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Wang M, Bo Z, Zhang C, Guo M, Wu Y, Zhang X. Deciphering the Genetic Variation: A Comparative Analysis of Parental and Attenuated Strains of the QXL87 Vaccine for Infectious Bronchitis. Animals (Basel) 2024; 14:1784. [PMID: 38929403 PMCID: PMC11200882 DOI: 10.3390/ani14121784] [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: 05/16/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The QXL87 live attenuated vaccine strain for infectious bronchitis represents the first approved QX type (GI-19 lineage) vaccine in China. This strain was derived from the parental strain CK/CH/JS/2010/12 through continuous passage in SPF chicken embryos. To elucidate the molecular mechanism behind its attenuation, whole-genome sequencing was conducted on both the parental and attenuated strains. Analysis revealed 145 nucleotide mutations in the attenuated strain, leading to 48 amino acid mutations in various proteins, including Nsp2 (26), Nsp3 (14), Nsp4 (1), S (4), 3a (1), E (1), and N (1). Additionally, a frameshift mutation caused by a single base insertion in the ORFX resulted in a six-amino-acid extension. Subsequent comparison of post-translational modification sites, protein structure, and protein-protein binding sites between the parental and attenuated strains identified three potential virulence genes: Nsp2, Nsp3, and S. The amino acid mutations in these proteins not only altered their conformation but also affected the distribution of post-translational modification sites and protein-protein interaction sites. Furthermore, three potential functional mutation sites-P106S, A352T, and L472F, all located in the Nsp2 protein-were identified through PROVEAN, PolyPhen, and I-Mutant. Overall, our findings suggest that Nsp2, Nsp3, and S proteins may play a role in modulating IBV pathogenicity, with a particular focus on the significance of the Nsp2 protein. This study contributes to our understanding of the molecular mechanisms underlying IBV attenuation and holds promise for the development of safer live attenuated IBV vaccines using reverse genetic approaches.
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Affiliation(s)
- Mengmeng Wang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
| | - Zongyi Bo
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Chengcheng Zhang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
| | - Mengjiao Guo
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
| | - Yantao Wu
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Xiaorong Zhang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.W.); (Z.B.); (C.Z.); (M.G.)
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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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Ramachandran B, Nadeem A, Mohanprasanth A, Saravanan M. Prediction of deleterious non-synonymous SNPs of TMPRSS2 protein combined with Molecular Dynamics Simulations and free energy analysis to identify the potential peptide substrates against SARS-CoV-2. J Biomol Struct Dyn 2024:1-15. [PMID: 38592189 DOI: 10.1080/07391102.2024.2330710] [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: 12/17/2023] [Accepted: 03/08/2024] [Indexed: 04/10/2024]
Abstract
Globally the SARS-CoV-2 viral infection demands for the new drugs, the TMPRSS2 target plays a vital role in facilitating the virus entry. The aim of the present study is to identify the potential peptide substrate from the Anti-viral database against TMPRSS2 of SARS-CoV-2. The compound screening and variation analysis were performed using molecular docking analysis and online tools such as PROVEAN and SNAP2 server, respectively. The re-docked crystal structure peptide substrate exhibits -128.151 kcal/mol whereas the RRKK peptide substrate shows -134.158 kcal/mol. Further, the selected compounds were proceeded with Molecular Dynamics Simulation, it explores the stability of the complex by revealing the hotspot residues (His296 and Ser441) were active for nucleophilic attack against TMPRSS2. The average Binding Free Energy values computed through MM/GBSA for RRKK, Camostat, and Crystal Structure were shown -69.9278 kcal/mol, -64.5983 kcal/mol, and -63.9755 kcal/mol, respectively against TMPRSS2. The 'rate of acylation' emerges as an indicator for RRKK's efficacy, it maintains the distance of 3.2 Å with Ser441 resembles, whilst its -NH backbone stabilizes at 2.5 Å 'Michaelis Complex' which leads to prevent the entry of SARS-CoV-2 to human cells. The sequence variation analysis explores that the V160 and G6 substitutions are essential to emphasize the uncover possibilities for the ongoing drug discovery research. Therefore, the identified peptide substrate found to be potent against SARS-CoV-2 and these results will be valuable for ongoing drug discovery research.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Balajee Ramachandran
- Structural and Computational Biology Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, Tamil Nadu, India
- Department of Pharmacology, Physiology and Biophysics, Boston University School of Medicine, Boston, MA, USA
| | - Ahmed Nadeem
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Aruchamy Mohanprasanth
- AMR & Nanotherapeutics Lab, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical, Sciences (SIMATS), Chennai, Tamil Nadu, India
| | - Muthupandian Saravanan
- AMR & Nanotherapeutics Lab, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical, Sciences (SIMATS), Chennai, Tamil Nadu, India
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Martínez-Gómez LE, Martinez-Armenta C, Tusie-Luna T, Vázquez-Cárdenas P, Vidal-Vázquez RP, Ramírez-Hinojosa JP, Gómez-Martín D, Vargas-Alarcón G, Posadas-Sánchez R, Fragoso JM, de la Peña A, Rodríguez-Pérez JM, Mata-Miranda MM, Vázquez-Zapién GJ, Martínez-Cuazitl A, Martínez-Ruiz FDJ, Zayago-Angeles DM, Ramos-Tavera L, Méndez-Aguilera A, Camacho-Rea MDC, Ordoñez-Sánchez ML, Segura-Kato Y, Suarez-Ahedo C, Olea-Torres J, Herrera-López B, Pineda C, Martínez-Nava GA, López-Reyes A. The fatal contribution of serine protease-related genetic variants to COVID-19 outcomes. Front Immunol 2024; 15:1335963. [PMID: 38601158 PMCID: PMC11004237 DOI: 10.3389/fimmu.2024.1335963] [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: 11/13/2023] [Accepted: 03/14/2024] [Indexed: 04/12/2024] Open
Abstract
Introduction Serine proteases play a critical role during SARS-CoV-2 infection. Therefore, polymorphisms of transmembrane protease serine 2 (TMPRSS2) and serpine family E member 1 (SERPINE1) could help to elucidate the contribution of variability to COVID-19 outcomes. Methods To evaluate the genetic variants of the genes previously associated with COVID-19 outcomes, we performed a cross-sectional study in which 1536 SARS-CoV-2-positive participants were enrolled. TMPRSS2 (rs2070788, rs75603675, rs12329760) and SERPINE1 (rs2227631, rs2227667, rs2070682, rs2227692) were genotyped using the Open Array Platform. The association of polymorphisms with disease outcomes was determined by logistic regression analysis adjusted for covariates (age, sex, hypertension, type 2 diabetes, and obesity). Results According to our codominant model, the GA genotype of rs2227667 (OR=0.55; 95% CI = 0.36-0.84; p=0.006) and the AG genotype of rs2227667 (OR=0.59; 95% CI = 0.38-0.91; p=0.02) of SERPINE1 played a protective role against disease. However, the rs2227692 T allele and TT genotype SERPINE1 (OR=1.45; 95% CI = 1.11-1.91; p=0.006; OR=2.08; 95% CI = 1.22-3.57; p=0.007; respectively) were associated with a decreased risk of death. Similarly, the rs75603675 AA genotype TMPRSS2 had an OR of 1.97 (95% CI = 1.07-3.6; p=0.03) for deceased patients. Finally, the rs2227692 T allele SERPINE1 was associated with increased D-dimer levels (OR=1.24; 95% CI = 1.03-1.48; p=0.02). Discussion Our data suggest that the rs75603675 TMPRSS2 and rs2227692 SERPINE1 polymorphisms are associated with a poor outcome. Additionally, rs2227692 SERPINE1 could participate in hypercoagulable conditions in critical COVID-19 patients, and this genetic variant could contribute to the identification of new pharmacological targets and treatment strategies to block the inhibition of TMPRSS2 entry into SARS-CoV-2.
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Affiliation(s)
- Laura Edith Martínez-Gómez
- Laboratorio de Gerociencias, Dirección General, Departamento de Reconstrucción Articular, Laboratorio Facilitador, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Secretaría de Salud, Mexico City, Mexico
| | - Carlos Martinez-Armenta
- Laboratorio de Gerociencias, Dirección General, Departamento de Reconstrucción Articular, Laboratorio Facilitador, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Secretaría de Salud, Mexico City, Mexico
| | - Teresa Tusie-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición, Salvador, Zubirán, Mexico City, Mexico
- Instituto de Investigaciones Biomédicas Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Paola Vázquez-Cárdenas
- Centro de Innovación Médica Aplicada, Hospital General Dr. Manuel Gea González, Mexico City, Mexico
| | - Rosa P. Vidal-Vázquez
- Centro de Innovación Médica Aplicada, Hospital General Dr. Manuel Gea González, Mexico City, Mexico
| | - Juan P. Ramírez-Hinojosa
- Centro de Innovación Médica Aplicada, Hospital General Dr. Manuel Gea González, Mexico City, Mexico
| | - Diana Gómez-Martín
- Department of Immunology and Rheumatology, Departamento de Inmunogenética, Departamento de Nutrición Animal, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Secretaría de Salud, Mexico City, Mexico
| | - Gilberto Vargas-Alarcón
- Departamento de Biología Molecular y Endocrinología, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Rosalinda Posadas-Sánchez
- Departamento de Biología Molecular y Endocrinología, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - José Manuel Fragoso
- Departamento de Biología Molecular y Endocrinología, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Aurora de la Peña
- Departamento de Farmacología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - José Manuel Rodríguez-Pérez
- Departamento de Biología Molecular y Endocrinología, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Mónica M. Mata-Miranda
- Laboratorio de Biología Celular y Tisular, Laboratorio de Embriología, Escuela Médico Militar, Universidad del Ejército y Fuerza Aérea, Mexico City, Mexico
| | - Gustavo J. Vázquez-Zapién
- Laboratorio de Biología Celular y Tisular, Laboratorio de Embriología, Escuela Médico Militar, Universidad del Ejército y Fuerza Aérea, Mexico City, Mexico
| | - Adriana Martínez-Cuazitl
- Laboratorio de Biología Celular y Tisular, Laboratorio de Embriología, Escuela Médico Militar, Universidad del Ejército y Fuerza Aérea, Mexico City, Mexico
| | - Felipe de J. Martínez-Ruiz
- Nuevo Hospital General Delegación Regional Sur de la Ciudad de México Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | - Dulce M. Zayago-Angeles
- Nuevo Hospital General Delegación Regional Sur de la Ciudad de México Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | - Luis Ramos-Tavera
- Department of Immunology and Rheumatology, Departamento de Inmunogenética, Departamento de Nutrición Animal, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Secretaría de Salud, Mexico City, Mexico
| | - Alberto Méndez-Aguilera
- Laboratorio de Gerociencias, Dirección General, Departamento de Reconstrucción Articular, Laboratorio Facilitador, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Secretaría de Salud, Mexico City, Mexico
| | - María del C. Camacho-Rea
- Department of Immunology and Rheumatology, Departamento de Inmunogenética, Departamento de Nutrición Animal, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Secretaría de Salud, Mexico City, Mexico
| | - María L. Ordoñez-Sánchez
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición, Salvador, Zubirán, Mexico City, Mexico
| | - Yayoi Segura-Kato
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición, Salvador, Zubirán, Mexico City, Mexico
| | - Carlos Suarez-Ahedo
- Laboratorio de Gerociencias, Dirección General, Departamento de Reconstrucción Articular, Laboratorio Facilitador, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Secretaría de Salud, Mexico City, Mexico
| | - Jessel Olea-Torres
- Laboratorio de Gerociencias, Dirección General, Departamento de Reconstrucción Articular, Laboratorio Facilitador, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Secretaría de Salud, Mexico City, Mexico
| | - Brígida Herrera-López
- Laboratorio de Gerociencias, Dirección General, Departamento de Reconstrucción Articular, Laboratorio Facilitador, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Secretaría de Salud, Mexico City, Mexico
| | - Carlos Pineda
- Laboratorio de Gerociencias, Dirección General, Departamento de Reconstrucción Articular, Laboratorio Facilitador, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Secretaría de Salud, Mexico City, Mexico
| | - Gabriela A. Martínez-Nava
- Laboratorio de Gerociencias, Dirección General, Departamento de Reconstrucción Articular, Laboratorio Facilitador, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Secretaría de Salud, Mexico City, Mexico
| | - Alberto López-Reyes
- Laboratorio de Gerociencias, Dirección General, Departamento de Reconstrucción Articular, Laboratorio Facilitador, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Secretaría de Salud, Mexico City, Mexico
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Duloquin G, Pommier T, Georges M, Giroud M, Guenancia C, Béjot Y, Laurent G, Rabec C. Is COVID-19 Infection a Multiorganic Disease? Focus on Extrapulmonary Involvement of SARS-CoV-2. J Clin Med 2024; 13:1397. [PMID: 38592697 PMCID: PMC10932259 DOI: 10.3390/jcm13051397] [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: 01/21/2024] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 04/10/2024] Open
Abstract
First described in December 2019 in Wuhan (China), COVID-19 disease rapidly spread worldwide, constituting the biggest pandemic in the last 100 years. Even if SARS-CoV-2, the agent responsible for COVID-19, is mainly associated with pulmonary injury, evidence is growing that this virus can affect many organs, including the heart and vascular endothelial cells, and cause haemostasis, CNS, and kidney and gastrointestinal tract abnormalities that can impact in the disease course and prognosis. In fact, COVID-19 may affect almost all the organs. Hence, SARS-CoV-2 is essentially a systemic infection that can present a large number of clinical manifestations, and it is variable in distribution and severity, which means it is potentially life-threatening. The goal of this comprehensive review paper in the series is to give an overview of non-pulmonary involvement in COVID-19, with a special focus on underlying pathophysiological mechanisms and clinical presentation.
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Affiliation(s)
- Gauthier Duloquin
- Department of Neurology, CHU Dijon-Bourgogne, 21000 Dijon, France; (G.D.); (M.G.); (Y.B.)
- Laboratory of Cerebro-Vascular Pathophysiology and Epidemiology (PEC2) EA 7460, University of Bourgogne, 21000 Dijon, France; (T.P.); (C.G.); (G.L.)
| | - Thibaut Pommier
- Laboratory of Cerebro-Vascular Pathophysiology and Epidemiology (PEC2) EA 7460, University of Bourgogne, 21000 Dijon, France; (T.P.); (C.G.); (G.L.)
- Department of Cardiology, University Hospital of Dijon, 21000 Dijon, France
| | - Marjolaine Georges
- Department of Pneumology and Intensive Care Unit, Reference Centre for Rare Lung Diseases, Dijon University Hospital, 14 Boulevard Gaffarel, 21000 Dijon, France;
- Centre des Sciences du Goût et de l’Alimentation, INRA, UMR 6265 CNRS 1234, University of Bourgogne Franche-Comté, 21000 Dijon, France
| | - Maurice Giroud
- Department of Neurology, CHU Dijon-Bourgogne, 21000 Dijon, France; (G.D.); (M.G.); (Y.B.)
- Laboratory of Cerebro-Vascular Pathophysiology and Epidemiology (PEC2) EA 7460, University of Bourgogne, 21000 Dijon, France; (T.P.); (C.G.); (G.L.)
| | - Charles Guenancia
- Laboratory of Cerebro-Vascular Pathophysiology and Epidemiology (PEC2) EA 7460, University of Bourgogne, 21000 Dijon, France; (T.P.); (C.G.); (G.L.)
- Department of Cardiology, University Hospital of Dijon, 21000 Dijon, France
| | - Yannick Béjot
- Department of Neurology, CHU Dijon-Bourgogne, 21000 Dijon, France; (G.D.); (M.G.); (Y.B.)
- Laboratory of Cerebro-Vascular Pathophysiology and Epidemiology (PEC2) EA 7460, University of Bourgogne, 21000 Dijon, France; (T.P.); (C.G.); (G.L.)
| | - Gabriel Laurent
- Laboratory of Cerebro-Vascular Pathophysiology and Epidemiology (PEC2) EA 7460, University of Bourgogne, 21000 Dijon, France; (T.P.); (C.G.); (G.L.)
- Department of Cardiology, University Hospital of Dijon, 21000 Dijon, France
| | - Claudio Rabec
- Department of Pneumology and Intensive Care Unit, Reference Centre for Rare Lung Diseases, Dijon University Hospital, 14 Boulevard Gaffarel, 21000 Dijon, France;
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Bashar NAS, Gohar NMAH, Tantawy AA, Kamel MHM. Evaluation of relationship between TMPRSS2 p.(Val197Met) variant and COVID-19 susceptibility and severity. BMC Infect Dis 2024; 24:112. [PMID: 38254046 PMCID: PMC10802041 DOI: 10.1186/s12879-024-08987-w] [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: 09/01/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND The World Health Organization (WHO) declared Coronavirus Disease 2019 (COVID-19) a global pandemic on March 11, 2020. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection has killed millions of people and had a terrible effect on society. The transmembrane protease serine 2 (TMPRSS2) enzyme is essential in the initial phases of the interplay between the SARSCoV-2 and the host cells by assisting viral entrance. METHODS This observational case-control study involved 150 participants, 100 adult patients with COVID-19, 50 of whom appeared healthy and had no history of or symptoms of COVID-19 infection when the study was conducted. Between January and April 2022, patients were taken as inpatients in isolation units or through recruitment from the COVID-19 clinic at Kasr Al-Ainy Cairo University Hospitals. According to the National Institutes of Health guidelines (2021), they were categorised into three categories: mild, moderate, and severe. TMPRSS2 p.(Val197Met) variant genotyping was evaluated using TaqMan Real-Time PCR. RESULTS The study showed a substantial difference between the mild and severe COVID-19 patient groups regarding their TMPRSS2 (p.Val197Met) genotypes (P value = 0.046). The C allele was significantly more prevalent in the mild, moderate and severe COVID-19 patient categories (77.8%, 89.7% and 91.7%, respectively) and the control group (80%). Meanwhile, the T allele was more prevalent in the mild (22.2%) and control (20%) groups. There was a statistically significant difference in allelic distribution between the mild and severe groups (P value = 0.034). CONCLUSION The study showed a connection between the TMPRSS2 gene variant p.(Val197Met) and the degree of illness. We concluded that the T(mutant) allele was protective against severe COVID-19 because it was linked to lesser disease severity.
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Affiliation(s)
- Nora Ahmed Saleh Bashar
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | | | - Ahmed A Tantawy
- Department of Pulmonary Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt.
| | - Mai Hamed Mohamed Kamel
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
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Yadav V, Ravichandran S. Significance of understanding the genomics of host-pathogen interaction in limiting antibiotic resistance development: lessons from COVID-19 pandemic. Brief Funct Genomics 2024; 23:69-74. [PMID: 36722037 DOI: 10.1093/bfgp/elad001] [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: 09/17/2022] [Revised: 12/15/2022] [Accepted: 01/09/2023] [Indexed: 02/02/2023] Open
Abstract
The entire world is facing the stiff challenge of COVID-19 pandemic. To overcome the spread of this highly infectious disease, several short-sighted strategies were adopted such as the use of broad-spectrum antibiotics and antifungals. However, the misuse and/or overuse of antibiotics have accentuated the emergence of the next pandemic: antimicrobial resistance (AMR). It is believed that pathogens while transferring between humans and the environment carry virulence and antibiotic-resistant factors from varied species. It is presumed that all such genetic factors are quantifiable and predictable, a better understanding of which could be a limiting step for the progression of AMR. Herein, we have reviewed how genomics-based understanding of host-pathogen interactions during COVID-19 could reduce the non-judicial use of antibiotics and prevent the eruption of an AMR-based pandemic in future.
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Affiliation(s)
- Vikas Yadav
- Department of Translational Medicine, Clinical Research Centre, Skaone University Hospital, Lund University, Malmo SE-20213, Sweden
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8
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Katsaouni N, Llavona P, Khodamoradi Y, Otto AK, Körber S, Geisen C, Seidl C, Vehreschild MJGT, Ciesek S, Ackermann J, Koch I, Schulz MH, Krause DS. Dataset of single nucleotide polymorphisms of immune-associated genes in patients with SARS-CoV-2 infection. PLoS One 2023; 18:e0287725. [PMID: 37971979 PMCID: PMC10653545 DOI: 10.1371/journal.pone.0287725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/09/2023] [Indexed: 11/19/2023] Open
Abstract
The SARS-CoV-2 pandemic has affected nations globally leading to illness, death, and economic downturn. Why disease severity, ranging from no symptoms to the requirement for extracorporeal membrane oxygenation, varies between patients is still incompletely understood. Consequently, we aimed at understanding the impact of genetic factors on disease severity in infection with SARS-CoV-2. Here, we provide data on demographics, ABO blood group, human leukocyte antigen (HLA) type, as well as next-generation sequencing data of genes in the natural killer cell receptor family, the renin-angiotensin-aldosterone and kallikrein-kinin systems and others in 159 patients with SARS-CoV-2 infection, stratified into seven categories of disease severity. We provide single-nucleotide polymorphism (SNP) data on the patients and a protein structural analysis as a case study on a SNP in the SIGLEC7 gene, which was significantly associated with the clinical score. Our data represent a resource for correlation analyses involving genetic factors and disease severity and may help predict outcomes in infections with future SARS-CoV-2 variants and aid vaccine adaptation.
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Affiliation(s)
- Nikoletta Katsaouni
- Computational Epigenomics & Systems Cardiology, Institute of Cardiovascular Regeneration, Goethe University and University Clinic, Frankfurt am Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, Frankfurt am Main, Germany
| | - Pablo Llavona
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Yascha Khodamoradi
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - Ann-Kathrin Otto
- Molecular Bioinformatics, Institute of Computer Science, Goethe University Frankfurt am Main, Germany
| | - Stephanie Körber
- German Red Cross Blood Donor Service Baden-Württemberg Hessen, Frankfurt am Main, Germany
| | - Christof Geisen
- German Red Cross Blood Donor Service Baden-Württemberg Hessen, Frankfurt am Main, Germany
| | - Christian Seidl
- German Red Cross Blood Donor Service Baden-Württemberg Hessen, Frankfurt am Main, Germany
| | - Maria J. G. T. Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital, Goethe University, Frankfurt, Germany
- German Centre for Infection Research, External Partner Site, Frankfurt, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine and Pharmacology, Frankfurt, Germany
| | - Jörg Ackermann
- Molecular Bioinformatics, Institute of Computer Science, Goethe University Frankfurt am Main, Germany
| | - Ina Koch
- Molecular Bioinformatics, Institute of Computer Science, Goethe University Frankfurt am Main, Germany
| | - Marcel H. Schulz
- Computational Epigenomics & Systems Cardiology, Institute of Cardiovascular Regeneration, Goethe University and University Clinic, Frankfurt am Main, Germany
- German Center for Cardiovascular Research (DZHK), Partner site Rhein Main, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, Frankfurt am Main, Germany
| | - Daniela S. Krause
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
- German Red Cross Blood Donor Service Baden-Württemberg Hessen, Frankfurt am Main, Germany
- Institute of Biochemistry II and Institute of General Pharmacology and Toxicology, Goethe-University, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Frankfurt, Germany
- Frankfurt Cancer Institute, Frankfurt am Main, Germany
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9
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Salihefendić L, Čeko I, Bešić L, Mulahuseinović N, Durgut S, Pećar D, Prnjavorac L, Kandić E, Meseldžić N, Bego T, Prnjavorac B, Marjanović D, Konjhodžić R, Ašić A. Identification of human genetic variants modulating the course of COVID-19 infection with importance in other viral infections. Front Genet 2023; 14:1240245. [PMID: 37795240 PMCID: PMC10545899 DOI: 10.3389/fgene.2023.1240245] [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: 06/14/2023] [Accepted: 08/11/2023] [Indexed: 10/06/2023] Open
Abstract
Introduction: COVID-19 has been a major focus of scientific research since early 2020. Due to its societal, economic, and clinical impact worldwide, research efforts aimed, among other questions, to address the effect of host genetics in susceptibility and severity of COVID-19. Methods: We, therefore, performed next-generation sequencing of coding and regulatory regions of 16 human genes, involved in maintenance of the immune system or encoding receptors for viral entry into the host cells, in a subset of 60 COVID-19 patients from the General Hospital Tešanj, Bosnia and Herzegovina, classified into three groups of clinical conditions of different severity ("mild," "moderate," and "severe"). Results: We confirmed that the male sex and older age are risk factors for severe clinical picture and identified 13 variants on seven genes (CD55, IL1B, IL4, IRF7, DDX58, TMPRSS2, and ACE2) with potential functional significance, either as genetic markers of modulated susceptibility to SARS-CoV-2 infection or modifiers of the infection severity. Our results include variants reported for the first time as potentially associated with COVID-19, but further research and larger patient cohorts are required to confirm their effect. Discussion: Such studies, focused on candidate genes and/or variants, have a potential to answer the questions regarding the effect of human genetic makeup on the expected infection outcome. In addition, loci we identified here were previously reported to have clinical significance in other diseases and viral infections, thus confirming a general, broader significance of COVID-19-related research results following the end of the pandemic period.
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Affiliation(s)
- Lana Salihefendić
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Ivana Čeko
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Larisa Bešić
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | | | - Selma Durgut
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
| | - Dino Pećar
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
| | | | - Enis Kandić
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
| | - Neven Meseldžić
- Department of Pharmaceutical Biochemistry and Laboratory Diagnostics, Faculty of Pharmacy, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Tamer Bego
- Department of Pharmaceutical Biochemistry and Laboratory Diagnostics, Faculty of Pharmacy, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | | | - Damir Marjanović
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
- Institute for Anthropological Research, University of Zagreb, Zagreb, Croatia
| | - Rijad Konjhodžić
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Adna Ašić
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
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10
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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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Ergoren MC, Akan G, Guler E, Tuncel G, Akovalı D, Evren EU, Evren H, Suer HK, Sanlidag T. Sex and ABO Blood Differences in SARS-CoV-2 Infection Susceptibility. Glob Med Genet 2023; 10:22-26. [PMID: 36727032 PMCID: PMC9886502 DOI: 10.1055/s-0043-1761202] [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: 02/01/2023] Open
Abstract
Data consisting of millions of cases cannot still explain the immunopathogenesis mechanism between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and host cell for ongoing coronavirus disease 2019 (COVID-19) pandemics. Epidemiological studies among different populations suggested different impacts of ABO and Rh antibodies on the COVID-19 susceptibility. Thus, the ABO blood group and the SARS-CoV-2 infection paradox remain unclear. Therefore, the present retrospective case-control study aimed to investigate the possible association between ABO blood groups and Rh blood types on SARS-CoV-2 infection in the Turkish Cypriot population. A total of 18,639 Turkish Cypriot subjects (297 SARS-CoV-2 COVID-19 patients and 18,342 healthy) were included in this study. Personal and clinical characteristics including age, gender, SARS-CoV-2 infection status, the ABO blood group and Rh blood types were evaluated and compared between two groups. As a result, ABO blood group was shown to be associated with a higher risk of SARS-CoV-2 infection as well as with male sex ( p = 0.018). There was no association between Rh blood type and COVID-19. Overall, this study is the first largest sample group study to show the distribution of ABO blood group and Rh blood types in the healthy Turkish Cypriot population. Based on the current evidence, there are insufficient data to guide public health policies regarding COVID-19 pathogenesis.
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Affiliation(s)
- Mahmut Cerkez Ergoren
- Department of Medical Genetics, Faculty of Medicine, Near East University, Nicosia, Cyprus,Address for correspondence Mahmut Cerkez Ergoren, PhD Department of Medical GeneticsFaculty of Medicine, Near East University, 99138 NicosiaCyprus
| | - Gokce Akan
- DESAM Research Institute, Near East University, Nicosia, Cyprus
| | - Emrah Guler
- DESAM Research Institute, Near East University, Nicosia, Cyprus,Department of Nutrition and Dietetics, Faculty of Health Sciences, Near East University, Nicosia, Cyprus
| | - Gulten Tuncel
- DESAM Research Institute, Near East University, Nicosia, Cyprus
| | - Damla Akovalı
- Blood Bank Unite, Near East University Hospital, Near East University, Nicosia, Cyprus
| | - Emine Unal Evren
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, University of Kyrenia, Kyrenia, Cyprus
| | - Hakan Evren
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, University of Kyrenia, Kyrenia, Cyprus
| | - Huseyin Kaya Suer
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Near East University, Nicosia, Cyprus
| | - Tamer Sanlidag
- DESAM Research Institute, Near East University, Nicosia, Cyprus
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12
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Ali S, Ali U, Qamar A, Zafar I, Yaqoob M, Ain QU, Rashid S, Sharma R, Nafidi HA, Bin Jardan YA, Bourhia M. Predicting the effects of rare genetic variants on oncogenic signaling pathways: A computational analysis of HRAS protein function. Front Chem 2023; 11:1173624. [PMID: 37153521 PMCID: PMC10160440 DOI: 10.3389/fchem.2023.1173624] [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: 02/24/2023] [Accepted: 04/10/2023] [Indexed: 05/09/2023] Open
Abstract
The HRAS gene plays a crucial role in regulating essential cellular processes for life, and this gene's misregulation is linked to the development of various types of cancers. Nonsynonymous single nucleotide polymorphisms (nsSNPs) within the coding region of HRAS can cause detrimental mutations that disrupt wild-type protein function. In the current investigation, we have employed in-silico methodologies to anticipate the consequences of infrequent genetic variations on the functional properties of the HRAS protein. We have discovered a total of 50 nsSNPs, of which 23 were located in the exon region of the HRAS gene and denoting that they were expected to cause harm or be deleterious. Out of these 23, 10 nsSNPs ([G60V], [G60D], [R123P], [D38H], [I46T], [G115R], [R123G], [P11OL], [A59L], and [G13R]) were identified as having the most delterious effect based on results of SIFT analysis and PolyPhen2 scores ranging from 0.53 to 69. The DDG values -3.21 kcal/mol to 0.87 kcal/mol represent the free energy change associated with protein stability upon mutation. Interestingly, we identified that the three mutations (Y4C, T58I, and Y12E) were found to improve the structural stability of the protein. We performed molecular dynamics (MD) simulations to investigate the structural and dynamic effects of HRAS mutations. Our results showed that the stable model of HRAS had a significantly lower energy value of -18756 kj/mol compared to the initial model of -108915 kj/mol. The RMSD value for the wild-type complex was 4.40 Å, and the binding energies for the G60V, G60D, and D38H mutants were -107.09 kcal/mol, -109.42 kcal/mol, and -107.18 kcal/mol, respectively as compared to wild-type HRAS protein had -105.85 kcal/mol. The result of our investigation presents convincing corroboration for the potential functional significance of nsSNPs in augmenting HRAS expression and adding to the activation of malignant oncogenic signalling pathways.
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Affiliation(s)
- Sadaqat Ali
- Medical Department, DHQ Hospital Bhawalnagr, Punjab, Pakistan
| | | | - Adeem Qamar
- Department of Pathology, Sahiwal Medical College Sahiwal, Punjab, Pakistan
| | - Imran Zafar
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Punjab, Pakistan
| | - Muhammad Yaqoob
- Department of Life Sciences, ARID University-Barani Institute of Sciences Burewala Campus, Punjab, Pakistan
| | - Qurat ul Ain
- Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Summya Rashid
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Punjab, Pakistan
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
- *Correspondence: Mohammed Bourhia, ; Rohit Sharma,
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec City, QC, Canada
| | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Bourhia
- Laboratory of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Agadir, Morocco
- *Correspondence: Mohammed Bourhia, ; Rohit Sharma,
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13
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Papageorgiou L, Papakonstantinou E, Diakou I, Pierouli K, Dragoumani K, Bacopoulou F, Chrousos GP, Eliopoulos E, Vlachakis D. Semantic and Population Analysis of the Genetic Targets Related to COVID-19 and Its Association with Genes and Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1423:59-78. [PMID: 37525033 DOI: 10.1007/978-3-031-31978-5_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
SARS-CoV-2 is a coronavirus responsible for one of the most serious, modern worldwide pandemics, with lasting and multifaceted effects. By late 2021, SARS-CoV-2 has infected more than 180 million people and has killed more than 3 million. The virus gains entrance to human cells through binding to ACE2 via its surface spike protein and causes a complex disease of the respiratory system, termed COVID-19. Vaccination efforts are being made to hinder the viral spread, and therapeutics are currently under development. Toward this goal, scientific attention is shifting toward variants and SNPs that affect factors of the disease such as susceptibility and severity. This genomic grammar, tightly related to the dark part of our genome, can be explored through the use of modern methods such as natural language processing. We present a semantic analysis of SARS-CoV-2-related publications, which yielded a repertoire of SNPs, genes, and disease ontologies. Population data from the 1000 Genomes Project were subsequently integrated into the pipeline. Data mining approaches of this scale have the potential to elucidate the complex interaction between COVID-19 pathogenesis and host genetic variation; the resulting knowledge can facilitate the management of high-risk groups and aid the efforts toward precision medicine.
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Affiliation(s)
- Louis Papageorgiou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Konstantina Dragoumani
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Flora Bacopoulou
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - George P Chrousos
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Elias Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece.
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece.
- Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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14
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Sekiya T, Ogura Y, Kai H, Kawaguchi A, Okawa S, Hirohama M, Kuroki T, Morii W, Hara A, Hiramatsu Y, Hitomi S, Kawakami Y, Arakawa Y, Maruo K, Chiba S, Suzuki H, Kojima H, Tachikawa H, Yamagata K. TMPRSS2 gene polymorphism common in East Asians confers decreased COVID-19 susceptibility. Front Microbiol 2022; 13:943877. [PMID: 36532428 PMCID: PMC9748344 DOI: 10.3389/fmicb.2022.943877] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 10/27/2022] [Indexed: 09/29/2023] Open
Abstract
COVID-19 has a wide range of clinical presentations, and the susceptibility to SARS-CoV-2 infection and the mortality rate also vary by region and ethnicity. Here, we found that rs12329760 in the TMPRSS2 gene, a missense variant common in East Asian populations, contributes to protection against SARS-CoV-2 infection. TMPRSS2 is a protease responsible for SARS-CoV-2 entry and syncytium formation. rs12329760 (c.478G>A, p. V160M) was associated with a reduced risk of moderate symptoms. The enzymatic activity of Met160-TMPRSS2 was lower than that of Val160-TMPRSS2, and thus the viral entry and the syncytium formation of SARS-CoV-2 were impaired. Collectively, these results indicate that the genetic variation in TMPRSS2, which is common in East Asians, is one of the molecular determinants of COVID-19 susceptibility.
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Affiliation(s)
- Takeshi Sekiya
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yukino Ogura
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Hirayasu Kai
- Department of Nephrology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Atsushi Kawaguchi
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Shino Okawa
- College of Biological Sciences, University of Tsukuba, Tsukuba, Japan
| | - Mikako Hirohama
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Takahiro Kuroki
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Wataru Morii
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Akira Hara
- Department of Otorhinolaryngology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yuji Hiramatsu
- Department of Cardiovascular Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shigemi Hitomi
- Department of Infectious Diseases, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yasushi Kawakami
- Department of Laboratory Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yoshihiro Arakawa
- Department of Medical Pharmacy, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kazushi Maruo
- Department of Biostatistics, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shigeru Chiba
- Department of Hematology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Hiromichi Suzuki
- Department of Infectious Diseases, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Hiroshi Kojima
- Ibaraki Clinical Education and Training Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Hirokazu Tachikawa
- Division of Clinical Medicine, Department of Disaster and Community Psychiatry, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kunihiro Yamagata
- Department of Nephrology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
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15
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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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16
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A Polymorphism in the TMPRSS2 Gene Increases the Risk of Death in Older Patients Hospitalized with COVID-19. Viruses 2022; 14:v14112557. [PMID: 36423166 PMCID: PMC9696669 DOI: 10.3390/v14112557] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/09/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Transmembrane serine protease type 2 (TMPRSS2) and angiotensin-converting enzyme 2 (ACE2) are the main molecules involved in the entry of SARS-CoV-2 into host cells. Changes in TMPRSS2 expression levels caused by single nucleotide polymorphisms (SNPs) may contribute to the outcome of COVID-19. The aim was to investigate the association between TMPRSS2 gene polymorphisms and the risk of death in hospitalized patients with COVID-19. METHODS We included patients with confirmed COVID-19, recruited from two hospitals in northeastern Brazil from August 2020 to July 2021. Two functional polymorphisms (rs2070788 and rs12329760) in TMPRSS2 were evaluated by real-time PCR. The Kaplan-Meier method was used to estimate death. The Cox's proportional hazards model was used to adjust for potentially confounding factors. RESULTS A total of 402 patients were followed prospectively. Survival analysis demonstrated that older patients carrying the rs2070788 GG genotype had shorter survival times when compared to those with AG or AA genotypes (p = 0.009). In multivariable analysis, the GG genotype was a factor independently associated with the risk of death in older individuals (hazard ratio = 4.03, 95% confidence interval 1.49 to 10.84). CONCLUSIONS The rs2070788 polymorphism in TMPRSS2 increases risk of death four-fold in older patients hospitalized with COVID-19.
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17
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Duman N, Tuncel G, Bisgin A, Bozdogan ST, Sag SO, Gul S, Kiraz A, Balta B, Erdogan M, Uyanik B, Canbek S, Ata P, Geckinli BB, Arslan Ates E, Alavanda C, Yesim Ozdemir S, Sezer O, Ozgon GO, Gurkan H, Guler K, Boga I, Kaya N, Alemdar A, Sayan M, Dundar M, Ergoren MC, Temel SG. Analysis of ACE2 and TMPRSS2 coding variants as a risk factor for SARS-CoV-2 from 946 whole-exome sequencing data in the Turkish population. J Med Virol 2022; 94:5225-5243. [PMID: 35811452 PMCID: PMC9349697 DOI: 10.1002/jmv.27976] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/14/2022] [Accepted: 07/02/2022] [Indexed: 12/15/2022]
Abstract
Heterogeneity in symptoms associated with COVID-19 in infected patients remains unclear. ACE2 and TMPRSS2 gene variants are considered possible risk factors for COVID-19. In this study, a retrospective comparative genome analysis of the ACE2 and TMPRSS2 variants from 946 whole-exome sequencing data was conducted. Allele frequencies of all variants were calculated and filtered to remove variants with allele frequencies lower than 0.003 and to prioritize functional coding variants. The majority of detected variants were intronic, only two ACE2 and three TMPRSS2 nonsynonymous variants were detected in the analyzed cohort. The main ACE2 variants that putatively have a protective or susceptibility effect on SARS-CoV-2 have not yet been determined in the Turkish population. The Turkish genetic makeup likely lacks any ACE2 variant that increases susceptibility to SARS-CoV-2 infection. TMPRSS2 rs75603675 and rs12329760 variants that were previously defined as common variants that have different allele frequencies among populations and may have a role in SARS-CoV-2 attachment to host cells were determined in the population. Overall, these data will contribute to the formation of a national variation database and may also contribute to further studies of ACE2 and TMPRSS2 in the Turkish population and differences in SARS-CoV-2 infection among other populations.
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Affiliation(s)
- Nilgun Duman
- Department of Medical Genetics, Faculty of MedicineBezmialem Vakif UniversityIstanbulTurkey
| | - Gulten Tuncel
- DESAM Research InstituteNear East UniversityNicosiaCyprus
| | - Atil Bisgin
- Department of Medical Genetics, Faculty of MedicineÇukurova UniversityAdanaTurkey,AGENTEM (Adana Genetic Diseases Diagnosis and Treatment Center)Cukurova UniversityAdanaTurkey
| | - Sevcan Tug Bozdogan
- Department of Medical Genetics, Faculty of MedicineÇukurova UniversityAdanaTurkey,AGENTEM (Adana Genetic Diseases Diagnosis and Treatment Center)Cukurova UniversityAdanaTurkey
| | - Sebnem Ozemri Sag
- Department of Medical Genetics, Faculty of MedicineBursa Uludag UniversityBursaTurkey
| | - Seref Gul
- Department of Biology, Biotechnology Division, Faculty of SciencesIstanbul UniversityIstanbulTurkey
| | - Aslihan Kiraz
- Department of Medical GeneticsKayseri Education and Research State HospitalKayseriTurkey
| | - Burhan Balta
- Department of Medical GeneticsKayseri Education and Research State HospitalKayseriTurkey
| | - Murat Erdogan
- Department of Medical GeneticsKayseri Education and Research State HospitalKayseriTurkey
| | - Bulent Uyanik
- Department of Medical GeneticsIstanbul Bakırkoy Dr. Sadi Konuk Education and Research HospitalIstanbulTurkey
| | - Sezin Canbek
- Department of Medical GeneticsUmraniye City HospitalIstanbulTurkey
| | - Pinar Ata
- Department of Medical Genetics, Faculty of MedicineMarmara UniversityIstanbulTurkey
| | | | - Esra Arslan Ates
- Department of Medical Genetics, Faculty of MedicineMarmara UniversityIstanbulTurkey
| | - Ceren Alavanda
- Department of Medical Genetics, Faculty of MedicineMarmara UniversityIstanbulTurkey
| | - Sevda Yesim Ozdemir
- Department of Medical Genetics, Faculty of MedicineUskudar UniversityİstanbulTurkey
| | - Ozlem Sezer
- Department of Medical GeneticsSamsun Education and Research HospitalSamsunTurkey
| | | | - Hakan Gurkan
- Department of Medical Genetics, Faculty of MedicineTrakya UniversityEdirneTurkey
| | - Kubra Guler
- Mikrogen Genetic Diagnostic CenterAnkaraTurkey
| | - Ibrahim Boga
- Department of Medical Genetics, Faculty of MedicineÇukurova UniversityAdanaTurkey,AGENTEM (Adana Genetic Diseases Diagnosis and Treatment Center)Cukurova UniversityAdanaTurkey
| | - Niyazi Kaya
- Department of Medical Genetics, Faculty of MedicineBursa Uludag UniversityBursaTurkey
| | - Adem Alemdar
- Department of Medical Genetics, Faculty of MedicineBursa Uludag UniversityBursaTurkey
| | - Murat Sayan
- DESAM Research InstituteNear East UniversityNicosiaCyprus,PCR Unit, Kocaeli University Education and Research HospitalKocaeliTurkey
| | - Munis Dundar
- Department of Medical Genetics, Faculty of MedicineErciyes UniversityKayseriTurkey
| | - Mahmut Cerkez Ergoren
- DESAM Research InstituteNear East UniversityNicosiaCyprus,Department of Medical Genetics, Faculty of MedicineNear East UniversityNicosiaCyprus
| | - Sehime Gulsun Temel
- Department of Medical Genetics, Faculty of MedicineBursa Uludag UniversityBursaTurkey,Department of Medical Genetics, Faculty of MedicineNear East UniversityNicosiaCyprus,Department of Histology and Embryology, Faculty of MedicineBursa Uludag UniversityBursaTurkey,Department of Translational Medicine, Institute of Health SciencesBursa Uludag UniversityBursaTurkey
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18
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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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19
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Karimian A, Behjati M, Karimian M. Molecular mechanisms involved in anosmia induced by SARS-CoV-2, with a focus on the transmembrane serine protease TMPRSS2. Arch Virol 2022; 167:1931-1946. [PMID: 35939103 PMCID: PMC9358639 DOI: 10.1007/s00705-022-05545-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/31/2022] [Indexed: 11/26/2022]
Abstract
Since 2020, SARS-CoV-2 has caused a pandemic virus that has posed many challenges worldwide. Infection with this virus can result in a number of symptoms, one of which is anosmia. Olfactory dysfunction can be a temporary or long-term viral complication caused by a disorder of the olfactory neuroepithelium. Processes such as inflammation, apoptosis, and neuronal damage are involved in the development of SARS-CoV-2-induced anosmia. One of the receptors that play a key role in the entry of SARS-CoV-2 into the host cell is the transmembrane serine protease TMPRSS2, which facilitates this process by cleaving the viral S protein. The gene encoding TMPRSS2 is located on chromosome 21. It contains 15 exons and has many genetic variations, some of which increase the risk of disease. Delta strains have been shown to be more dependent on TMPRSS2 for cell entry than Omicron strains. Blockade of this receptor by serine protease inhibitors such as camostat and nafamostat can be helpful for treating SARS-CoV-2 symptoms, including anosmia. Proper understanding of the different functional aspects of this serine protease can help to overcome the therapeutic challenges of SARS-CoV-2 symptoms, including anosmia. In this review, we describe the cellular and molecular events involved in anosmia induced by SARS-CoV-2 with a focus on the function of the TMPRSS2 receptor.
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Affiliation(s)
- Ali Karimian
- Department of Otorhinolaryngology, School of Medicine, Kashan University of Medical Science, Kashan, Iran
| | - Mohaddeseh Behjati
- Cellular, Molecular and Genetics Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Karimian
- Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, 47416-95447, Iran.
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20
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Association of the Transmembrane Serine Protease-2 (TMPRSS2) Polymorphisms with COVID-19. Viruses 2022; 14:v14091976. [PMID: 36146782 PMCID: PMC9505830 DOI: 10.3390/v14091976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 uses the ACE2 receptor and the cellular protease TMPRSS2 for entry into target cells. The present study aimed to establish if the TMPRSS2 polymorphisms are associated with COVID-19 disease. The study included 609 patients with COVID-19 confirmed by RT-PCR test and 291 individuals negative for the SARS-CoV-2 infection confirmed by RT-PCR test and without antibodies anti-SARS-CoV-2. Four TMPRSS2 polymorphisms (rs12329760, rs2298659, rs456298, and rs462574) were determined using the 5′exonuclease TaqMan assays. Under different inheritance models, the rs2298659 (pcodominant2 = 0.018, precessive = 0.006, padditive = 0.019), rs456298 (pcodominant1 = 0.014, pcodominant2 = 0.004; pdominant = 0.009, precessive = 0.004, padditive = 0.0009), and rs462574 (pcodominant1 = 0.017, pcodominant2 = 0.004, pdominant = 0.041, precessive = 0.002, padditive = 0.003) polymorphisms were associated with high risk of developing COVID-19. Two risks (ATGC and GAAC) and two protectives (GAGC and GAGT) haplotypes were detected. High levels of lactic acid dehydrogenase (LDH) were observed in patients with the rs462574AA and rs456298TT genotypes (p = 0.005 and p = 0.020, respectively), whereas, high heart rate was present in patients with the rs462574AA genotype (p = 0.028). Our data suggest that the rs2298659, rs456298, and rs462574 polymorphisms independently and as haplotypes are associated with the risk of COVID-19. The rs456298 and rs462574 genotypes are related to high levels of LDH and heart rate.
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21
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Zhang L, Sarangi V, Liu D, Ho MF, Grassi AR, Wei L, Moon I, Vierkant RA, Larson NB, Lazaridis KN, Athreya AP, Wang L, Weinshilboum R. ACE2 and TMPRSS2 SARS-CoV-2 infectivity genes: deep mutational scanning and characterization of missense variants. Hum Mol Genet 2022; 31:4183-4192. [PMID: 35861636 PMCID: PMC9759330 DOI: 10.1093/hmg/ddac157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/18/2022] [Accepted: 07/05/2022] [Indexed: 01/21/2023] Open
Abstract
The human angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) proteins play key roles in the cellular internalization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the coronavirus responsible for the coronavirus disease of 2019 (COVID-19) pandemic. We set out to functionally characterize the ACE2 and TMPRSS2 protein abundance for variant alleles encoding these proteins that contained non-synonymous single-nucleotide polymorphisms (nsSNPs) in their open reading frames (ORFs). Specifically, a high-throughput assay, deep mutational scanning (DMS), was employed to test the functional implications of nsSNPs, which are variants of uncertain significance in these two genes. Specifically, we used a 'landing pad' system designed to quantify the protein expression for 433 nsSNPs that have been observed in the ACE2 and TMPRSS2 ORFs and found that 8 of 127 ACE2, 19 of 157 TMPRSS2 isoform 1 and 13 of 149 TMPRSS2 isoform 2 variant proteins displayed less than ~25% of the wild-type protein expression, whereas 4 ACE2 variants displayed 25% or greater increases in protein expression. As a result, we concluded that nsSNPs in genes encoding ACE2 and TMPRSS2 might potentially influence SARS-CoV-2 infectivity. These results can now be applied to DNA sequence data for patients infected with SARS-CoV-2 to determine the possible impact of patient-based DNA sequence variation on the clinical course of SARS-CoV-2 infection.
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Affiliation(s)
- Lingxin Zhang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Vivekananda Sarangi
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Duan Liu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Ming-Fen Ho
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Angela R Grassi
- Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Lixuan Wei
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Irene Moon
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Robert A Vierkant
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas B Larson
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA,Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Arjun P Athreya
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA,Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA,Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Richard Weinshilboum
- To whom correspondence should be addressed at: Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic 200 First Street SW, Rochester, MN 55905, USA. Tel: +1 5072842246;
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22
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Saengsiwaritt W, Jittikoon J, Chaikledkaew U, Udomsinprasert W. Genetic polymorphisms of ACE1, ACE2, and TMPRSS2 associated with COVID-19 severity: A systematic review with meta-analysis. Rev Med Virol 2022; 32:e2323. [PMID: 34997794 DOI: 10.1002/rmv.2323] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 12/17/2022]
Abstract
Novel coronavirus disease 2019 (COVID-19) poses a global threat, due to its fluctuating frequency and lethality. Published data revealed associations of COVID-19 susceptibility and severity with host genetic polymorphisms in renin-angiotensin-aldosterone system (RAAS)-related genes including angiotensin-converting enzyme (ACE)1, ACE2, and transmembrane protease (TMPRSS)2. However, the findings remain inconclusive. Accordingly, we aimed to clarify associations of genetic variants in those genes with COVID-19 susceptibility and severity using a systematic review with meta-analysis. From inception through 1 July 2021, a literature search was performed using PubMed, Scopus, Web of Science, and Cochrane Library databases. Allelic distributions for each polymorphism were calculated as pooled odds ratios (OR) with 95% confidence intervals (CI) to assess the strength of association. A total of 3333 COVID-19 patients and 5547 controls from 11 eligible studies were included. From a systematic review, ACE1 rs1799752, ACE1 rs4646994, ACE2 rs2285666, and TMPRSS2 rs12329760 were identified as common polymorphisms of RAAS-related genes. Meta-analysis showed a significant association between TMPRSS2 rs12329760 C-allele and an increased risk of developing severe COVID-19 (OR = 1.32, 95% CI: 1.01, 1.73). Likewise, additional meta-analyses uncovered that both ACE1 rs4646994 DD-genotype and ACE2 rs2285666 GG-genotype carriers had a significantly increased risk of developing severe COVID-19 (OR = 2.06, 95% CI: 1.45, 2.93; OR = 2.14, 95% CI: 1.26, 3.66; respectively). Genetic polymorphisms of ACE1 rs4646994 DD-genotype, ACE2 rs2285666 GG-genotype, and TMPRSS2 rs12329760 CC-genotype and C-allele may serve as predictive models of COVID-19 severity.
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Affiliation(s)
| | - Jiraphun Jittikoon
- Department of Biochemistry, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Usa Chaikledkaew
- Social and Administrative Pharmacy Division, Department of Pharmacy, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Mahidol University Health Technology Assessment (MUHTA) Graduate Program, Mahidol University, Bangkok, Thailand
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23
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Ishak A, Mehendale M, AlRawashdeh MM, Sestacovschi C, Sharath M, Pandav K, Marzban S. The association of COVID-19 severity and susceptibility and genetic risk factors: A systematic review of the literature. Gene 2022; 836:146674. [PMID: 35714803 PMCID: PMC9195407 DOI: 10.1016/j.gene.2022.146674] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/27/2022] [Accepted: 06/10/2022] [Indexed: 11/15/2022]
Abstract
Background COVID-19 is associated with several risk factors such as distinct ethnicities (genetic ancestry), races, sexes, age, pre-existing comorbidities, smoking, and genetics. The authors aim to evaluate the correlation between variability in the host genetics and the severity and susceptibility towards COVID-19 in this study. Methods Following the PRISMA guidelines, we retrieved all the relevant articles published until September 15, 2021, from two online databases: PubMed and Scopus. Findings High-risk HLA haplotypes, higher expression of ACE polymorphisms, and several genes of cellular proteases such as TMPRSS2, FURIN, TLL-1 increase the risk of susceptibility and severity of COVID-19. In addition, upregulation of several genes encoding for both innate and acquired immune systems proteins, mainly CCR5, IFNs, TLR, DPPs, and TNF, positively correlate with COVID-19 severity. However, reduced expression or polymorphisms in genes affecting TLR and IFNλ increase COVID-19 severity. Conclusion Higher expression, polymorphisms, mutations, and deletions of several genes are linked with the susceptibility, severity, and clinical outcomes of COVID-19. Early treatment and vaccination of individuals with genetic predisposition could help minimize the severity and mortality associated with COVID-19.
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Affiliation(s)
- Angela Ishak
- Department of Research & Academic Affairs, Larkin Community Hospital, South Miami, Florida, USA.
| | - Meghana Mehendale
- Department of Research & Academic Affairs, Larkin Community Hospital, South Miami, Florida, USA
| | - Mousa M AlRawashdeh
- Department of Research & Academic Affairs, Larkin Community Hospital, South Miami, Florida, USA; European University Cyprus - School of Medicine, Nicosia, Cyprus
| | - Cristina Sestacovschi
- Department of Research & Academic Affairs, Larkin Community Hospital, South Miami, Florida, USA
| | - Medha Sharath
- Department of Research & Academic Affairs, Larkin Community Hospital, South Miami, Florida, USA; Bangalore Medical College and Research Institute, Bangalore, Karnataka, India
| | - Krunal Pandav
- Department of Research & Academic Affairs, Larkin Community Hospital, South Miami, Florida, USA
| | - Sima Marzban
- Department of Research & Academic Affairs, Larkin Community Hospital, South Miami, Florida, USA
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24
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Epigenetics at the Intersection of COVID-19 Risk and Environmental Chemical Exposures. Curr Environ Health Rep 2022; 9:477-489. [PMID: 35648356 PMCID: PMC9157479 DOI: 10.1007/s40572-022-00353-9] [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] [Accepted: 04/08/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE OF REVIEW Several environmental contaminants have been implicated as contributors to COVID-19 susceptibility and severity. Immunomodulation and epigenetic regulation have been hypothesized as mediators of this relationship, but the precise underlying molecular mechanisms are not well-characterized. This review examines the evidence for epigenetic modification at the intersection of COVID-19 and environmental chemical exposures. RECENT FINDINGS Numerous environmental contaminants including air pollutants, toxic metal(loid)s, per- and polyfluorinated substances, and endocrine disrupting chemicals are hypothesized to increase susceptibility to the SARS-CoV-2 virus and the risk of severe COVID-19, but few studies currently exist. Drawing on evidence that many environmental chemicals alter the epigenetic regulation of key immunity genes and pathways, we discuss how exposures likely perturb host antiviral responses. Specific mechanisms vary by contaminant but include general immunomodulation as well as regulation of viral entry and recognition, inflammation, and immunologic memory pathways, among others. Associations between environmental contaminants and COVID-19 are likely mediated, in part, by epigenetic regulation of key immune pathways involved in the host response to SARS-CoV-2.
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25
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Antioxidant Genetic Profile Modifies Probability of Developing Neurological Sequelae in Long-COVID. Antioxidants (Basel) 2022; 11:antiox11050954. [PMID: 35624818 PMCID: PMC9138155 DOI: 10.3390/antiox11050954] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/06/2022] [Accepted: 05/08/2022] [Indexed: 02/06/2023] Open
Abstract
Understanding the sequelae of COVID-19 is of utmost importance. Neuroinflammation and disturbed redox homeostasis are suggested as prevailing underlying mechanisms in neurological sequelae propagation in long-COVID. We aimed to investigate whether variations in antioxidant genetic profile might be associated with neurological sequelae in long-COVID. Neurological examination and antioxidant genetic profile (SOD2, GPXs and GSTs) determination, as well as, genotype analysis of Nrf2 and ACE2, were conducted on 167 COVID-19 patients. Polymorphisms were determined by the appropriate PCR methods. Only polymorphisms in GSTP1AB and GSTO1 were independently associated with long-COVID manifestations. Indeed, individuals carrying GSTP1 Val or GSTO1 Asp allele exhibited lower odds of long-COVID myalgia development, both independently and in combination. Furthermore, the combined presence of GSTP1 Ile and GSTO1 Ala alleles exhibited cumulative risk regarding long-COVID myalgia in carriers of the combined GPX1 LeuLeu/GPX3 CC genotype. Moreover, individuals carrying combined GSTM1-null/GPX1LeuLeu genotype were more prone to developing long-COVID “brain fog”, while this probability further enlarged if the Nrf2 A allele was also present. The fact that certain genetic variants of antioxidant enzymes, independently or in combination, affect the probability of long-COVID manifestations, further emphasizes the involvement of genetic susceptibility when SARS-CoV-2 infection is initiated in the host cells, and also months after.
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David A, Parkinson N, Peacock TP, Pairo-Castineira E, Khanna T, Cobat A, Tenesa A, Sancho-Shimizu V, Casanova JL, Abel L, Barclay WS, Baillie JK, Sternberg MJ. A common TMPRSS2 variant has a protective effect against severe COVID-19. Curr Res Transl Med 2022; 70:103333. [PMID: 35104687 PMCID: PMC8743599 DOI: 10.1016/j.retram.2022.103333] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/22/2021] [Accepted: 01/06/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND The human protein transmembrane protease serine type 2 (TMPRSS2) plays a key role in SARS-CoV-2 infection, as it is required to activate the virus' spike protein, facilitating entry into target cells. We hypothesized that naturally-occurring TMPRSS2 human genetic variants affecting the structure and function of the TMPRSS2 protein may modulate the severity of SARS-CoV-2 infection. METHODS We focused on the only common TMPRSS2 non-synonymous variant predicted to be damaging (rs12329760 C>T, p.V160M), which has a minor allele frequency ranging from 0.14 in Ashkenazi Jewish to 0.38 in East Asians. We analysed the association between the rs12329760 and COVID-19 severity in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units recruited as part of the GenOMICC (Genetics Of Mortality In Critical Care) study. Logistic regression analyses were adjusted for sex, age and deprivation index. For in vitro studies, HEK293 cells were co-transfected with ACE2 and either TMPRSS2 wild type or mutant (TMPRSS2V160M). A SARS-CoV-2 pseudovirus entry assay was used to investigate the ability of TMPRSS2V160M to promote viral entry. RESULTS We show that the T allele of rs12329760 is associated with a reduced likelihood of developing severe COVID-19 (OR 0.87, 95%CI:0.79-0.97, p = 0.01). This association was stronger in homozygous individuals when compared to the general population (OR 0.65, 95%CI:0.50-0.84, p = 1.3 × 10-3). We demonstrate in vitro that this variant, which causes the amino acid substitution valine to methionine, affects the catalytic activity of TMPRSS2 and is less able to support SARS-CoV-2 spike-mediated entry into cells. CONCLUSION TMPRSS2 rs12329760 is a common variant associated with a significantly decreased risk of severe COVID-19. Further studies are needed to assess the expression of TMPRSS2 across different age groups. Moreover, our results identify TMPRSS2 as a promising drug target, with a potential role for camostat mesilate, a drug approved for the treatment of chronic pancreatitis and postoperative reflux esophagitis, in the treatment of COVID-19. Clinical trials are needed to confirm this.
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Affiliation(s)
- Alessia David
- Centre for Integrative System Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
| | - Nicholas Parkinson
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Thomas P Peacock
- Department of Infectious Diseases, Imperial College London, London, W2 1PG, UK
| | | | - Tarun Khanna
- Centre for Integrative System Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Aurelie Cobat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, EU France; University of Paris, Imagine Institute, Paris, EU France
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Vanessa Sancho-Shimizu
- Department of Paediatric Infectious Diseases & Virology, Imperial College London, London, UK; Centre for Paediatrics and Child Health, Faculty of Medicine, Imperial College London, London, UK
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, EU France; University of Paris, Imagine Institute, Paris, EU France; Howard Hughes Medical Institute, New York, NY, USA
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, EU France; University of Paris, Imagine Institute, Paris, EU France
| | - Wendy S Barclay
- Department of Infectious Diseases, Imperial College London, London, W2 1PG, UK
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK; Intenstive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK
| | - Michael Je Sternberg
- Centre for Integrative System Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
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27
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Figueiredo DLA, Ximenez JPB, Seiva FRF, Panis C, Bezerra RDS, Ferrasa A, Cecchini AL, de Medeiros AI, Almeida AMF, Ramão A, Boldt ABW, Moya CF, Chin CM, de Paula D, Rech D, Gradia DF, Malheiros D, Venturini D, Tavares ER, Carraro E, Ribeiro EMDSF, Pereira EM, Tuon FF, Follador FAC, Fernandes GSA, Volpato H, Cólus IMDS, de Oliveira JC, Rodrigues JHDS, dos Santos JL, Visentainer JEL, Brandi JC, Serpeloni JM, Bonini JS, de Oliveira KB, Fiorentin K, Lucio LC, Faccin-Galhardi LC, Ferreto LED, Lioni LMY, Consolaro MEL, Vicari MR, Arbex MA, Pileggi M, Watanabe MAE, Costa MAR, Giannini MJSM, Amarante MK, Khalil NM, de Lima QA, Herai RH, Guembarovski RL, Shinsato RN, Mainardes RM, Giuliatti S, Yamada-Ogatta SF, Gerber VKDQ, Pavanelli WR, da Silva WC, Petzl-Erler ML, Valente V, Soares CP, Cavalli LR, Silva WA. COVID-19: The question of genetic diversity and therapeutic intervention approaches. Genet Mol Biol 2022; 44:e20200452. [PMID: 35421211 PMCID: PMC9075701 DOI: 10.1590/1678-4685-gmb-2020-0452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 12/24/2021] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2), is the largest pandemic in modern history with very high infection rates and considerable mortality. The disease, which emerged in China's Wuhan province, had its first reported case on December 29, 2019, and spread rapidly worldwide. On March 11, 2020, the World Health Organization (WHO) declared the COVID-19 outbreak a pandemic and global health emergency. Since the outbreak, efforts to develop COVID-19 vaccines, engineer new drugs, and evaluate existing ones for drug repurposing have been intensively undertaken to find ways to control this pandemic. COVID-19 therapeutic strategies aim to impair molecular pathways involved in the virus entrance and replication or interfere in the patients' overreaction and immunopathology. Moreover, nanotechnology could be an approach to boost the activity of new drugs. Several COVID-19 vaccine candidates have received emergency-use or full authorization in one or more countries, and others are being developed and tested. This review assesses the different strategies currently proposed to control COVID-19 and the issues or limitations imposed on some approaches by the human and viral genetic variability.
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Affiliation(s)
- David Livingstone Alves Figueiredo
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Medicina, Guarapuava, PR, Brazil
- Instituto para Pesquisa do Câncer (IPEC), Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - João Paulo Bianchi Ximenez
- Universidade de São Paulo, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Departamento de Análises Clínicas, Toxicologia e Ciência de Alimentos, Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Fábio Rodrigues Ferreira Seiva
- Universidade Estadual do Norte do Paraná (UENP), Centro de Ciências Biológicas, Bandeirantes, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Carolina Panis
- Universidade Estadual do Oeste do Paraná, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Rafael dos Santos Bezerra
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro Regional de Ribeirão Preto, Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Adriano Ferrasa
- Universidade Estadual de Ponta Grossa, Ponta Grossa, Programa de Pós Graduação em Computação Aplicada, Ponta Grossa, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Alessandra Lourenço Cecchini
- Universidade Estadual de Londrina, Departamento de Patologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Alexandra Ivo de Medeiros
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Ana Marisa Fusco Almeida
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Anelisa Ramão
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Ciências Biológicas, Guarapuava, PR, Brazil
| | - Angelica Beate Winter Boldt
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Carla Fredrichsen Moya
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Medicina Veterinária, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Chung Man Chin
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Fármacos e Medicamentos, Araraquara, SP, Brazil
- União das Faculdades dos Grandes Lagos (UNILAGO), Centro de Pesquisa Avançada em Medicina, São José do Rio Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Daniel de Paula
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Farmácia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Daniel Rech
- Universidade Estadual do Oeste do Paraná (UNIOESTE), Hospital do Câncer Francisco Beltrão, Laboratório de Biologia de Tumores, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Daniela Fiori Gradia
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Danielle Malheiros
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Danielle Venturini
- Universidade Estadual de Londrina, Centro de Ciências da Saúde, Departamento de patologia, clínica e toxicologia, Laboratório de bioquímica clínica, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Eliandro Reis Tavares
- Universidade Estadual de Londrina, Departamento de Microbiologia, Centro de Ciências Biológicas, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Emerson Carraro
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Laboratório de Virologia Clínica, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Enilze Maria de Souza Fonseca Ribeiro
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Evani Marques Pereira
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Enfermagem, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Felipe Francisco Tuon
- Universidade Católica do Paraná, Laboratório de Doenças Infecciosas Emergentes, Pontifícia Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Franciele Aní Caovilla Follador
- Universidade Estadual do Oeste do Paraná, Departamento de Ciências da Vida, Programa de Pós-Graduação em Ciências Aplicadas à Saúde, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Glaura Scantamburlo Alves Fernandes
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Hélito Volpato
- Universidade Estadual do Paraná (UNESPAR), Faculdade de Ciências Biológicas, Centro de Ciências Humanas e Educação, Paranavaí, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Ilce Mara de Syllos Cólus
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Jaqueline Carvalho de Oliveira
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Jean Henrique da Silva Rodrigues
- Universidade do Estado de São Paulo (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Fármacos e Medicamentos, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Jean Leandro dos Santos
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Fármacos e Medicamentos, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Jeane Eliete Laguila Visentainer
- Universidade Estadual de Maringá, Laboratório de Imunogenética, Maringá, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Juliana Cristina Brandi
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Juliana Mara Serpeloni
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Juliana Sartori Bonini
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Laboratório de Neuropsicofarmacologia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Karen Brajão de Oliveira
- Universidade Estadual de Londrina, Departamento de Ciências Patológicas, Centro de Ciências Biológicas, Laboratório de Genética Molecular e Imunologia, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Karine Fiorentin
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Léia Carolina Lucio
- Universidade Estadual do Oeste do Paraná, Programa de Pós-Graduação em Ciências Aplicadas à Saúde, Centro de Ciências da Saúde, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Ligia Carla Faccin-Galhardi
- Universidade Estadual de Londrina, Departamento de Microbiologia, Centro de Ciências Biológicas, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Lirane Elize Defante Ferreto
- Universidade Estadual do Oeste do Paraná, Programa de Pós-Graduação em Ciências Aplicadas à Saúde, Centro de Ciências da Saúde, Francisco Beltrão, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Lucy Megumi Yamauchi Lioni
- Universidade Estadual do Norte do Paraná (UENP), Centro de Ciências Biológicas, Bandeirantes, PR, Brazil
- Universidade Estadual de Londrina, Departamento de Microbiologia, Centro de Ciências Biológicas, Londrina, PR, Brazil
| | - Marcia Edilaine Lopes Consolaro
- Universidade Estadual de Maringá, Departamento de Análises Clínicas e Biomedicina, Maringá, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Marcelo Ricardo Vicari
- Universidade Estadual de Ponta Grossa, Departamento de Biologia e Genética Estrutural e Molecular, Ponta Grossa, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Marcos Abdo Arbex
- Universidade de Araraquara, Faculdade de Medicina, Área temática de Pneumologia, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Marcos Pileggi
- Universidade Estadual de Ponta Grossa, Departamento de Biologia e Genética Estrutural e Molecular, Ponta Grossa, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Maria Angelica Ehara Watanabe
- Universidade Estadual de Londrina, Departamento de Ciências Patológicas, Centro de Ciências Biológicas, Laboratório de Imunologia, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Maria Antônia Ramos Costa
- Universidade do Estado do Paraná, Colegiada de Enfermagem, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Maria José S. Mendes Giannini
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Marla Karine Amarante
- Universidade Estadual de Londrina, Departamento de Ciências Patológicas, Centro de Ciências Biológicas, Laboratório de Imunologia, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Najeh Maissar Khalil
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Farmácia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Quirino Alves de Lima
- Universidade Estadual de Maringá, Laboratório de Imunogenética, Maringá, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Roberto H. Herai
- Universidade Católica do Paraná (PUCPR), Faculdade de Medicina, Programa de Pós-Graduação em Ciências da Saúde, Laboratório Experimental Multiusuário, Curitiba, PR, Brazil
- Universitário Católico Salesiano Auxilium (UNISALESIANO), Faculdade de Medicina, Centro Araçatuba, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Roberta Losi Guembarovski
- Universidade Estadual de Londrina, Departamento de Biologia Geral, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Rogério N. Shinsato
- Universidade Católica do Paraná (PUCPR), Faculdade de Medicina, Programa de Pós-Graduação em Ciências da Saúde, Laboratório Experimental Multiusuário, Curitiba, PR, Brazil
- Universitário Católico Salesiano Auxilium (UNISALESIANO), Faculdade de Medicina, Centro Araçatuba, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Rubiana Mara Mainardes
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Farmácia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Silvana Giuliatti
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro Regional de Ribeirão Preto, Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Sueli Fumie Yamada-Ogatta
- Universidade Estadual de Londrina, Departamento de Microbiologia, Centro de Ciências Biológicas, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Viviane Knuppel de Quadros Gerber
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Enfermagem, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Wander Rogério Pavanelli
- Universidade Estadual de Londrina, Laboratório de Imunoparasitologia de Doenças Negligenciadas e Câncer, Londrina, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Weber Claudio da Silva
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Departamento de Farmácia, Guarapuava, PR, Brazil
- Universidade Estadual do Centro-Oeste do Paraná (UNICENTRO), Laboratório de Neuropsicofarmacologia, Guarapuava, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Maria Luiza Petzl-Erler
- Universidade Federal do Paraná, Programa de Pós-Graduação em Genética, Departamento de Genética, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Valeria Valente
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
- Faculdade de Medicina de Ribeirão Preto, Centro de Terapia Celular (CEPID/FAPESP), Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Christiane Pienna Soares
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Luciane Regina Cavalli
- Faculdades Pequeno Príncipe, Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, PR, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
| | - Wilson Araujo Silva
- Instituto para Pesquisa do Câncer (IPEC), Guarapuava, PR, Brazil
- Faculdade de Medicina de Ribeirão Preto, Centro de Terapia Celular (CEPID/FAPESP), Ribeirão Preto, SP, Brazil
- Instituto Nacional de Ciência e Tecnologia em Células-Tronco e Terapia Celular (INCT/CNPq), Ribeirão Preto, SP, Brazil
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil
- Novos Arranjos de Pesquisa e Inovação - Genômica (NAPI-Genômica), Fundação Araucária, PR, Brazil
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Rokni M, Heidari Nia M, Sarhadi M, Mirinejad S, Sargazi S, Moudi M, Saravani R, Rahdar S, Kargar M. Association of TMPRSS2 Gene Polymorphisms with COVID-19 Severity and Mortality: a Case-Control Study with Computational Analyses. Appl Biochem Biotechnol 2022; 194:3507-3526. [PMID: 35386063 PMCID: PMC8986508 DOI: 10.1007/s12010-022-03885-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/14/2022] [Indexed: 12/12/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is a severe disease caused by a new variant of beta-coronavirus that first appeared in China. Human genetic factors, including polymorphisms, serve pivotal roles in the high transmission of SARS-CoV-2 and the stubbornly progressing sickness seen in a small but significant percentage of infected people; however, but these factors remain ill-defined. A total of 288 COVID-19 patients and 288 controls were genotyped for TMPRSS2 polymorphisms using both restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR) and amplification refractory mutation system (ARMS)-PCR techniques. Different genotypes of TMPRSS2 polymorphisms were compared in terms of disease susceptibility and mortality. The statistical analysis showed that minor alleles of all studied variants statistically increased the risk of COVID-19, except for the rs75603675 C > A variant. The T allele of rs12329760 conferred an increased risk of COVID-19. Moreover, the AG/AC/TT/AG combination of genotypes significantly enhanced the risk of COVID-19 in our population. Different haplotypes of rs17854725/rs75603675/rs12329760/rs4303795 polymorphisms, including GACA, GACG, GATG, GATA, AATA, ACCG, ACTG, ACTA, GCCA, and GCTG, were found to be associated with increased risk of the disease (odds ratio > 1). Regarding the clinical and paraclinical characteristics, a statistically significant difference was found between non-severe and severe forms except for gender, platelet, C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), and underlying diseases. In addition, case genotypes of TMPRSS2 rs17854725 A > G, rs12329760 C > T, and rs4303795 A > G were significantly different regarding severe and non-severe forms of the disease (P-value < 0.001). Specifically, death was more frequent in carriers of the AG genotype of rs17854725 A > G (P-value = 0.022). Patients who carry the minor alleles of the four studied TMPRSS2 variants were rather vulnerable to COVID-19 infection. Our findings indicated that rs17854725 A > G (AA vs. AG and AA vs. GG), rs12329760 C > T (CC vs. CT and CC vs. TT), and rs4303795 A > G (AA vs. AG) genotypes of TMPRSS2 variations are associated with a more invasive disorder pattern. More studies on larger populations are needed to confirm our results.
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Affiliation(s)
- Mohsen Rokni
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Milad Heidari Nia
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, 9816743463, Iran
| | - Mohammad Sarhadi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, 9816743463, Iran
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, 9816743463, Iran
| | - Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, 9816743463, Iran.
| | - Mahdiyeh Moudi
- Genetics of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ramin Saravani
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, 9816743463, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Sara Rahdar
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, 9816743463, Iran
| | - Maryam Kargar
- Department of Laboratory Hematology and Blood Bank, School of Allied Medical Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Abstract
Coronavirus disease (COVID-19) is an infectious disease caused by a newly discovered coronavirus, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). There is growing evidence that host genetics play an important role in COVID-19 severity. Based on current knowledge about the human protein machinery for SARS-CoV-2 entry, the host innate immune response, and virus-host interactions, the potential effects of human genetic polymorphisms, which may contribute to clinical differences in SARS-CoV-2 pathogenesis, may help to determine the individual risk for COVID-19 infection and outcome.
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Affiliation(s)
- Joris R Delanghe
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.
| | - Marijn M Speeckaert
- Department of Nephrology, Ghent University Hospital, Ghent, Belgium; Research Foundation-Flanders (FWO), Brussels, Belgium
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30
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Pandey RK, Srivastava A, Singh PP, Chaubey G. Genetic association of TMPRSS2 rs2070788 polymorphism with COVID-19 case fatality rate among Indian populations. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 98:105206. [PMID: 34995811 PMCID: PMC8730738 DOI: 10.1016/j.meegid.2022.105206] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/30/2021] [Accepted: 01/03/2022] [Indexed: 11/17/2022]
Abstract
SARS-CoV-2, the causative agent for COVID-19, an ongoing pandemic, engages the ACE2 receptor to enter the host cell through S protein priming by a serine protease, TMPRSS2. Variation in the TMPRSS2 gene may account for the disparity in disease susceptibility between populations. Therefore, in the present study, we have used next-generation sequencing (NGS) data of world populations from 393 individuals and analyzed the TMPRSS2 gene using a haplotype-based approach with a major focus on South Asia to study its phylogenetic structure and their haplotype sharing among various populations worldwide. Our analysis of phylogenetic relatedness showed a closer affinity of South Asians with the West Eurasian populations therefore, host disease susceptibility and severity particularly in the context of TMPRSS2 will be more akin to West Eurasian instead of East Eurasian. This is in contrast to our prior study on the ACE2 gene which shows South Asian haplotypes have a strong affinity towards West Eurasians. Thus ACE2 and TMPRSS2 have an antagonistic genetic relatedness among South Asians. Considering the significance of the TMPRSS2 gene in the SARS-CoV-2 pathogenicity, COVID-19 infection and intensity trends could be directly associated with increased expression therefore, we have also tested the SNPs frequencies of this gene among various Indian state populations with respect to the case fatality rate (CFR). Interestingly, we found a significant positive association between the rs2070788 SNP (G Allele) and the CFR among Indian populations. Further our cis eQTL analysis of rs2070788 shows that the GG genotype of the rs2070788 tends to have a significantly higher expression of TMPRSS2 gene in the lung compared to the AG and AA genotypes thus validating the previous observation and therefore it might play a vital part in determining differential disease vulnerability. We trust that this information will be useful in understanding the role of the TMPRSS2 variant in COVID-19 susceptibility and using it as a biomarker may help to predict populations at risk.
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Affiliation(s)
- Rudra Kumar Pandey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, India.
| | - Anshika Srivastava
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, India
| | - Prajjval Pratap Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, India.
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31
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In Silico Molecular Characterization of Human TMPRSS2 Protease Polymorphic Variants and Associated SARS-CoV-2 Susceptibility. Life (Basel) 2022; 12:life12020231. [PMID: 35207518 PMCID: PMC8876804 DOI: 10.3390/life12020231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/19/2022] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
The 2019 coronavirus disease (COVID-19) pandemic continues to challenge health care systems worldwide. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for the cause of global pandemic. Type 2 transmembrane serine protease (TMPRSS2) is important in the cell entry and spread of SARS-CoV-2 and plays a crucial role in the proteolytic cleavage of SARS-CoV-2 spike (S) glycoprotein. Here, using reported structural data, we analyzed the molecular complex of TMPRSS2 and the S glycoprotein and further examined intermolecular interactions of natural TMPRSS2 polymorphic variants. We identified several TMPRSS2 variants that could possibly alter host susceptibility to the SARS-CoV-2 infection. Molecular docking analysis revealed that G462D/G462S variants were predicted to be protective variants, whereas Q438E and S339F variants were predicted to increase susceptibility. In addition, we examined intermolecular interactions between TMPRSS2 and its two potential serine protease inhibitors, camostat mesylate and nafamostat. Further, we investigated the effect of TMPRSS2 variants on these interactions. Our structural analysis revealed that G462D, C297S and S460R variants had possibly altered the interactions with the protease inhibitors. Our results identified important TMPRSS2 variations that could be useful to develop high affinity and personalized drugs for treating COVID-19 patients.
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32
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Sarubbo F, El Haji K, Vidal-Balle A, Bargay Lleonart J. Neurological consequences of COVID-19 and brain related pathogenic mechanisms: A new challenge for neuroscience. Brain Behav Immun Health 2022; 19:100399. [PMID: 34870247 PMCID: PMC8629776 DOI: 10.1016/j.bbih.2021.100399] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 12/15/2022] Open
Abstract
Due to the infection by the SARS-CoV-2 virus (COVID-19) there were also reported neurological symptoms, being the most frequent and best cited those that affect the cerebrovascular, sensorial, cognitive and motor functions, together with the neurological diffuse symptoms as for examples headache or dizziness. Besides, some of them behave high risk of mortality. Consequently, it is crucial to elucidate the mechanisms of action in brain of SARS-CoV-2 virus in order to create new therapeutic targets to fight against this new disease. Since now the mechanisms of arrival to the brain seems to be related with the following processes: blood brain barrier (BBB) disruption together with nervous or axonal transport of the virus by the trigeminal nerve, the vagus nerve, or the brain-gut-axis. Being two the mechanisms of brain affectation most cited: a direct affectation of the virus in the brain through neuroinvasion and an indirect mechanism of action due to the effects of the systemic infection. Both processes include the triggering of inflammation, hypoxia and the increased likelihood of secondary infections. This topic supposes a major novel challenge for neuroscience. Therefore, the aim of this review is to provide summarized information about the neurological symptomatology and the brain pathogenic mechanisms involved and reported in COVID-19.
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Affiliation(s)
- Fiorella Sarubbo
- Research Unit, University Hospital Son Llàtzer, Health Research Institute of the Balearic Islands (IdISBa), Crta, Manacor Km 4, 07198, Palma, Spain
- University of the Balearic Islands (UIB), Biology Department, Mallorca, Spain
- University of the Balearic Islands (UIB), Medicine Faculty, Mallorca, Spain
| | - Khaoulah El Haji
- Research Unit, University Hospital Son Llàtzer, Health Research Institute of the Balearic Islands (IdISBa), Crta, Manacor Km 4, 07198, Palma, Spain
| | - Aina Vidal-Balle
- Research Unit, University Hospital Son Llàtzer, Health Research Institute of the Balearic Islands (IdISBa), Crta, Manacor Km 4, 07198, Palma, Spain
| | - Joan Bargay Lleonart
- Research Unit, University Hospital Son Llàtzer, Health Research Institute of the Balearic Islands (IdISBa), Crta, Manacor Km 4, 07198, Palma, Spain
- University of the Balearic Islands (UIB), Medicine Faculty, Mallorca, Spain
- Hematology Department, University Hospital Son Llàtzer, Crta, Manacor Km 4, 07198, Palma, Spain
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Zepeda-Cervantes J, Martínez-Flores D, Ramírez-Jarquín JO, Tecalco-Cruz ÁC, Alavez-Pérez NS, Vaca L, Sarmiento-Silva RE. Implications of the Immune Polymorphisms of the Host and the Genetic Variability of SARS-CoV-2 in the Development of COVID-19. Viruses 2022; 14:94. [PMID: 35062298 PMCID: PMC8778858 DOI: 10.3390/v14010094] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 01/08/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current pandemic affecting almost all countries in the world. SARS-CoV-2 is the agent responsible for coronavirus disease 19 (COVID-19), which has claimed millions of lives around the world. In most patients, SARS-CoV-2 infection does not cause clinical signs. However, some infected people develop symptoms, which include loss of smell or taste, fever, dry cough, headache, severe pneumonia, as well as coagulation disorders. The aim of this work is to report genetic factors of SARS-CoV-2 and host-associated to severe COVID-19, placing special emphasis on the viral entry and molecules of the immune system involved with viral infection. Besides this, we analyze SARS-CoV-2 variants and their structural characteristics related to the binding to polymorphic angiotensin-converting enzyme type 2 (ACE2). Additionally, we also review other polymorphisms as well as some epigenetic factors involved in the immunopathogenesis of COVID-19. These factors and viral variability could explain the increment of infection rate and/or in the development of severe COVID-19.
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Affiliation(s)
- Jesús Zepeda-Cervantes
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Daniel Martínez-Flores
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Josué Orlando Ramírez-Jarquín
- Departamento de Neuropatología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Ángeles C. Tecalco-Cruz
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), Mexico City 06720, Mexico;
| | - Noé Santiago Alavez-Pérez
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07340, Mexico;
| | - Luis Vaca
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Rosa Elena Sarmiento-Silva
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
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34
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Jeon S, Blazyte A, Yoon C, Ryu H, Jeon Y, Bhak Y, Bolser D, Manica A, Shin ES, Cho YS, Kim BC, Ryoo N, Choi H, Bhak J. Regional TMPRSS2 V197M Allele Frequencies Are Correlated with COVID-19 Case Fatality Rates. Mol Cells 2021; 44:680-687. [PMID: 34588322 PMCID: PMC8490206 DOI: 10.14348/molcells.2021.2249] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 06/14/2021] [Accepted: 07/10/2021] [Indexed: 02/08/2023] Open
Abstract
Coronavirus disease, COVID-19 (coronavirus disease 2019), caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), has a higher case fatality rate in European countries than in others, especially East Asian ones. One potential explanation for this regional difference is the diversity of the viral infection efficiency. Here, we analyzed the allele frequencies of a nonsynonymous variant rs12329760 (V197M) in the TMPRSS2 gene, a key enzyme essential for viral infection and found a significant association between the COVID-19 case fatality rate and the V197M allele frequencies, using over 200,000 present-day and ancient genomic samples. East Asian countries have higher V197M allele frequencies than other regions, including European countries which correlates to their lower case fatality rates. Structural and energy calculation analysis of the V197M amino acid change showed that it destabilizes the TMPRSS2 protein, possibly negatively affecting its ACE2 and viral spike protein processing.
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Affiliation(s)
- Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, UNIST, Ulsan 44919, Korea
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, UNIST, Ulsan 44919, Korea
| | - Changhan Yoon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, UNIST, Ulsan 44919, Korea
| | - Hyojung Ryu
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, UNIST, Ulsan 44919, Korea
| | - Yeonsu Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, UNIST, Ulsan 44919, Korea
| | - Youngjune Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, UNIST, Ulsan 44919, Korea
| | | | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Eun-Seok Shin
- Division of Cardiology, Department of Internal Medicine, Ulsan Medical Center, Ulsan 44686, Korea
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Cheongju 28160, Korea
| | | | | | - Namhee Ryoo
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu 42601, Korea
| | - Hansol Choi
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, UNIST, Ulsan 44919, Korea
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, UNIST, Ulsan 44919, Korea
- Geromics, Ltd., Cambridge CB1 3NF, UK
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Cheongju 28160, Korea
- Clinomics, Inc., Ulsan 44919, Korea
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35
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Paniri A, Hosseini MM, Akhavan-Niaki H. Impact of new UK (B.1.1.7) SARS-Cov-2 variant on interacting with ACE2 and host immune response. GENE REPORTS 2021; 25:101342. [PMID: 34493993 PMCID: PMC8414842 DOI: 10.1016/j.genrep.2021.101342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 07/28/2021] [Accepted: 08/31/2021] [Indexed: 11/25/2022]
Affiliation(s)
- Alireza Paniri
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran.,Genetics Department, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
| | | | - Haleh Akhavan-Niaki
- Genetics Department, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.,Zoonoses Research Center, Pasteur Institute of Iran, Amol, Iran
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36
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Rahbar Saadat Y, Hosseiniyan Khatibi SM, Zununi Vahed S, Ardalan M. Host Serine Proteases: A Potential Targeted Therapy for COVID-19 and Influenza. Front Mol Biosci 2021; 8:725528. [PMID: 34527703 PMCID: PMC8435734 DOI: 10.3389/fmolb.2021.725528] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/11/2021] [Indexed: 12/23/2022] Open
Abstract
The ongoing pandemic illustrates limited therapeutic options for controlling SARS-CoV-2 infections, calling a need for additional therapeutic targets. The viral spike S glycoprotein binds to the human receptor angiotensin-converting enzyme 2 (ACE2) and then is activated by the host proteases. Based on the accessibility of the cellular proteases needed for SARS-S activation, SARS-CoV-2 entrance and activation can be mediated by endosomal (such as cathepsin L) and non-endosomal pathways. Evidence indicates that in the non-endosomal pathway, the viral S protein is cleaved by the furin enzyme in infected host cells. To help the virus enter efficiently, the S protein is further activated by the serine protease 2 (TMPRSS2), provided that the S has been cleaved by furin previously. In this review, important roles for host proteases within host cells will be outlined in SARS-CoV-2 infection and antiviral therapeutic strategies will be highlighted. Although there are at least five highly effective vaccines at this time, the appearance of the new viral mutations demands the development of therapeutic agents. Targeted inhibition of host proteases can be used as a therapeutic approach for viral infection.
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37
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Quimque MTJ, Notarte KIR, Fernandez RAT, Mendoza MAO, Liman RAD, Lim JAK, Pilapil LAE, Ong JKH, Pastrana AM, Khan A, Wei DQ, Macabeo APG. Virtual screening-driven drug discovery of SARS-CoV2 enzyme inhibitors targeting viral attachment, replication, post-translational modification and host immunity evasion infection mechanisms. J Biomol Struct Dyn 2021; 39:4316-4333. [PMID: 32476574 PMCID: PMC7309309 DOI: 10.1080/07391102.2020.1776639] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 05/25/2020] [Indexed: 01/01/2023]
Abstract
The novel coronavirus SARS-CoV2, the causative agent of the pandemic disease COVID-19, emerged in December 2019 forcing lockdown of communities in many countries. The absence of specific drugs and vaccines, the rapid transmission of the virus, and the increasing number of deaths worldwide necessitated the discovery of new substances for anti-COVID-19 drug development. With the aid of bioinformatics and computational modelling, ninety seven antiviral secondary metabolites from fungi were docked onto five SARS-CoV2 enzymes involved in viral attachment, replication, post-translational modification, and host immunity evasion infection mechanisms followed by molecular dynamics simulation and in silico ADMET prediction (absorption, distribution, metabolism, excretion and toxicity) of the hit compounds. Thus, three fumiquinazoline alkaloids scedapin C (15), quinadoline B (19) and norquinadoline A (20), the polyketide isochaetochromin D1 (8), and the terpenoid 11a-dehydroxyisoterreulactone A (11) exhibited high binding affinities on the target proteins, papain-like protease (PLpro), chymotrypsin-like protease (3CLpro), RNA-directed RNA polymerase (RdRp), non-structural protein 15 (nsp15), and the spike binding domain to GRP78. Molecular dynamics simulation was performed to optimize the interaction and investigate the stability of the top-scoring ligands in complex with the five target proteins. All tested complexes were found to have dynamic stability. Of the five top-scoring metabolites, quinadoline B (19) was predicted to confer favorable ADMET values, high gastrointestinal absorptive probability and poor blood-brain barrier crossing capacities.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mark Tristan J. Quimque
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Chemistry Department, College of Science and Mathematics, Mindanao State University – Iligan Institute of Technology, Tibanga, Iligan City, Philippines
| | | | | | - Mark Andrew O. Mendoza
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | | | - Justin Allen K. Lim
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Luis Agustin E. Pilapil
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Jehiel Karsten H. Ong
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Adriel M. Pastrana
- Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines
| | - Abbas Khan
- Department of Bioinformatics and Biostatistics, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biostatistics, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, China
| | - Allan Patrick G. Macabeo
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
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Kucher AN, Babushkina NP, Sleptcov AA, Nazarenko MS. Genetic Control of Human Infection with SARS-CoV-2. RUSS J GENET+ 2021; 57:627-641. [PMID: 34248311 PMCID: PMC8254434 DOI: 10.1134/s1022795421050057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/26/2020] [Accepted: 08/25/2020] [Indexed: 01/21/2023]
Abstract
In 2019, the SARS-CoV-2 beta-coronavirus, which caused a pandemic of severe acute respiratory viral infection COVID-19 (from COronaVIrus Disease 2019), was first detected. The susceptibility to SARS-CoV-2 and the nature of the course of the COVID-19 clinical picture are determined by many factors, including genetic characteristics of both the pathogen and the human. The SARS-CoV-2 genome has a similarity to the genomes of other coronaviruses, which are pathogenic for humans and cause a severe course of infection: 79% to the SARS-CoV genome and 50% to the MERS-CoV genome. The most significant differences between SARS-CoV-2 and other coronaviruses are recorded in the structure of the gene of the S protein, a key protein responsible for the virus binding to the receptor of the host organism cells. In particular, substitutions in the S protein of SARS-CoV-2, leading to the formation of the furin cleavage site that is absent in other SARS-like coronaviruses, were identified, which may explain the high pathogenicity of SARS-CoV-2. In humans, the genes that are significant for the initial stages of infection include ACE2, ANPEP, DPP4 (encode receptors for coronavirus binding); TMPRSS2, FURIN, TMPRSS11D, CTSL, CTSB (encode proteases involved in the entry of the coronavirus into the cell); DDX1 (the gene of ATP-dependent RNA helicase DDX1, which promotes replication of coronaviruses); and IFITM1, IFITM2, and IFITM3 (encode interferon-induced transmembrane proteins with an antiviral effect). These genes are expressed in many tissues (including those susceptible to the effects of SARS-CoV-2); rare and frequent variants that affect the structure of the encoded protein and its properties and expression level are described in them. A number of common genetic variants with proven functional significance are characterized by the variability in the allele frequency in the world's populations, which can determine interpopulation differences in the prevalence of COVID-19 and in the clinical features of the course of this pathology. The expression level of genes that are important for the formation of the susceptibility to SARS-CoV-2 is affected by epigenetic modifications, comorbidities at the time of infection, taking medications, and bad habits.
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Affiliation(s)
- A. N. Kucher
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, 634050 Tomsk, Russia
| | - N. P. Babushkina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, 634050 Tomsk, Russia
| | - A. A. Sleptcov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, 634050 Tomsk, Russia
| | - M. S. Nazarenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, 634050 Tomsk, Russia
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Yildirim Z, Sahin OS, Yazar S, Bozok Cetintas V. Genetic and epigenetic factors associated with increased severity of Covid-19. Cell Biol Int 2021; 45:1158-1174. [PMID: 33590936 PMCID: PMC8014716 DOI: 10.1002/cbin.11572] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 02/14/2021] [Indexed: 01/07/2023]
Abstract
Since December 2019, a new form of severe acute respiratory syndrome (SARS) from a novel strain of coronavirus (SARS coronavirus 2 [SARS-CoV-2]) has been spreading worldwide. The disease caused by SARS-CoV-2 was named Covid-19 and declared as a pandemic by the World Health Organization in March 2020. Clinical symptoms of Covid-19 range from common cold to more severe disease defined as pneumonia, hypoxia, and severe respiratory distress. In the next stage, disease can become more critical with respiratory failure, sepsis, septic shock, and/or multiorgan failure. Outcomes of Covid-19 indicate large gaps between the male-female and the young-elder groups. Several theories have been proposed to explain variations, such as gender, age, comorbidity, and genetic factors. It is likely that mixture of genetic and nongenetic factors interplays between virus and host genetics and determines the severity of disease outcome. In this review, we aimed to summarize current literature in terms of potential host genetic and epigenetic factors that associated with increased severity of Covid-19. Several studies indicated that the genetic variants of the SARS-CoV-2 entry mechanism-related (angiotensin-converting enzymes, transmembrane serine protease-2, furin) and host innate immune response-related genes (interferons [IFNs], interleukins, toll-like receptors), and human leukocyte antigen, ABO, 3p21.31, and 9q34.2 loci are critical host determinants related to Covid-19 severity. Epigenetic mechanisms also affect Covid-19 outcomes by regulating IFN signaling, angiotensin-converting enzyme-2, and immunity-related genes that particularly escape from X chromosome inactivation. Enhanced understanding of host genetic and epigenetic factors and viral interactions of SARS-CoV-2 is critical for improved prognostic tools and innovative therapeutics.
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Affiliation(s)
- Zafer Yildirim
- Department of Medical Biology, Faculty of MedicineEge UniversityIzmirTurkey
| | - Oyku Semahat Sahin
- Department of Medical Biology, Faculty of MedicineEge UniversityIzmirTurkey
| | - Seyhan Yazar
- Garvan‐Weizmann Centre for Cellular GenomicsGarvan Institute of Medical ResearchSydneyNew South WalesAustralia
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Lui GCY, Yip TCF, Wong VWS, Chow VCY, Ho THY, Li TCM, Tse YK, Chan HLY, Hui DSC, Wong GLH. Significantly Lower Case-fatality Ratio of Coronavirus Disease 2019 (COVID-19) than Severe Acute Respiratory Syndrome (SARS) in Hong Kong-A Territory-Wide Cohort Study. Clin Infect Dis 2021; 72:e466-e475. [PMID: 33005933 PMCID: PMC7543259 DOI: 10.1093/cid/ciaa1187] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/10/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The case-fatality ratios (CFR) of coronavirus disease 2019 (COVID-19) and severe acute respiratory syndrome (SARS) appeared to differ substantially. We aimed to compare the CFR and its predictors of COVID-19 and SARS patients using a territory-wide cohort in Hong Kong. METHODS This was a territory-wide retrospective cohort study using data captured from all public hospitals in Hong Kong. Laboratory-confirmed COVID-19 and SARS patients were identified. The primary endpoint was a composite endpoint of intensive care unit admission, use of mechanical ventilation, and/or death. RESULTS We identified 1013 COVID-19 patients (mean age, 38.4 years; 53.9% male) diagnosed from 23 January to 14 April 2020 and 1670 SARS patients (mean age, 44.4 years; 44.0% male) from March to June 2003. Fifty-five (5.4%) COVID-19 patients and 432 (25.9%) SARS patients had reached the primary endpoint in 30 days. By 30 June 2003, 286 SARS patients had died (CFR, 17.1%). By 7 June 2020, 4 COVID-19 patients had died (CFR, 0.4%). After adjusting for demographic and clinical parameters, COVID-19 was associated with a 71% lower risk of primary endpoint compared with SARS (adjusted hazard ratio, 0.29; 95% confidence interval, .21-.40; P < .0001). Age, diabetes mellitus, and laboratory parameters (high lactate dehydrogenase, high C-reactive protein, and low platelet count) were independent predictors of the primary endpoint in COVID-19 patients, whereas use of antiviral treatments was not associated with primary endpoint. CONCLUSIONS The CFR of COVID-19 was 0.4%. Age and diabetes were associated with worse outcomes, whereas antiviral treatments were not.
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Affiliation(s)
- Grace Chung-Yan Lui
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Medical Data Analytic Centre (MDAC), The Chinese University of Hong Kong, Hong Kong SAR, China
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Terry Cheuk-Fung Yip
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Medical Data Analytic Centre (MDAC), The Chinese University of Hong Kong, Hong Kong SAR, China
- Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, Chinaand
| | - Vincent Wai-Sun Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Medical Data Analytic Centre (MDAC), The Chinese University of Hong Kong, Hong Kong SAR, China
- Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, Chinaand
| | | | - Tracy Hang-Yee Ho
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Timothy Chun-Man Li
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yee-Kit Tse
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Medical Data Analytic Centre (MDAC), The Chinese University of Hong Kong, Hong Kong SAR, China
- Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, Chinaand
| | - Henry Lik-Yuen Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Medical Data Analytic Centre (MDAC), The Chinese University of Hong Kong, Hong Kong SAR, China
- Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, Chinaand
| | - David Shu-Cheong Hui
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Medical Data Analytic Centre (MDAC), The Chinese University of Hong Kong, Hong Kong SAR, China
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Grace Lai-Hung Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Medical Data Analytic Centre (MDAC), The Chinese University of Hong Kong, Hong Kong SAR, China
- Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, Chinaand
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41
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Wulandari L, Hamidah B, Pakpahan C, Damayanti NS, Kurniati ND, Adiatmaja CO, Wigianita MR, Soedarsono, Husada D, Tinduh D, Prakoeswa CRS, Endaryanto A, Puspaningsih NNT, Mori Y, Lusida MI, Shimizu K, Oceandy D. Initial study on TMPRSS2 p.Val160Met genetic variant in COVID-19 patients. Hum Genomics 2021; 15:29. [PMID: 34001248 PMCID: PMC8127183 DOI: 10.1186/s40246-021-00330-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/04/2021] [Indexed: 11/19/2022] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) is a global health problem that causes millions of deaths worldwide. The clinical manifestation of COVID-19 widely varies from asymptomatic infection to severe pneumonia and systemic inflammatory disease. It is thought that host genetic variability may affect the host’s response to the virus infection and thus cause severity of the disease. The SARS-CoV-2 virus requires interaction with its receptor complex in the host cells before infection. The transmembrane protease serine 2 (TMPRSS2) has been identified as one of the key molecules involved in SARS-CoV-2 virus receptor binding and cell invasion. Therefore, in this study, we investigated the correlation between a genetic variant within the human TMPRSS2 gene and COVID-19 severity and viral load. Results We genotyped 95 patients with COVID-19 hospitalised in Dr Soetomo General Hospital and Indrapura Field Hospital (Surabaya, Indonesia) for the TMPRSS2 p.Val160Met polymorphism. Polymorphism was detected using a TaqMan assay. We then analysed the association between the presence of the genetic variant and disease severity and viral load. We did not observe any correlation between the presence of TMPRSS2 genetic variant and the severity of the disease. However, we identified a significant association between the p.Val160Met polymorphism and the SARS-CoV-2 viral load, as estimated by the Ct value of the diagnostic nucleic acid amplification test. Furthermore, we observed a trend of association between the presence of the C allele and the mortality rate in patients with severe COVID-19. Conclusion Our data indicate a possible association between TMPRSS2 p.Val160Met polymorphism and SARS-CoV-2 infectivity and the outcome of COVID-19. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-021-00330-7.
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Affiliation(s)
- Laksmi Wulandari
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Airlangga/Dr Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Berliana Hamidah
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Cennikon Pakpahan
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.,Andrology Program, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | | | - Neneng Dewi Kurniati
- Department of Medical Microbiology, Faculty of Medicine, Universitas Airlangga/Clinical Microbiology Unit, Central Laboratory Installation, Dr Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Christophorus Oetama Adiatmaja
- Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.,Clinical Pathology Program, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | | | - Soedarsono
- Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Airlangga/Dr Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Dominicus Husada
- Department of Child Health, Faculty of Medicine, Universitas Airlangga/Dr Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Damayanti Tinduh
- Department of Physical Medicine and Rehabilitation, Faculty of Medicine, Universitas Airlangga/Dr Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Cita Rosita Sigit Prakoeswa
- Department of Dermatology Venerology, Faculty of Medicine, Universitas Airlangga/Dr. Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Anang Endaryanto
- Department of Child Health, Faculty of Medicine, Universitas Airlangga/Dr Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Ni Nyoman Tri Puspaningsih
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia.,Laboratory of Proteomic, University CoE-Research Center for Bio-Molecule Engineering, Universitas Airlangga, Surabaya, Indonesia
| | - Yasuko Mori
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kusunoki-cho, Chuo-ku, Kobe, Japan
| | - Maria Inge Lusida
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Department of Microbiology, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Kazufumi Shimizu
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kusunoki-cho, Chuo-ku, Kobe, Japan.,CRC-ERID, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Delvac Oceandy
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
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42
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Andolfo I, Russo R, Lasorsa VA, Cantalupo S, Rosato BE, Bonfiglio F, Frisso G, Abete P, Cassese GM, Servillo G, Esposito G, Gentile I, Piscopo C, Villani R, Fiorentino G, Cerino P, Buonerba C, Pierri B, Zollo M, Iolascon A, Capasso M. Common variants at 21q22.3 locus influence MX1 and TMPRSS2 gene expression and susceptibility to severe COVID-19. iScience 2021; 24:102322. [PMID: 33748697 PMCID: PMC7968217 DOI: 10.1016/j.isci.2021.102322] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/15/2021] [Accepted: 03/15/2021] [Indexed: 12/15/2022] Open
Abstract
The established risk factors of coronavirus disease 2019 (COVID-19) are advanced age, male sex, and comorbidities, but they do not fully explain the wide spectrum of disease manifestations. Genetic factors implicated in the host antiviral response provide for novel insights into its pathogenesis. We performed an in-depth genetic analysis of chromosome 21 exploiting the genome-wide association study data, including 6,406 individuals hospitalized for COVID-19 and 902,088 controls with European genetic ancestry from the COVID-19 Host Genetics Initiative. We found that five single nucleotide polymorphisms within TMPRSS2 and near MX1 gene show associations with severe COVID-19. The minor alleles of the five single nucleotide polymorphisms (SNPs) correlated with a reduced risk of developing severe COVID-19 and high level of MX1 expression in blood. Our findings demonstrate that host genetic factors can influence the different clinical presentations of COVID-19 and that MX1 could be a potential therapeutic target.
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Affiliation(s)
- Immacolata Andolfo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Roberta Russo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Vito Alessandro Lasorsa
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Sueva Cantalupo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Barbara Eleni Rosato
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Ferdinando Bonfiglio
- Dipartimento di Ingegneria chimica, dei Materiali e della Produzione industriale, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Giulia Frisso
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Pasquale Abete
- COVID Hospital, P.O.S. Anna e SS. Madonna della Neve di Boscotrecase, Ospedali Riuniti Area Vesuviana, Napoli, Italy
| | - Gian Marco Cassese
- COVID Hospital, P.O.S. Anna e SS. Madonna della Neve di Boscotrecase, Ospedali Riuniti Area Vesuviana, Napoli, Italy
| | - Giuseppe Servillo
- Dipartimento di Neuroscienze e Scienze riproduttive ed odontostomatologiche, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Gabriella Esposito
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Ivan Gentile
- Dipartimento di Medicina clinica e Chirurgia, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Carmelo Piscopo
- Medical and Laboratory Genetics Unit, A.O.R.N. ‘Antonio Cardarelli’, Napoli, Italy
| | - Romolo Villani
- Poison Centre, A.O.R.N. ‘Antonio Cardarelli’, Napoli, Italy
| | | | - Pellegrino Cerino
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Napoli, Italy
| | - Carlo Buonerba
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Napoli, Italy
| | - Biancamaria Pierri
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Napoli, Italy
- Dipartimento di Medicina, Chirurgia e Odontoiatria "Scuola Medica Salernitana", Università di Salerno, Baronissi, Italy
| | - Massimo Zollo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Achille Iolascon
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
| | - Mario Capasso
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples, Federico II, 80145 Naples, Italy
- CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Napoli, Italy
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Schönfelder K, Breuckmann K, Elsner C, Dittmer U, Fistera D, Herbstreit F, Risse J, Schmidt K, Sutharsan S, Taube C, Jöckel KH, Siffert W, Kribben A, Möhlendick B. Transmembrane serine protease 2 Polymorphisms and Susceptibility to Severe Acute Respiratory Syndrome Coronavirus Type 2 Infection: A German Case-Control Study. Front Genet 2021; 12:667231. [PMID: 33968142 PMCID: PMC8097083 DOI: 10.3389/fgene.2021.667231] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/29/2021] [Indexed: 12/22/2022] Open
Abstract
The transmembrane serine protease 2 (TMPRSS2) is the major host protease that enables entry of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) into host cells by spike (S) protein priming. Single nucleotide polymorphisms (SNPs) in the gene TMPRSS2 have been associated with susceptibility to and severity of H1N1 or H1N9 influenza A virus infections. Functional variants may influence SARS-CoV-2 infection risk and severity of Coronavirus disease 2019 (COVID-19) as well. Therefore, we analyzed the role of SNPs in the gene TMPRSS2 in a German case-control study. We performed genotyping of the SNPs rs2070788, rs383510, and rs12329760 in the gene TMPRSS2 in 239 SARS-CoV-2-positive and 253 SARS-CoV-2-negative patients. We analyzed the association of the SNPs with susceptibility to SARS-CoV-2 infection and severity of COVID-19. SARS-CoV-2-positive and SARS-CoV-2-negative patients did not differ regarding their demographics. The CC genotype of TMPRSS2 rs383510 was associated with a 1.73-fold increased SARS-CoV-2 infection risk, but was not correlated to severity of COVID-19. Neither TMPRSS2 rs2070788 nor rs12329760 polymorphisms were related to SARS-CoV-2 infection risk or severity of COVID-19. In a multivariable analysis (MVA), the rs383510 CC genotype remained an independent predictor for a 2-fold increased SARS-CoV-2 infection risk. In summary, our report appears to be the first showing that the intron variant rs383510 in the gene TMPRSS2 is associated with an increased risk to SARS-CoV-2 infection in a German cohort.
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Affiliation(s)
- Kristina Schönfelder
- Department of Nephrology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Katharina Breuckmann
- Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Carina Elsner
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - David Fistera
- Center of Emergency Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Frank Herbstreit
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Joachim Risse
- Center of Emergency Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Karsten Schmidt
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sivagurunathan Sutharsan
- Department of Pulmonary Medicine, Ruhrlandklinik, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Christian Taube
- Department of Pulmonary Medicine, Ruhrlandklinik, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Karl-Heinz Jöckel
- Institute of Medical Informatics, Biometry and Epidemiology, University of Duisburg-Essen, Essen, Germany
| | - Winfried Siffert
- Institute of Pharmacogenetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Andreas Kribben
- Department of Nephrology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Birte Möhlendick
- Institute of Pharmacogenetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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44
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Monticelli M, Hay Mele B, Benetti E, Fallerini C, Baldassarri M, Furini S, Frullanti E, Mari F, Andreotti G, Cubellis MV, Renieri A. Protective Role of a TMPRSS2 Variant on Severe COVID-19 Outcome in Young Males and Elderly Women. Genes (Basel) 2021; 12:596. [PMID: 33921689 PMCID: PMC8073081 DOI: 10.3390/genes12040596] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 04/09/2021] [Indexed: 02/06/2023] Open
Abstract
The protease encoded by the TMPRSS2 gene facilitates viral infections and has been implicated in the pathogenesis of SARS-CoV-2. We analyzed the TMPRSS2 sequence and correlated the protein variants with the clinical features of a cohort of 1177 patients affected by COVID-19 in Italy. Nine relatively common variants (allele frequency > 0.01) and six missense variants which may affect the protease activity according to PolyPhen-2 in HumVar-trained mode were identified. Among them, p.V197M (p.Val197Met) (rs12329760) emerges as a common variant that has a deleterious effect on the protease and a protective effect on the patients. Its role appears particularly relevant in two subgroups of patients-young males and elderly women-and among those affected by co-morbidities, where the variant frequency is higher among individuals who were mildly affected by the disease and did not need hospitalization or oxygen therapy than among those more severely affected, who required oxygen therapy, ventilation or intubation. This study provides useful information for the identification of patients at risk of developing a severe form of COVID-19, and encourages the usage of drugs affecting the expression of TMPRSS2 or inhibiting protein activity.
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Affiliation(s)
- Maria Monticelli
- Department of Biology, Università Federico II, 80126 Napoli, Italy; (M.M.); (B.H.M.)
| | - Bruno Hay Mele
- Department of Biology, Università Federico II, 80126 Napoli, Italy; (M.M.); (B.H.M.)
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Elisa Benetti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (C.F.); (M.B.); (S.F.); (E.F.); (F.M.); (A.R.)
| | - Chiara Fallerini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (C.F.); (M.B.); (S.F.); (E.F.); (F.M.); (A.R.)
- Medical Genetics, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Margherita Baldassarri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (C.F.); (M.B.); (S.F.); (E.F.); (F.M.); (A.R.)
- Medical Genetics, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Simone Furini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (C.F.); (M.B.); (S.F.); (E.F.); (F.M.); (A.R.)
| | - Elisa Frullanti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (C.F.); (M.B.); (S.F.); (E.F.); (F.M.); (A.R.)
- Medical Genetics, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Francesca Mari
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (C.F.); (M.B.); (S.F.); (E.F.); (F.M.); (A.R.)
- Medical Genetics, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, 53100 Siena, Italy
| | | | | | - Maria Vittoria Cubellis
- Department of Biology, Università Federico II, 80126 Napoli, Italy; (M.M.); (B.H.M.)
- Istituto di Chimica Biomolecolare—CNR, 80078 Pozzuoli, Italy
| | - Alessandra Renieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (E.B.); (C.F.); (M.B.); (S.F.); (E.F.); (F.M.); (A.R.)
- Medical Genetics, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, 53100 Siena, Italy
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45
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Marchi R, Sugita B, Centa A, Fonseca AS, Bortoletto S, Fiorentin K, Ferreira S, Cavalli LR. The role of microRNAs in modulating SARS-CoV-2 infection in human cells: a systematic review. INFECTION GENETICS AND EVOLUTION 2021; 91:104832. [PMID: 33812037 PMCID: PMC8012164 DOI: 10.1016/j.meegid.2021.104832] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 03/11/2021] [Accepted: 03/27/2021] [Indexed: 12/11/2022]
Abstract
MicroRNAs are gene expression regulators, associated with several human pathologies, including the ones caused by virus infections. Although their role in infection diseases is not completely known, they can exert double functions in the infected cell, by mediating the virus infection and/or regulating the immunity-related gene targets through complex networks of virus-host cell interactions. In this systematic review, the Pubmed, EMBASE, Scopus, Lilacs, Scielo, and EBSCO databases were searched for research articles published until October 22nd, 2020 that focused on describing the role, function, and/or association of miRNAs in SARS-CoV-2 human infection and COVID-19. Following the PRISMA 2009 protocol, 29 original research articles were selected. Most of the studies reported miRNA data based on the genome sequencing of SARS-CoV-2 isolates and computational prediction analysis. The latter predicted, by at least one independent study, 1266 host miRNAs to target the viral genome. Thirteen miRNAs were identified by four independent studies to target SARS-CoV-2 specific genes, suggested to act by interfering with their cleavage and/or translation process. The studies selected also reported on viral and host miRNAs that targeted host genes, on the expression levels of miRNAs in biological specimens of COVID-19 patients, and on the impact of viral genome mutations on miRNA function. Also, miRNAs that regulate the expression levels of the ACE2 and TMPRSS2 proteins, which are critical for the virus entrance in the host cells, were reported. In conclusion, despite the limited number of studies identified, based on the search terms and eligibility criteria applied, this systematic review provides evidence on the impact of miRNAs on SARS-CoV-2 infection and COVID-19. Although most of the reported viral/host miRNAs interactions were based on in silico prediction analysis, they demonstrate the relevance of the viral/host miRNA interaction for viral activity and host responses. In addition, the identified studies highlight the potential use of miRNAs as therapeutic targets against COVID-19, and other viral human diseases (This review was registered at the International Prospective Register of Systematic Reviews (PROSPERO) database (#CRD42020199290).
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Affiliation(s)
- Rafael Marchi
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Bruna Sugita
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Ariana Centa
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Aline S Fonseca
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Stefanne Bortoletto
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Karine Fiorentin
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Solange Ferreira
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil
| | - Luciane R Cavalli
- Research Institute Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba, PR, Brazil.
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46
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Huang SW, Wang SF. SARS-CoV-2 Entry Related Viral and Host Genetic Variations: Implications on COVID-19 Severity, Immune Escape, and Infectivity. Int J Mol Sci 2021; 22:3060. [PMID: 33802729 PMCID: PMC8002537 DOI: 10.3390/ijms22063060] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/15/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved to display particular patterns of genetic diversity in the genome across geographical regions. These variations in the virus and genetic variation in human populations can determine virus transmissibility and coronavirus disease 2019 (COVID-19) severity. Genetic variations and immune differences in human populations could be the driving forces in viral evolution. Recently emerged SARS-CoV-2 variants show several mutations at the receptor binding domain in the spike (S) glycoprotein and contribute to immune escape and enhanced binding with angiotensin 1-converting enzyme 2 (ACE2). Since ACE2 and transmembrane protease serine 2 (TMPRSS2) play important roles in SARS-CoV-2 entry into the cell, genetic variation in these host entry-related proteins may be a driving force for positive selection in the SARS-CoV-2 S glycoprotein. Dendritic or liver/lymph cell-specific intercellular adhesion molecule (ICAM)-3-grabbing non-integrin is also known to play vital roles in several pathogens. Genetic variations of these host proteins may affect the susceptibility to SARS-CoV-2. This review summarizes the latest research to describe the impacts of genetic variation in the viral S glycoprotein and critical host proteins and aims to provide better insights for understanding transmission and pathogenesis and more broadly for developing vaccine/antiviral drugs and precision medicine strategies, especially for high risk populations with genetic risk variants.
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Affiliation(s)
- Szu-Wei Huang
- Model Development Section, Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Sheng-Fan Wang
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Clinical Microbiology Laboratory, Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
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47
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Senapati S, Banerjee P, Bhagavatula S, Kushwaha PP, Kumar S. Contributions of human ACE2 and TMPRSS2 in determining host–pathogen interaction of COVID-19. J Genet 2021. [PMID: 33707363 PMCID: PMC7904510 DOI: 10.1007/s12041-021-01262-w] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is at present an emerging global public health crisis. Angiotensin converting enzyme 2 (ACE2) and trans-membrane protease serine 2 (TMPRSS2) are the two major host factors that contribute to the virulence of SARS-CoV-2 and pathogenesis of coronavirus disease-19 (COVID-19). Transmission of SARS-CoV-2 from animal to human is considered a rare event that necessarily requires strong evolutionary adaptations. Till date no other human cellular receptors are identified beside ACE2 for SARS-CoV-2 entry inside the human cell. Proteolytic cleavage of viral spike (S)-protein and ACE2 by TMPRSS2 began the entire host–pathogen interaction initiated with the physical binding of ACE2 to S-protein. SARS-CoV-2 S-protein binds to ACE2 with much higher affinity and stability than that of SARS-CoVs. Molecular interactions between ACE2-S and TMPRSS2-S are crucial and preciously mediated by specific residues. Structural stability, binding affinity and level of expression of these three interacting proteins are key susceptibility factors for COVID-19. Specific protein–protein interactions (PPI) are being identified that explains uniqueness of SARS-CoV-2 infection. Amino acid substitutions due to naturally occurring genetic polymorphisms potentially alter these PPIs and poses further clinical heterogeneity of COVID-19. Repurposing of several phytochemicals and approved drugs against ACE2, TMPRSS2 and S-protein have been proposed that could inhibit PPI between them. We have also identified some novel lead phytochemicals present in Azadirachta indica and Aloe barbadensis which could be utilized for further in vitro and in vivo anti-COVID-19 drug discovery. Uncovering details of ACE2-S and TMPRSS2-S interactions would further contribute to future research on COVID-19.
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Affiliation(s)
- Sabyasachi Senapati
- Immunogenomics Laboratory, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda 151 401, India.
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48
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Al-Mulla F, Mohammad A, Al Madhoun A, Haddad D, Ali H, Eaaswarkhanth M, John SE, Nizam R, Channanath A, Abu-Farha M, Ahmad R, Abubaker J, Thanaraj TA. ACE2 and FURIN variants are potential predictors of SARS-CoV-2 outcome: A time to implement precision medicine against COVID-19. Heliyon 2021; 7:e06133. [PMID: 33532652 PMCID: PMC7843038 DOI: 10.1016/j.heliyon.2021.e06133] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/23/2020] [Accepted: 01/26/2021] [Indexed: 01/08/2023] Open
Abstract
The severity of the new COVID-19 pandemic caused by the SARS-CoV-2 virus is strikingly variable in different global populations. SARS-CoV-2 uses ACE2 as a cell receptor, TMPRSS2 protease, and FURIN peptidase to invade human cells. Here, we investigated 1,378 whole-exome sequences of individuals from the Middle Eastern populations (Kuwait, Qatar, and Iran) to explore natural variations in the ACE2, TMPRSS2, and FURIN genes. We identified two activating variants (K26R and N720D) in the ACE2 gene that are more common in Europeans than in the Middle Eastern, East Asian, and African populations. We postulate that K26R can activate ACE2 and facilitate binding to S-protein RBD while N720D enhances TMPRSS2 cutting and, ultimately, viral entry. We also detected deleterious variants in FURIN that are frequent in the Middle Eastern but not in the European populations. This study highlights specific genetic variations in the ACE2 and FURIN genes that may explain SARS-CoV-2 clinical disparity. We showed structural evidence of the functionality of these activating variants that increase the SARS-CoV-2 aggressiveness. Finally, our data illustrate a significant correlation between ACE2 variants identified in people from Middle Eastern origins that can be further explored to explain the variation in COVID-19 infection and mortality rates globally.
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Affiliation(s)
- Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Ashraf Al Madhoun
- Department of Animal and Imaging Core Facilities, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Dania Haddad
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Hamad Ali
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Health Sciences Center (HSC), Kuwait University, Jabriya, Kuwait
| | | | - Sumi Elsa John
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Rasheeba Nizam
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Arshad Channanath
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Mohamed Abu-Farha
- Department of Special Services Facilities, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Rasheed Ahmad
- Department of Immunology & Microbiology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
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49
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Pereira NL, Ahmad F, Byku M, Cummins NW, Morris AA, Owens A, Tuteja S, Cresci S. COVID-19: Understanding Inter-Individual Variability and Implications for Precision Medicine. Mayo Clin Proc 2021; 96:446-463. [PMID: 33549263 PMCID: PMC7713605 DOI: 10.1016/j.mayocp.2020.11.024] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/09/2020] [Accepted: 11/30/2020] [Indexed: 02/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is characterized by heterogeneity in susceptibility to the disease and severity of illness. Understanding inter-individual variation has important implications for not only allocation of resources but also targeting patients for escalation of care, inclusion in clinical trials, and individualized medical therapy including vaccination. In addition to geographic location and social vulnerability, there are clear biological differences such as age, sex, race, presence of comorbidities, underlying genetic variation, and differential immune response that contribute to variability in disease manifestation. These differences may have implications for precision medicine. Specific examples include the observation that androgens regulate the expression of the enzyme transmembrane protease, serine 2 which facilitates severe acute respiratory syndrome coronavirus 2 viral entry into the cell; therefore, androgen deprivation therapy is being explored as a treatment option in males infected with COVID-19. An immunophenotyping study of COVID-19 patients has shown that a subset develop T cytopenia which has prompted a clinical trial that is testing the efficacy of interleukin-7 in these patients. Predicting which COVID-19 patients will develop progressive disease that will require hospitalization has important implications for clinical trials that target outpatients. Enrollment of patients at low risk for progression of disease and hospitalization would likely not result in such therapy demonstrating efficacy. There are efforts to use artificial intelligence to integrate digital data from smartwatch applications or digital monitoring systems and biological data to enable identification of the high risk COVID-19 patient. The ultimate goal of precision medicine using such modern technology is to recognize individual differences to improve health for all.
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Affiliation(s)
- Naveen L Pereira
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN.
| | - Ferhaan Ahmad
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Iowa Carver College of Medicine Iowa City, IA
| | - Mirnela Byku
- Department of Medicine, Division of Cardiology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Anjali Owens
- Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Sony Tuteja
- Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Sharon Cresci
- Department of Medicine and Genetics, Washington University, St Louis, MO
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50
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Population-Specific ACE2 Single-Nucleotide Polymorphisms Have Limited Impact on SARS-CoV-2 Infectivity In Vitro. Viruses 2021; 13:v13010067. [PMID: 33418950 PMCID: PMC7825141 DOI: 10.3390/v13010067] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 12/25/2020] [Accepted: 12/30/2020] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), employs host-cell angiotensin-converting enzyme 2 (ACE2) for cell entry. Genetic analyses of ACE2 have identified several single-nucleotide polymorphisms (SNPs) specific to different human populations. Molecular dynamics simulations have indicated that several of these SNPs could affect interactions between SARS-CoV-2 and ACE2, thereby providing a partial explanation for the regional differences observed in SARS-CoV-2 infectivity and severity. However, the significance of population-specific ACE2 SNPs in SARS-CoV-2 infectivity is unknown, as no in vitro validation studies have been performed. Here, we analyzed the impact of eight SNPs found in specific populations on receptor binding and cell entry in vitro. Except for a SNP causing a nonsense mutation that reduced ACE2 expression, none of the selected SNPs markedly altered the interaction between ACE2 and the SARS-CoV-2 spike protein (SARS-2-S), which is responsible for receptor recognition and cell entry, or the efficiency of viral cell entry mediated by SARS-2-S. Our findings indicate that ACE2 polymorphisms have limited impact on the ACE2-dependent cell entry of SARS-CoV-2 and underscore the importance of future studies on the involvement of population-specific SNPs of other host genes in susceptibility toward SARS-CoV-2 infection.
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