype frequencies in the control population represented by 475 people from the Russian population. Although the obtained data revealed no significant differences between the samples at a locus level, they allowed one to uncover a set of notable alleles potentially contributing to the COVID-19 outcome. Our results did not only confirm the previously discovered fatal role of age or association of DRB1*01:01:01G and DRB1*01:02:01G alleles with severe symptoms and survival, but also allowed us to single out the DQB1*05:03:01G allele and B*14:02:01G~C*08:02:01G haplotype, which were associated with survival. Our findings showed that not only separate allele, but also their haplotype, could serve as potential markers of COVID-19 outcome and be used during triage for hospital admission.
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Chung HY, Jian M, Chang CK, Chen CS, Li SY, Lin JC, Yeh KM, Yang YS, Chen CW, Hsieh SS, Tang SH, Perng CL, Hung KS, Chang FY, Shang HS. The application of a novel 5-in-1 multiplex reverse transcriptase-polymerase chain reaction assay for rapid detection of SARS-CoV-2 and differentiation between variants of concern. Int J Infect Dis 2023; 127:56-62. [PMID: 36455809 PMCID: PMC9703862 DOI: 10.1016/j.ijid.2022.11.027] [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: 06/05/2022] [Revised: 10/24/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES We have established a novel 5-in-1 VOC assay to rapidly detect SARS-CoV-2 and immediately distinguish whether positive samples represent variants of concern (VOCs). METHODS This assay could distinguish among five VOCs: Alpha, Beta, Gamma, Delta, and Omicron, in a single reaction tube. The five variants exhibit different single nucleotide polymorphisms (SNPs) in their viral genome, which can be used to distinguish them. We selected target SNPs in the spike gene, including N501Y, P681R, K417N, and deletion H69/V70 for the assay. RESULTS The limit of detection of each gene locus was 80 copies per polymerase chain reaction. We observed a high consistency among the results when comparing the performance of our 5-in-1 VOC assay, whole gene sequencing, and the Roche VirSNiP SARS-CoV-2 test in retrospectively analyzing 150 clinical SARS-CoV-2 variant positive samples. The 5-in-1 VOC assay offers an alternative and rapid high-throughput test for most diagnostic laboratories in a flexible sample-to-result platform. CONCLUSION The assay can also be applied in a commercial platform with the completion of the SARS-CoV-2 confirmation test and identification of its variant within 2.5 hours.
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Affiliation(s)
- Hsing-Yi Chung
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan,Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
| | - Ming Jian
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Kai Chang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chi-Sheng Chen
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Shih-Yi Li
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Jung-Chung Lin
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Kuo-Ming Yeh
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Ya-Sung Yang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chien-Wen Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Shan-Shan Hsieh
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Sheng-Hui Tang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Kuo-Sheng Hung
- Center for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Feng-Yee Chang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan,Corresponding author
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Jin X, Liu X, Shen C. A systemic review of T-cell epitopes defined from the proteome of SARS-CoV-2. Virus Res 2023; 324:199024. [PMID: 36526016 PMCID: PMC9757803 DOI: 10.1016/j.virusres.2022.199024] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/10/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection remains in a global pandemic, and no eradicative therapy is currently available. Host T cells have been shown to play a crucial role in the antiviral immune protection and pathology in Coronavirus disease 2019 (COVID-19) patients; thus, identifying sufficient T-cell epitopes from the SARS-CoV-2 proteome can contribute greatly to the development of T-cell epitope vaccines and the precise evaluation of host SARS-CoV-2-specific cellular immunity. This review presents a comprehensive map of T-cell epitopes functionally validated from SARS-CoV-2 antigens, the human leukocyte antigen (HLA) supertypes to present these epitopes, and the strategies to screen and identify T-cell epitopes. To the best of our knowledge, a total of 1349 CD8+ T-cell epitopes and 790 CD4+ T-cell epitopes have been defined by functional experiments thus far, but most are presented by approximately twenty common HLA supertypes, such as HLA-A0201, A2402, B0702, DR15, DR7 and DR11 molecules, and 74-80% of the T-cell epitopes are derived from S protein and nonstructural protein. These data provide useful insight into the development of vaccines and specific T-cell detection systems. However, the currently defined T-cell epitope repertoire cannot cover the HLA polymorphism of major populations in an indicated geographic region. More research is needed to depict an overall landscape of T-cell epitopes, which covers the overall SARS-CoV-2 proteome and global patients.
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Affiliation(s)
- Xiaoxiao Jin
- Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, China 225002; Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, Jiangsu, China 210009
| | - Xiaotao Liu
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, Jiangsu, China 210009
| | - Chuanlai Shen
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing, Jiangsu, China 210009.
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Azimi S, Saghafi F, Mohammadi MH, Moghimi MH, Akhavan SA, Khataminia M, Shirvani M, Sohrevardi SM, Jamialahmadi T, Sahebnasagh A, Sahebkar A. The Potential of Cannabidiol for Acute Respiratory Distress Syndrome in COVID-19. Curr Pharm Des 2023; 29:2291-2296. [PMID: 37818584 DOI: 10.2174/0113816128275803230920094909] [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: 08/05/2023] [Accepted: 08/22/2023] [Indexed: 10/12/2023]
Abstract
COVID-19 disease manifests itself in a wide range of signs and symptoms, beginning with mild symptoms, such as fever, cough, and dyspnea, progressing to acute respiratory distress syndrome (ARDS) and death in some cases. The cytokine storm, or an excess of cytokines released locally, is assumed to be the primary cause of ARDS and mortality in COVID-19 patients. To enhance the survival rate of COVID-19 patients, early management of the cytokine storm with immunomodulators is crucial. Although the effectiveness of some immunosuppressants, such as corticosteroids and tocilizumab, has been studied in clinical trials, the administration of these drugs should be exercised cautiously. Cannabidiol (CBD) is a non-psychotropic phytocannabinoid from Cannabis sativa extracts with anti-inflammatory properties. This review is intended to discuss the possible utility of CBD for the management of COVID-19 patients, particularly those with ARDS.
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Affiliation(s)
- Saeid Azimi
- Student Research Committee, Faculty of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Saghafi
- Department of Clinical Pharmacy, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | - Mohammad Hossein Moghimi
- Student Research Committee, Faculty of Pharmacy, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Seyed Ali Akhavan
- Student Research Committee, Faculty of Pharmacy, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Masoud Khataminia
- Student Research Committee, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Maria Shirvani
- Clinical Research Development Center, Imam Reza Hospital, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Seyed Mojtaba Sohrevardi
- Department of Clinical Pharmacy, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Tannaz Jamialahmadi
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Adeleh Sahebnasagh
- Department of Internal Medicine, Clinical Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
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35
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Queiroz MAF, Santiago AM, Brito WRDS, Pereira KAS, de Brito WB, Torres MKDS, Lopes JDC, dos Santos EF, da Costa FP, de Sarges KML, Cantanhede MHD, de Brito MTFM, da Silva ALS, Leite MDM, Viana MDNDSDA, Rodrigues FBB, da Silva R, Viana GMR, Chaves TDSS, Veríssimo ADOL, Carvalho MDS, Henriques DF, dos Santos CP, Nunes JAL, Costa IB, Amoras EDSG, Lima SS, Cayres-Vallinoto IMV, Brasil-Costa I, Quaresma JAS, Falcão LFM, dos Santos EJM, Vallinoto ACR. Polymorphisms in the MBL2 gene are associated with the plasma levels of MBL and the cytokines IL-6 and TNF-α in severe COVID-19. Front Immunol 2023; 14:1151058. [PMID: 37138871 PMCID: PMC10149935 DOI: 10.3389/fimmu.2023.1151058] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/29/2023] [Indexed: 05/05/2023] Open
Abstract
Introduction Mannose-binding lectin (MBL) promotes opsonization, favoring phagocytosis and activation of the complement system in response to different microorganisms, and may influence the synthesis of inflammatory cytokines. This study investigated the association of MBL2 gene polymorphisms with the plasma levels of MBL and inflammatory cytokines in COVID-19. Methods Blood samples from 385 individuals (208 with acute COVID-19 and 117 post-COVID-19) were subjected to real-time PCR genotyping. Plasma measurements of MBL and cytokines were performed by enzyme-linked immunosorbent assay and flow cytometry, respectively. Results The frequencies of the polymorphic MBL2 genotype (OO) and allele (O) were higher in patients with severe COVID-19 (p< 0.05). The polymorphic genotypes (AO and OO) were associated with lower MBL levels (p< 0.05). IL-6 and TNF-α were higher in patients with low MBL and severe COVID-19 (p< 0.05). No association of polymorphisms, MBL levels, or cytokine levels with long COVID was observed. Discussion The results suggest that, besides MBL2 polymorphisms promoting a reduction in MBL levels and therefore in its function, they may also contribute to the development of a more intense inflammatory process responsible for the severity of COVID-19.
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Affiliation(s)
- Maria Alice Freitas Queiroz
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- *Correspondence: Maria Alice Freitas Queiroz,
| | - Angélica Menezes Santiago
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Virology, Evandro Chagas Institute, Department of Science, Technology, Innovation and Strategic Health Inputs, Ministry of Health of Brazil, Ananindeua, Brazil
| | - Wandrey Roberto dos Santos Brito
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
| | - Keise Adrielle Santos Pereira
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
| | - William Botelho de Brito
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Virology, Evandro Chagas Institute, Department of Science, Technology, Innovation and Strategic Health Inputs, Ministry of Health of Brazil, Ananindeua, Brazil
| | - Maria Karoliny da Silva Torres
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
| | - Jeferson da Costa Lopes
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
| | - Erika Ferreira dos Santos
- Graduate Program in Biology of Infectious and Parasitic Agents, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Laboratory of Genetics of Complex Diseases, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Flávia Póvoa da Costa
- Graduate Program in Biology of Infectious and Parasitic Agents, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Laboratory of Genetics of Complex Diseases, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Kevin Matheus Lima de Sarges
- Graduate Program in Biology of Infectious and Parasitic Agents, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Laboratory of Genetics of Complex Diseases, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Marcos Henrique Damasceno Cantanhede
- Graduate Program in Biology of Infectious and Parasitic Agents, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Laboratory of Genetics of Complex Diseases, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | | | | | - Mauro de Meira Leite
- Laboratory of Genetics of Complex Diseases, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Maria de Nazaré do Socorro de Almeida Viana
- Graduate Program in Biology of Infectious and Parasitic Agents, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Laboratory of Genetics of Complex Diseases, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Fabíola Brasil Barbosa Rodrigues
- Graduate Program in Biology of Infectious and Parasitic Agents, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Laboratory of Genetics of Complex Diseases, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Rosilene da Silva
- Graduate Program in Biology of Infectious and Parasitic Agents, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Laboratory of Genetics of Complex Diseases, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Giselle Maria Rachid Viana
- Laboratory of Basic Research in Malaria, Parasitology Section, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Brazil
| | - Tânia do Socorro Souza Chaves
- Laboratory of Basic Research in Malaria, Parasitology Section, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Ananindeua, Brazil
- School of Medicine, Institute of Medical Sciences, Federal University of Pará, Pará, Brazil
| | | | | | - Daniele Freitas Henriques
- Laboratory of Immunology, Section of Virology, Instituto Evandro Chagas, Health and Environment Arbovirology and Hemorrhagic Fevers Section, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ananindeua, Brazil
| | - Carla Pinheiro dos Santos
- Laboratory of Immunology, Section of Virology, Instituto Evandro Chagas, Health and Environment Arbovirology and Hemorrhagic Fevers Section, Evandro Chagas Institute, Health and Environment Surveillance Secretariat, Ananindeua, Brazil
| | - Juliana Abreu Lima Nunes
- Laboratory of Immunology, Section of Virology, Instituto Evandro Chagas, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Brazilian Ministry of Health, Ananindeua, Brazil
| | - Iran Barros Costa
- Graduate Program in Virology, Evandro Chagas Institute, Department of Science, Technology, Innovation and Strategic Health Inputs, Ministry of Health of Brazil, Ananindeua, Brazil
- Laboratory of Immunology, Section of Virology, Instituto Evandro Chagas, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Brazilian Ministry of Health, Ananindeua, Brazil
| | | | - Sandra Souza Lima
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
| | - Izaura Maria Vieira Cayres-Vallinoto
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
| | - Igor Brasil-Costa
- Graduate Program in Virology, Evandro Chagas Institute, Department of Science, Technology, Innovation and Strategic Health Inputs, Ministry of Health of Brazil, Ananindeua, Brazil
- Laboratory of Immunology, Section of Virology, Instituto Evandro Chagas, Health and Environment Surveillance Secretariat, Brazilian Ministry of Health, Brazilian Ministry of Health, Ananindeua, Brazil
| | | | | | - Eduardo José Melo dos Santos
- Graduate Program in Biology of Infectious and Parasitic Agents, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Laboratory of Genetics of Complex Diseases, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Antonio Carlos Rosário Vallinoto
- Laboratory of Virology, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Graduate Program in Biology of Infectious and Parasitic Agents, Institute of Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
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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
- grid.31143.340000 0001 2168 4024Research Laboratory in Oral Biology and Biotechnology, Faculty of Dental Medicine, Mohammed V University in Rabat, Rabat, Morocco
| | - Hayat Caidi
- grid.416738.f0000 0001 2163 0069NARST Surveillance Unit, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Khalid Sadki
- grid.31143.340000 0001 2168 4024Research Laboratory in Oral Biology and Biotechnology, Faculty of Dental Medicine, Mohammed V University in Rabat, Rabat, Morocco
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Dieter C, de Almeida Brondani L, Lemos NE, Schaeffer AF, Zanotto C, Ramos DT, Girardi E, Pellenz FM, Camargo JL, Moresco KS, da Silva LL, Aubin MR, de Oliveira MS, Rech TH, Canani LH, Gerchman F, Leitão CB, Crispim D. Polymorphisms in ACE1, TMPRSS2, IFIH1, IFNAR2, and TYK2 Genes Are Associated with Worse Clinical Outcomes in COVID-19. Genes (Basel) 2022; 14:genes14010029. [PMID: 36672770 PMCID: PMC9858252 DOI: 10.3390/genes14010029] [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: 10/28/2022] [Revised: 11/29/2022] [Accepted: 12/10/2022] [Indexed: 12/25/2022] Open
Abstract
Although advanced age, male sex, and some comorbidities impact the clinical course of COVID-19, these factors only partially explain the inter-individual variability in disease severity. Some studies have shown that genetic polymorphisms contribute to COVID-19 severity; however, the results are inconclusive. Thus, we investigated the association between polymorphisms in ACE1, ACE2, DPP9, IFIH1, IFNAR2, IFNL4, TLR3, TMPRSS2, and TYK2 and the clinical course of COVID-19. A total of 694 patients with COVID-19 were categorized as: (1) ward inpatients (moderate symptoms) or patients admitted at the intensive care unit (ICU; severe symptoms); and (2) survivors or non-survivors. In females, the rs1990760/IFIH1 T/T genotype was associated with risk of ICU admission and death. Moreover, the rs1799752/ACE1 Ins and rs12329760/TMPRSS2 T alleles were associated with risk of ICU admission. In non-white patients, the rs2236757/IFNAR2 A/A genotype was associated with risk of ICU admission, while the rs1799752/ACE1 Ins/Ins genotype, rs2236757/IFNAR2 A/A genotype, and rs12329760/TMPRSS2 T allele were associated with risk of death. Moreover, some of the analyzed polymorphisms interact in the risk of worse COVID-19 outcomes. In conclusion, this study shows an association of rs1799752/ACE1, rs1990760/IFIH1, rs2236757/IFNAR2, rs12329760/TMPRSS2, and rs2304256/TYK2 polymorphisms with worse COVID-19 outcomes, especially among female and non-white patients.
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Affiliation(s)
- Cristine Dieter
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
| | - Leticia de Almeida Brondani
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Natália Emerim Lemos
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Ariell Freires Schaeffer
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
| | - Caroline Zanotto
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Denise Taurino Ramos
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Eliandra Girardi
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Felipe Mateus Pellenz
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
| | - Joiza Lins Camargo
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
- Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Diabetes and Metabolism Group, Centro de Pesquisa Clínica, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Karla Suzana Moresco
- Campus Realeza, Universidade Federal da Fronteira Sul, Realeza 85770-000, PR, Brazil
| | - Lucas Lima da Silva
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Mariana Rauback Aubin
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Mayara Souza de Oliveira
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
| | - Tatiana Helena Rech
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
- Diabetes and Metabolism Group, Centro de Pesquisa Clínica, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Luís Henrique Canani
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
- Diabetes and Metabolism Group, Centro de Pesquisa Clínica, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Fernando Gerchman
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
- Diabetes and Metabolism Group, Centro de Pesquisa Clínica, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Cristiane Bauermann Leitão
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
- Diabetes and Metabolism Group, Centro de Pesquisa Clínica, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
| | - Daisy Crispim
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Post-Graduate Program in Medical Sciences, Endocrinology, Department of Internal Medicine, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
- Diabetes and Metabolism Group, Centro de Pesquisa Clínica, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, RS, Brazil
- Correspondence:
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Nekrasova LA, Shmakova AA, Samokhodskaya LM, Kirillova KI, Stoyanova SS, Mershina EA, Nazarova GB, Rubina KA, Semina EV, Kamalov AA. The Association of PLAUR Genotype and Soluble suPAR Serum Level with COVID-19-Related Lung Damage Severity. Int J Mol Sci 2022; 23:ijms232416210. [PMID: 36555850 PMCID: PMC9785175 DOI: 10.3390/ijms232416210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Uncovering the risk factors for acute respiratory disease coronavirus 2019 (COVID-19) severity may help to provide a valuable tool for early patient stratification and proper treatment implementation, improving the patient outcome and lowering the burden on the healthcare system. Here we report the results of a single-center retrospective cohort study on 151 severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-infected symptomatic hospitalized adult patients. We assessed the association of several blood test measurements, soluble urokinase receptor (uPAR) serum level and specific single nucleotide polymorphisms of ACE (I/D), NOS3 (rs2070744, rs1799983), SERPINE1 (rs1799768), PLAU (rs2227564) and PLAUR (rs344781, rs2302524) genes, with the disease severity classified by the percentage of lung involvement on computerized tomography scans. Our findings reveal that the T/C genotype of PLAUR rs2302524 was independently associated with a less severe lung damage (odds ratio 0.258 [0.071-0.811]). Along with high C-reactive protein, fibrinogen and soluble uPAR serum levels turned out to be independently associated with more severe lung damage in COVID-19 patients. The identified factors may be further employed as predictors of a possibly severe COVID-19 clinical course.
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Affiliation(s)
- Ludmila A. Nekrasova
- Medical Scientific and Educational Centre, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Anna A. Shmakova
- Koltzov Institute of Developmental Biology, 117334 Moscow, Russia
| | - Larisa M. Samokhodskaya
- Medical Scientific and Educational Centre, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Karina I. Kirillova
- Medical Scientific and Educational Centre, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Simona S. Stoyanova
- Medical Scientific and Educational Centre, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Elena A. Mershina
- Medical Scientific and Educational Centre, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Galina B. Nazarova
- Medical Scientific and Educational Centre, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Kseniya A. Rubina
- Faculty of Medicine, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Ekaterina V. Semina
- Medical Scientific and Educational Centre, Lomonosov Moscow State University, 119192 Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, 119192 Moscow, Russia
- Institute of Experimental Cardiology, National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia
- Correspondence:
| | - Armais A. Kamalov
- Medical Scientific and Educational Centre, Lomonosov Moscow State University, 119192 Moscow, Russia
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Srivastava A, Hollenbach JA. The immunogenetics of COVID-19. Immunogenetics 2022; 75:309-320. [PMID: 36534127 PMCID: PMC9762652 DOI: 10.1007/s00251-022-01284-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/19/2022] [Indexed: 12/23/2022]
Abstract
The worldwide coronavirus disease 2019 pandemic was sparked by the severe acute respiratory syndrome caused by coronavirus 2 (SARS-CoV-2) that first surfaced in December 2019 (COVID-19). The effects of COVID-19 differ substantially not just between patients individually but also between populations with different ancestries. In humans, the human leukocyte antigen (HLA) system coordinates immune regulation. Since HLA molecules are a major component of antigen-presenting pathway, they play an important role in determining susceptibility to infectious disease. It is likely that differential susceptibility to SARS-CoV-2 infection and/or disease course in COVID-19 in different individuals could be influenced by the variations in the HLA genes which are associated with various immune responses to SARS-CoV-2. A growing number of studies have identified a connection between HLA variation and diverse COVID-19 outcomes. Here, we review research investigating the impact of HLA on individual responses to SARS-CoV-2 infection and/or progression, also discussing the significance of MHC-related immunological patterns and its use in vaccine design.
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Affiliation(s)
- Anshika Srivastava
- grid.266102.10000 0001 2297 6811University of California San Francisco, San Francisco, CA USA
| | - Jill A. Hollenbach
- grid.266102.10000 0001 2297 6811University of California San Francisco, San Francisco, CA USA
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40
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Rabaan AA, Mutair AA, Aljeldah M, Shammari BRA, Sulaiman T, Alshukairi AN, Alfaresi M, Al-Jishi JM, Al Bati NA, Al-Mozaini MA, Bshabshe AA, Almatouq JA, Abuzaid AA, Alfaraj AH, Al-Adsani W, Alabdullah M, Alwarthan S, Alsalman F, Alwashmi ASS, Alhumaid S. Genetic Variants and Protective Immunity against SARS-CoV-2. Genes (Basel) 2022; 13:genes13122355. [PMID: 36553622 PMCID: PMC9778397 DOI: 10.3390/genes13122355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/16/2022] Open
Abstract
The novel coronavirus-19 (SARS-CoV-2), has infected numerous individuals worldwide, resulting in millions of fatalities. The pandemic spread with high mortality rates in multiple waves, leaving others with moderate to severe symptoms. Co-morbidity variables, including hypertension, diabetes, and immunosuppression, have exacerbated the severity of COVID-19. In addition, numerous efforts have been made to comprehend the pathogenic and host variables that contribute to COVID-19 susceptibility and pathogenesis. One of these endeavours is understanding the host genetic factors predisposing an individual to COVID-19. Genome-Wide Association Studies (GWAS) have demonstrated the host predisposition factors in different populations. These factors are involved in the appropriate immune response, their imbalance influences susceptibility or resistance to viral infection. This review investigated the host genetic components implicated at the various stages of viral pathogenesis, including viral entry, pathophysiological alterations, and immunological responses. In addition, the recent and most updated genetic variations associated with multiple host factors affecting COVID-19 pathogenesis are described in the study.
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Affiliation(s)
- Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
- Correspondence:
| | - Abbas Al Mutair
- Research Center, Almoosa Specialist Hospital, Al-Ahsa 36342, Saudi Arabia
- College of Nursing, Princess Norah Bint Abdulrahman University, Riyadh 11564, Saudi Arabia
- School of Nursing, Wollongong University, Wollongong, NSW 2522, Australia
- Nursing Department, Prince Sultan Military College of Health Sciences, Dhahran 33048, Saudi Arabia
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Basim R. Al Shammari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Tarek Sulaiman
- Infectious Diseases Section, Medical Specialties Department, King Fahad Medical City, Riyadh 12231, Saudi Arabia
| | - Abeer N. Alshukairi
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah 21499, Saudi Arabia
| | - Mubarak Alfaresi
- Department of Pathology and Laboratory Medicine, Sheikh Khalifa General Hospital, Umm Al Quwain 499, United Arab Emirates
- Department of Pathology, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai 505055, United Arab Emirates
| | - Jumana M. Al-Jishi
- Internal Medicine Department, Qatif Central Hospital, Qatif 35342, Saudi Arabia
| | - Neda A. Al Bati
- Medical and Clinical Affairs, Rural Health Network, Eastern Health Cluster, Dammam 31444, Saudi Arabia
| | - Maha A. Al-Mozaini
- Immunocompromised Host Research Section, Department of Infection and Immunity, King Faisal, Specialist Hospital and Research Centre, Riyadh 11564, Saudi Arabia
| | - Ali Al Bshabshe
- Adult Critical Care Department of Medicine, Division of Adult Critical Care, College of Medicine, King Khalid University, Abha 62561, Saudi Arabia
| | - Jenan A. Almatouq
- Department of Clinical Laboratory Sciences, Mohammed Al-Mana College of Health Sciences, Dammam 34222, Saudi Arabia
| | - Abdulmonem A. Abuzaid
- Medical Microbiology Department, Security Forces Hospital Programme, Dammam 32314, Saudi Arabia
| | - Amal H. Alfaraj
- Pediatric Department, Abqaiq General Hospital, First Eastern Health Cluster, Abqaiq 33261, Saudi Arabia
| | - Wasl Al-Adsani
- Department of Medicine, Infectious Diseases Hospital, Kuwait City 63537, Kuwait
- Department of Infectious Diseases, Hampton Veterans Administration Medical Center, Hampton, VA 23667, USA
| | - Mohammed Alabdullah
- Department of Infectious Diseases, Almoosa Specialist Hospital, Al Mubarraz 36342, Saudi Arabia
| | - Sara Alwarthan
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Fatimah Alsalman
- Department of Emergency Medicine, Oyun City Hospital, Al-Ahsa 36312, Saudi Arabia
| | - Ameen S. S. Alwashmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Saad Alhumaid
- Administration of Pharmaceutical Care, Al-Ahsa Health Cluster, Ministry of Health, Al-Ahsa 31982, Saudi Arabia
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Chen LC, Nersisyan S, Wu CJ, Chang CM, Tonevitsky A, Guo CL, Chang WC. On the peptide binding affinity changes in population-specific HLA repertoires to the SARS-CoV-2 variants Delta and Omicron. J Autoimmun 2022; 133:102952. [PMID: 36427410 PMCID: PMC9650568 DOI: 10.1016/j.jaut.2022.102952] [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: 08/24/2022] [Revised: 11/05/2022] [Accepted: 11/06/2022] [Indexed: 11/13/2022]
Abstract
OBJECTIVE To investigate the changes of Spike protein-HLA binding affinity profiles between the Wuhan strain and two dominant variants, the Delta and the Omicron strains, among the Taiwanese, the British and the Russian populations. METHODS The HLA frequencies and the HLA-peptide binding affinity profiles in the T-CoV database were combined to conduct the study. We focused on the public alleles in the three populations (HLA-A, HLA-B, HLA-C, HLA-DRB1, and/or HLA-DPA1/DPB1 alleles) and the altered peptides of the spike protein (compared to the Wuhan strain) in the Delta G/478K·V1 (B.1.617.2 + AY.1 + AY.2) and the Omicron (BA.1) strains. RESULTS For the Delta strain, tight bindings of the altered peptides to the HLA alleles decrease in all three populations and almost vanish in the Taiwanese population. For the Omicron strain, tight bindings are mostly preserved for both HLA classes and in the Taiwanese and the British populations, with a slight reduction in HLA class II in the Taiwanese (1.4%), while the Russian population preserves a relatively high fraction of tight bindings for both HLA classes. CONCLUSION We comprehensively reported the changes in the HLA-associated SARS-CoV-2 Spike protein peptide binding profiles among the Taiwanese, the British, and the Russian populations. Further studies are needed to understand the immunological mechanisms and the clinical value of our findings.
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Affiliation(s)
- Lu-Chun Chen
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Institute of Molecular Biology, The National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia,Armenian Bioinformatics Institute (ABI), Yerevan, Armenia
| | - Chang-Jiun Wu
- Department of Genomic Medicine, University of Texas, MD Anderson Cancer Center. Houston Texas, USA
| | - Che-Mai Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Chin-Lin Guo
- Institute of Physics, Academia Sinica, Taipei, Taiwan,Corresponding author. Institute of Physics, Academia Sinica, No. 128, Sec. 2, Academia Rd., Nangang Dist., Taipei City 115201, Taiwan. Tel.: (886) 988545414
| | - Wei-Chiao Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan,Department of Medical Education and Research, Integrative Research Center for Critical Care, Wan fang Hospital, Taipei Medical University, Taipei, Taiwan,Master Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan,Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan,Corresponding author. Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, No. 250 Wuxing St., Xinyi Dist., Taipei City 110, Taiwan. Tel.: (886) 928121979
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Samlali K, Thornbury M, Venter A. Community-led risk analysis of direct-to-consumer whole-genome sequencing. Biochem Cell Biol 2022; 100:499-509. [PMID: 35939839 DOI: 10.1139/bcb-2021-0506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Direct-to-consumer (DTC) genetic testing is cheaper and more accessible than ever before; however, the intention to combine, reuse, and resell this genetic information as powerful data sets is generally hidden from the consumer. This financial gain is creating a competitive DTC market, reducing the price of whole-genome sequencing (WGS) to under 300 USD. Entering this transition from single-nucleotide polymorphism-based DTC testing to WGS DTC testing, individuals looking for access to their whole-genomic information face new privacy and security risks. Differences between WGS and other methods of consumer genetic tests are left unexplored by regulation, leading to the application of legal data anonymization methods on whole-genome data, and questionable consent methods. Large representative genomic data sets are important for research and improve the standard of medicine and personalized care. However, these data can also be used by market players, law enforcement, and governments for surveillance, population analyses, marketing purposes, and discrimination. Here, we present a summary of the state of WGS DTC genetic testing and its current regulation, through a community-based lens to expose dual-use risks in consumer-facing biotechnologies.
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Affiliation(s)
- Kenza Samlali
- BricoBio Community Biology Lab, Montréal, QC, Canada.,Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, Canada.,Department of Electrical and Computer Engineering, Concordia University, Montréal, QC, Canada
| | - Mackenzie Thornbury
- BricoBio Community Biology Lab, Montréal, QC, Canada.,Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, Canada.,Department of Biology, Concordia University, Montréal, QC, Canada
| | - Andrei Venter
- BricoBio Community Biology Lab, Montréal, QC, Canada
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Gupta K, Kaur G, Pathak T, Banerjee I. Systematic review and meta-analysis of human genetic variants contributing to COVID-19 susceptibility and severity. Gene 2022; 844:146790. [PMID: 35987511 PMCID: PMC9384365 DOI: 10.1016/j.gene.2022.146790] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/25/2022] [Accepted: 08/05/2022] [Indexed: 12/12/2022]
Abstract
The COVID-19 pandemic has spawned global health crisis of unprecedented magnitude, claiming millions of lives and pushing healthcare systems in many countries to the brink. Among several factors that contribute to an increased risk of COVID-19 and progression to exacerbated manifestations, host genetic landscape is increasingly being recognized as a critical determinant of susceptibility/resistance to infection and a prognosticator of clinical outcomes in infected individuals. Recently, several case-control association studies investigated the influence of human gene variants on COVID-19 susceptibility and severity to identify the culpable mutations. However, a comprehensive synthesis of the recent advances in COVID-19 host genetics research was lacking, and the inconsistent findings of the association studies required reliable evaluation of the strength of association with greater statistical power. In this study, we embarked on a systematic search of all possible reports of genetic association with COVID-19 till April 07, 2022, and performed meta-analyses of all the genetic polymorphisms that were examined in at least three studies. After identifying a total of 84 studies that investigated the association of 130 polymorphisms in 61 genes, we performed meta-analyses of all the eligible studies. Seven genetic polymorphisms involving 15,550 cases and 444,007 controls were explored for association with COVID-19 susceptibility, of which, ACE1 I/D rs4646994/rs1799752, APOE rs429358, CCR5 rs333, and IFITM3 rs12252 showed increased risk of infection. Meta-analyses of 11 gene variants involving 6702 patients with severe COVID-19 and 8640 infected individuals with non-severe manifestations revealed statistically significant association of ACE2 rs2285666, ACE2 rs2106809, ACE2 rs2074192, AGTR1 rs5186, and TNFA rs1800629 with COVID-19 severity. Overall, our study presents a synthesis of evidence on all the genetic determinants implicated in COVID-19 to date, and provides evidence of correlation between the above polymorphisms with COVID-19 susceptibility and severity.
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Affiliation(s)
| | | | | | - Indranil Banerjee
- Cellular Virology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali (IISER Mohali), Sector 81, S.A.S Nagar, Mohali 140306, India.
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44
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Li P, Ke Y, Shen W, Shi S, Wang Y, Lin K, Guo X, Wang C, Zhang Y, Zhao Z. Targeted screening of genetic associations with COVID-19 susceptibility and severity. Front Genet 2022; 13:1073880. [PMID: 36531218 PMCID: PMC9747945 DOI: 10.3389/fgene.2022.1073880] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/18/2022] [Indexed: 07/26/2023] Open
Abstract
The COVID-19 pandemic has resulted in great morbidity and mortality worldwide and human genetic factors have been implicated in the susceptibility and severity of COVID-19. However, few replicate researches have been performed, and studies on associated genes mainly focused on genic regions while regulatory regions were a lack of in-depth dissection. Here, based on previously reported associated variants and genes, we designed a capture panel covering 1,238 candidate variants and 25 regulatory regions of 19 candidate genes and targeted-sequenced 96 mild and 145 severe COVID-19 patients. Genetic association analysis was conducted between mild and severe COVID-19 patients, between all COVID-19 patients and general population, or between severe COVID-19 patients and general population. A total of 49 variants were confirmed to be associated with susceptibility or severity of COVID-19 (p < 0.05), corresponding to 18 independent loci. Specifically, rs1799964 in the promoter of inflammation-related gene TNF, rs9975538 in the intron of interferon receptor gene IFNAR2, rs429358 in the exon of APOE, rs1886814 in the intron of FOXP4-AS1 and a list of variants in the widely reported 3p21.31 and ABO gene were confirmed. It is worth noting that, for the confirmed variants, the phenotypes of the cases and controls were highly consistent between our study and previous reports, and the confirmed variants identified between mild and severe patients were quite different from those identified between patients and general population, suggesting the genetic basis of susceptibility and severity of SARS-CoV-2 infection might be quite different. Moreover, we newly identified 67 significant associated variants in the 12 regulatory regions of 11 candidate genes (p < 0.05). Further annotation by RegulomeDB database and GTEx eQTL data filtered out two variants (rs11246060 and rs28655829) in the enhancer of broad-spectrum antiviral gene IFITM3 that might affect disease severity by regulating the gene expression. Collectively, we confirmed a list of previously reported variants and identified novel regulatory variants associated with susceptibility and severity of COVID-19, which might provide biological and clinical insights into COVID-19 pathogenesis and treatment.
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Affiliation(s)
- Ping Li
- Beijing Institute of Biotechnology, Beijing, China
| | - Yuehua Ke
- Center for Disease Control and Prevention of PLA, Beijing, China
| | - Wenlong Shen
- Beijing Institute of Biotechnology, Beijing, China
| | - Shu Shi
- Beijing Institute of Biotechnology, Beijing, China
| | - Yahao Wang
- Beijing Institute of Biotechnology, Beijing, China
| | - Kailin Lin
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Xinjie Guo
- Beijing Institute of Biotechnology, Beijing, China
| | - Changjun Wang
- Center for Disease Control and Prevention of PLA, Beijing, China
| | - Yan Zhang
- Beijing Institute of Biotechnology, Beijing, China
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, Beijing, China
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45
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Beheshti Shirazi SS, Sakhaee F, Sotoodehnejadnematalahi F, Zamani MS, Ahmadi I, Anvari E, Fateh A. rs12329760 Polymorphism in Transmembrane Serine Protease 2 Gene and Risk of Coronavirus Disease 2019 Mortality. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7841969. [PMID: 36457338 PMCID: PMC9708353 DOI: 10.1155/2022/7841969] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/04/2022] [Accepted: 11/12/2022] [Indexed: 08/29/2023]
Abstract
The protease produced by the transmembrane serine protease 2 (TMPRSS2) gene enhances viral infections and has been linked to severe acute respiratory syndrome coronavirus 2 pathogenesis. Therefore, this study evaluated the association between TMPRSS2 and coronavirus disease 2019 (COVID-19) mortality. TMPRSS2 rs12329760 polymorphism was genotyped using the tetraprimer amplification refractory mutation system-polymerase chain reaction method in 592 dead and 693 improved patients. In the current study, the frequency of TMPRSS2 rs12329760 CC than TT genotypes was significantly lower in improved patients than in dead patients. According to the findings of the multivariate logistic regression test, higher levels of mean age, creatinine, erythrocyte sedimentation rate, C-reactive protein, aspartate aminotransferase, lower levels of 25-hydroxyvitamin D, uric acid, and real-time PCR Ct values and TMPRSS2 rs12329760 CC genotype were observed to be associated with increased COVID-19 mortality rates. In conclusion, the TMPRSS2 rs12329760 CC genotype was a polymorphism linked to a significantly higher incidence of severe COVID-19. Further studies are required to corroborate the obtained findings.
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Affiliation(s)
| | - 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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Abolhassani H, Delavari S, Landegren N, Shokri S, Bastard P, Du L, Zuo F, Hajebi R, Abolnezhadian F, Iranparast S, Modaresi M, Vosughimotlagh A, Salami F, Aranda-Guillén M, Cobat A, Marcotte H, Zhang SY, Zhang Q, Rezaei N, Casanova JL, Kämpe O, Hammarström L, Pan-Hammarström Q. Genetic and immunologic evaluation of children with inborn errors of immunity and severe or critical COVID-19. J Allergy Clin Immunol 2022; 150:1059-1073. [PMID: 36113674 PMCID: PMC9472457 DOI: 10.1016/j.jaci.2022.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Most severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected individuals are asymptomatic or only exhibit mild disease. In about 10% of cases, the infection leads to hypoxemic pneumonia, although it is much more rare in children. OBJECTIVE We evaluated 31 young patients aged 0.5 to 19 years who had preexisting inborn errors of immunity (IEI) but lacked a molecular diagnosis and were later diagnosed with coronavirus disease 2019 (COVID-19) complications. METHODS Genetic evaluation by whole-exome sequencing was performed in all patients. SARS-CoV-2-specific antibodies, autoantibodies against type I IFN (IFN-I), and inflammatory factors in plasma were measured. We also reviewed COVID-19 disease severity/outcome in reported IEI patients. RESULTS A potential genetic cause of the IEI was identified in 28 patients (90.3%), including mutations that may affect IFN signaling, T- and B-cell function, the inflammasome, and the complement system. From tested patients 65.5% had detectable virus-specific antibodies, and 6.8% had autoantibodies neutralizing IFN-I. Five patients (16.1%) fulfilled the diagnostic criteria of multisystem inflammatory syndrome in children. Eleven patients (35.4%) died of COVID-19 complications. All together, at least 381 IEI children with COVID-19 have been reported in the literature to date. Although many patients with asymptomatic or mild disease may not have been reported, severe presentation of COVID-19 was observed in 23.6% of the published cases, and the mortality rate was 8.7%. CONCLUSIONS Young patients with preexisting IEI may have higher mortality than children without IEI when infected with SARS-CoV-2. Elucidating the genetic basis of IEI patients with severe/critical COVID-19 may help to develop better strategies for prevention and treatment of severe COVID-19 disease and complications in pediatric patients.
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Affiliation(s)
- Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Huddinge, Sweden; Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Samaneh Delavari
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Nils Landegren
- Centre for Molecular Medicine, Department of Medicine (Solna), Karolinska Institutet, Stockholm, Sweden; Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Sima Shokri
- Department of Pediatrics, School of Medicine, Hazrat-e Rasool General Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Paul Bastard
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Necker Hospital for Sick Children, Paris, France; University of Paris, Imagine Institute, Paris, France
| | - Likun Du
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Huddinge, Sweden
| | - Fanglei Zuo
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Huddinge, Sweden
| | - Reza Hajebi
- Department of General Surgery, School of Medicine, Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Farhad Abolnezhadian
- Department of Pediatrics, Abuzar Children's Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sara Iranparast
- Department of Immunology, Faculty of Medical Sciences, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammadreza Modaresi
- Division of Pediatrics Pulmonary Disease, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Vosughimotlagh
- Department of Pediatrics, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Fereshte Salami
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maribel Aranda-Guillén
- Centre for Molecular Medicine, Department of Medicine (Solna), Karolinska Institutet, Stockholm, Sweden
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Necker Hospital for Sick Children, Paris, France; University of Paris, Imagine Institute, Paris, France
| | - Harold Marcotte
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Huddinge, Sweden
| | - Shen-Ying Zhang
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Necker Hospital for Sick Children, Paris, France; University of Paris, Imagine Institute, Paris, France
| | - Qian Zhang
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Necker Hospital for Sick Children, Paris, France
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Necker Hospital for Sick Children, Paris, France; University of Paris, Imagine Institute, Paris, France; Howard Hughes Medical Institute, New York, NY
| | - Olle Kämpe
- Centre for Molecular Medicine, Department of Medicine (Solna), Karolinska Institutet, Stockholm, Sweden; Department of Endocrinology, Metabolism and Diabetes, Karolinska University Hospital, Stockholm, Sweden
| | - Lennart Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Huddinge, Sweden.
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Huddinge, Sweden.
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Vázquez-Coto D, Albaiceta GM, Amado-Rodríguez L, Clemente MG, Cuesta-Llavona E, Gómez J, Coto E. Common mitochondrial haplogroups as modifiers of the onset-age for critical COVID-19. Mitochondrion 2022; 67:1-5. [PMID: 36115538 PMCID: PMC9474411 DOI: 10.1016/j.mito.2022.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/09/2022] [Indexed: 02/08/2023]
Abstract
As a key regulator of innate immunity, mitochondrial function is essential to maintain antiviral activities. Common mitochondrial DNA variants (haplogroups) have been associated with different physiological capacities and the nrisk of developing several diseases. Haplogroup H was associated with increased survival among sepsis patients, and lower risk of progression toward AIDS in HIV infected and lower manifestation of severe manifestation of herpex virus disease. We studied 316 Spanish with critical COVID-19, and found that the 7028C (haplogroup H) was protective among patients with early-onset disease (≤65 vs > 65 years, p = 0.01), while the ancestral 16223T was a risk factor for early-onset critical COVID-19 (OR = 3.36, 95 %CI = 1.49-7.54). Our work suggested that common mitochondrial variants may serve as predictors of COVID-19 severity. Additional studies to confirm this effect from other populations are of special interest.
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Affiliation(s)
| | - Guillermo M. Albaiceta
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central Asturias, Oviedo, Spain,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain,Universidad de Oviedo, Oviedo, Spain,CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain,Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
| | - Laura Amado-Rodríguez
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central Asturias, Oviedo, Spain,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain,Universidad de Oviedo, Oviedo, Spain,CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain,Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
| | - Marta G. Clemente
- Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain,Neumología, Hospital Universitario Central Asturias, Oviedo, Spain
| | - Elías Cuesta-Llavona
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain
| | - Juan Gómez
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain,CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Eliecer Coto
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain,Universidad de Oviedo, Oviedo, Spain,Corresponding author at: Genética Molecular-HUCA, Oviedo, Spain
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48
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Gustiananda M, Julietta V, Hermawan A, Febriana GG, Hermantara R, Kristiani L, Sidhartha E, Sutejo R, Agustriawan D, Andarini S, Parikesit AA. Immunoinformatics Identification of the Conserved and Cross-Reactive T-Cell Epitopes of SARS-CoV-2 with Human Common Cold Coronaviruses, SARS-CoV, MERS-CoV and Live Attenuated Vaccines Presented by HLA Alleles of Indonesian Population. Viruses 2022; 14:v14112328. [PMID: 36366426 PMCID: PMC9699331 DOI: 10.3390/v14112328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/13/2022] [Accepted: 10/16/2022] [Indexed: 02/01/2023] Open
Abstract
Reports on T-cell cross-reactivity against SARS-CoV-2 epitopes in unexposed individuals have been linked with prior exposure to the human common cold coronaviruses (HCCCs). Several studies suggested that cross-reactive T-cells response to live attenuated vaccines (LAVs) such as BCG (Bacillus Calmette-Guérin), OPV (Oral Polio Vaccine), and MMR (measles, mumps, and rubella) can limit the development and severity of COVID-19. This study aims to identify potential cross-reactivity between SARS-CoV-2, HCCCs, and LAVs in the context of T-cell epitopes peptides presented by HLA (Human Leukocyte Antigen) alleles of the Indonesian population. SARS-CoV-2 derived T-cell epitopes were predicted using immunoinformatics tools and assessed for their conservancy, variability, and population coverage. Two fully conserved epitopes with 100% similarity and nine heterologous epitopes with identical T-cell receptor (TCR) contact residues were identified from the ORF1ab fragment of SARS-CoV-2 and all HCCCs. Cross-reactive epitopes from various proteins of SARS-CoV-2 and LAVs were also identified (15 epitopes from BCG, 7 epitopes from MMR, but none from OPV). A majority of the identified epitopes were observed to belong to ORF1ab, further suggesting the vital role of ORF1ab in the coronaviruses family and suggesting it as a candidate for a potential universal coronavirus vaccine that protects against severe disease by inducing cell mediated immunity.
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Affiliation(s)
- Marsia Gustiananda
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
- Correspondence:
| | - Vivi Julietta
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
| | - Angelika Hermawan
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
| | - Gabriella Gita Febriana
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
| | - Rio Hermantara
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
| | - Lidya Kristiani
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
| | - Elizabeth Sidhartha
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
| | - Richard Sutejo
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
| | - David Agustriawan
- Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
| | - Sita Andarini
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine University of Indonesia, Persahabatan Hospital, Jl. Persahabatan Raya 1, Jakarta 13230, Indonesia
| | - Arli Aditya Parikesit
- Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jl. Pulomas Barat Kav 88, Jakarta 13210, Indonesia
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49
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Nhung VP, Ton ND, Ngoc TTB, Thuong MTH, Hai NTT, Oanh KTP, Hien LTT, Thach PN, Hai NV, Ha NH. Host Genetic Risk Factors Associated with COVID-19 Susceptibility and Severity in Vietnam. Genes (Basel) 2022; 13:genes13101884. [PMID: 36292769 PMCID: PMC9601961 DOI: 10.3390/genes13101884] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 11/16/2022] Open
Abstract
Since the emergence and rapid transmission of SARS-CoV-2, numerous scientific reports have searched for the association of host genetic variants with COVID-19, but the data are mostly acquired from Europe. In the current work, we explored the link between host genes (SARS-CoV-2 entry and immune system related to COVID-19 sensitivity/severity) and ABO blood types with COVID-19 from whole-exome data of 200 COVID-19 patients and 100 controls in Vietnam. The O blood type was found to be a protective factor that weakens the worst outcomes of infected individuals. For SARS-CoV-2 susceptibility, rs2229207 (TC genotype, allele C) and rs17860118 (allele T) of IFNAR2 increased the risk of infection, but rs139940581 (CT genotype, allele T) of SLC6A20 reduced virus sensitivity. For COVID-19 progress, the frequencies of rs4622692 (TG genotype) and rs1048610 (TC genotype) of ADAM17 were significantly higher in the moderate group than in the severe/fatal group. The variant rs12329760 (AA genotype) of TMPRSS2 was significantly associated with asymptomatic/mild symptoms. Additionally, rs2304255 (CT genotype, allele T) of TYK2 and rs2277735 (AG genotype) of DPP9 were associated with severe/fatal outcomes. Studies on different populations will give better insights into the pathogenesis, which is ethnic-dependent, and thus decipher the genetic factor’s contribution to mechanisms that predispose people to being more vulnerable to COVID-19.
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Affiliation(s)
- Vu Phuong Nhung
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Nguyen Dang Ton
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Tran Thi Bich Ngoc
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Ma Thi Huyen Thuong
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Nguyen Thi Thanh Hai
- National Hospital for Tropical Disease, Kim Chung, Dong Anh, Hanoi 100000, Vietnam
- Department of Biochemistry, Hanoi Medical University, 1 Ton That Tung, Dong Da, Hanoi 100000, Vietnam
| | - Kim Thi Phuong Oanh
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Le Thi Thu Hien
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Pham Ngoc Thach
- National Hospital for Tropical Disease, Kim Chung, Dong Anh, Hanoi 100000, Vietnam
| | - Nong Van Hai
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
| | - Nguyen Hai Ha
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Faculty of Biotechnology, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi 100000, Vietnam
- Correspondence: ; Tel.: +84-385-368-368
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50
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Tziastoudi M, Cholevas C, Stefanidis I, Theoharides TC. Genetics of COVID-19 and myalgic encephalomyelitis/chronic fatigue syndrome: a systematic review. Ann Clin Transl Neurol 2022; 9:1838-1857. [PMID: 36204816 PMCID: PMC9639636 DOI: 10.1002/acn3.51631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 01/08/2023] Open
Abstract
COVID‐19 and ME/CFS present with some similar symptoms, especially physical and mental fatigue. In order to understand the basis of these similarities and the possibility of underlying common genetic components, we performed a systematic review of all published genetic association and cohort studies regarding COVID‐19 and ME/CFS and extracted the genes along with the genetic variants investigated. We then performed gene ontology and pathway analysis of those genes that gave significant results in the individual studies to yield functional annotations of the studied genes using protein analysis through evolutionary relationships (PANTHER) VERSION 17.0 software. Finally, we identified the common genetic components of these two conditions. Seventy‐one studies for COVID‐19 and 26 studies for ME/CFS were included in the systematic review in which the expression of 97 genes for COVID‐19 and 429 genes for ME/CFS were significantly affected. We found that ACE, HLA‐A, HLA‐C, HLA‐DQA1, HLA‐DRB1, and TYK2 are the common genes that gave significant results. The findings of the pathway analysis highlight the contribution of inflammation mediated by chemokine and cytokine signaling pathways, and the T cell activation and Toll receptor signaling pathways. Protein class analysis revealed the contribution of defense/immunity proteins, as well as protein‐modifying enzymes. Our results suggest that the pathogenesis of both syndromes could involve some immune dysfunction.
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Affiliation(s)
- Maria Tziastoudi
- Department of Nephrology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Christos Cholevas
- First Department of Ophthalmology, Faculty of Health Sciences, Aristotle University, AHEPA Hospital, Thessaloniki, Greece
| | - Ioannis Stefanidis
- Department of Nephrology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Theoharis C Theoharides
- Institute of Neuro-Immune Medicine, Nova Southeastern University, Clearwater, FL, USA.,Laboratory of Molecular Immunopharmacology and Drug Discovery, Department of Immunology, Tufts University School of Medicine, Boston, Massachusetts, USA.,School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA.,Departments of Internal Medicine and Psychiatry, Tufts University School of Medicine and Tufts Medical Center, Boston, Massachusetts, USA
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