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Alghamdi S, Baeissa HM, Azhar Kamal M, Rafeeq MM, Al Zahrani A, Maslum AA, Hakeem IJ, Alazragi RS, Alam Q. Unveiling the multitargeted potency of Sodium Danshensu against cervical cancer: a multitargeted docking-based, structural fingerprinting and molecular dynamics simulation study. J Biomol Struct Dyn 2024; 42:8268-8280. [PMID: 37599470 DOI: 10.1080/07391102.2023.2248260] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/30/2023] [Indexed: 08/22/2023]
Abstract
Cervical Cancer (CC) is one of the most common types of cancer in women worldwide, with a significant number of deaths reported yearly. Despite the various treatment options available, the high mortality rate associated with CC highlights the need to develop new and effective therapeutic agents. In this study, we have screened the complete prepared FDA library against the Mitotic kinesin-like protein 1, Cyclin B1, DNA polymerase, and MCM10-ID using three glide-based molecular docking algorithms: HTVS, SP and XP to produce a robust calculation. All four proteins are crucial proteins that actively participate in CC development, and inhibiting them together can be a game-changer step for multitargeted drug designing. Our multitargeted screening identified Sodium (Na) Danshensu, a natural FDA-approved phenolic compound of caffeic acid derivatives isolated from Salvia miltiorrhiza. The docking score ranges from -5.892 to -13.103 Kcal/mol, and the screening study was evaluated with the pharmacokinetics and interaction fingerprinting to identify the pattern of interactions that revealed that the compound has bound to the best site it can be fitted to where maximum bonds were created to make the complex stable. The molecular dynamics simulations for 100 ns were then extended to validate the stability of the protein-ligand complexes. The results provide insight into the repurposing, and Na-danshensu exhibited strong binding affinity and stable complex formation with the target proteins, indicating its potential as a multitargeted drug against CC.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia
| | - Hanadi M Baeissa
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Kingdom of Saudi Arabia
| | - Mohammad Azhar Kamal
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Kingdom of Saudi Arabia
| | - Misbahuddin M Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Abdullah Al Zahrani
- Central Military Laboratory and Blood Bank Department - Microbiology Division, Prince Sultan Military Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Ali Ahmed Maslum
- Central Military Laboratory and Blood Bank Department - Microbiology Division, Prince Sultan Military Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Israa J Hakeem
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Kingdom of Saudi Arabia
| | - Reem S Alazragi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Kingdom of Saudi Arabia
| | - Qamre Alam
- Department of Molecular Genomics and Precision Medicine, ExpressMed Laboratories, Zinj, Kingdom of Bahrain
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Xu Y, Li H, Santosa A, Wettermark B, Fall T, Björk J, Börjesson M, Gisslén M, Nyberg F. Cardiovascular events following coronavirus disease 2019 vaccination in adults: a nationwide Swedish study. Eur Heart J 2024:ehae639. [PMID: 39344920 DOI: 10.1093/eurheartj/ehae639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/27/2024] [Accepted: 09/07/2024] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND AND AIMS While the rationale for coronavirus disease 2019 (COVID-19) vaccination is to reduce complications and overall mortality, some cardiovascular complications from the vaccine itself have been demonstrated. Myocarditis and pericarditis are recognized as rare acute adverse events after mRNA vaccines in young males, while evidence regarding other cardiovascular events remains limited and inconsistent. This study assessed the risks of several cardiovascular and cerebrovascular events in a Swedish nationwide register-based cohort. METHODS Post-vaccination risk of myocarditis/pericarditis, dysrhythmias, heart failure, myocardial infarction, and cerebrovascular events (transient ischaemic attack and stroke) in several risk windows after each vaccine dose were assessed among all Swedish adults (n = 8 070 674). Hazard ratios (HRs) with 95% confidence intervals (95% CIs) compared with unvaccinated were estimated from Cox regression models adjusted for potential confounders. RESULTS For most studied outcomes, decreased risks of cardiovascular events post-vaccination were observed, especially after dose three (HRs for dose three ranging from .69 to .81), while replicating the increased risk of myocarditis and pericarditis 1-2 weeks after COVID-19 mRNA vaccination. Slightly increased risks, similar across vaccines, were observed for extrasystoles [HR 1.17 (95% CI 1.06-1.28) for dose one and HR 1.22 (95% CI 1.10-1.36) for dose two, stronger in elderly and males] but not for arrhythmias and for transient ischaemic attack [HR 1.13 (95% CI 1.05-1.23), mainly in elderly] but not for stroke. CONCLUSIONS Risk of myopericarditis (mRNA vaccines only), extrasystoles, and transient ischaemic attack was transiently increased after COVID-19 vaccination, but full vaccination substantially reduced the risk of several more severe COVID-19-associated cardiovascular outcomes, underscoring the protective benefits of complete vaccination.
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Affiliation(s)
- Yiyi Xu
- School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, BOX 414, 40 530 Gothenburg, Sweden
| | - Huiqi Li
- School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, BOX 414, 40 530 Gothenburg, Sweden
| | - Ailiana Santosa
- School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, BOX 414, 40 530 Gothenburg, Sweden
| | - Björn Wettermark
- Pharmacoepidemiology and Social Pharmacy, Department of Pharmacy, Uppsala University, Uppsala, Sweden
- Pharmacy Centre, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Tove Fall
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jonas Björk
- Department of Laboratory Medicine, Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden
- Clinical Studies Sweden, Forum South, Skåne University Hospital, Lund, Sweden
| | - Mats Börjesson
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Lifestyle Intervention, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Magnus Gisslén
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
- Public Health Agency of Sweden, Solna, Sweden
| | - Fredrik Nyberg
- School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, BOX 414, 40 530 Gothenburg, Sweden
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Ahmad S, Bano N, Khanna K, Gupta D, Raza K. Reporting multitargeted potency of Tiaprofenic acid against lung cancer: Molecular fingerprinting, MD simulation, and MTT-based cell viability assay studies. Int J Biol Macromol 2024; 276:133872. [PMID: 39019378 DOI: 10.1016/j.ijbiomac.2024.133872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/08/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024]
Abstract
Lung Cancer (LC) is among the most death-causing cancers, has caused the most destruction and is a gender-neutral cancer, and WHO has kept this cancer on its priority list to find the cure. We have used high-throughput virtual screening, standard precision docking, and extra precise docking for extensive screening of Drug Bank compounds, and the uniqueness of this study is that it considers multiple protein targets of prognosis and metastasis of LC. The docking and MM\GBSA calculation scores for the Tiaprofenic acid (DB01600) against all ten proteins range from -8.422 to -5.727 kcal/mol and - 47.43 to -25.72 kcal/mol, respectively. Also, molecular fingerprinting helped us to understand the interaction pattern of Tiaprofenic acid among all the proteins. Further, we extended our analysis to the molecular dynamic simulation in a neutralised SPC water medium for 100 ns. We analysed the root mean square deviation, fluctuations, and simulative interactions among the protein, ligand, water molecules, and protein-ligand complexes. Most complexes have shown a deviation of <2 Å as cumulative understanding. Also, the fluctuations were lesser, and only a few residues showed the fluctuation with a huge web of interaction between the protein and ligand, providing an edge that supports that the protein and ligand complexes were stable. In the MTT-based Cell Viability Assay, Tiaprofenic Acid exhibited concentration-dependent anti-cancer efficacy against A549 lung cancer cells, significantly reducing viability at 100 μg/mL. These findings highlight its potential as a therapeutic candidate, urging further exploration into the underlying molecular mechanisms for lung cancer treatment.
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Affiliation(s)
- Shaban Ahmad
- Computational Intelligence and Bioinformatics Lab, Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India.
| | - Nagmi Bano
- Computational Intelligence and Bioinformatics Lab, Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India; Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India.
| | - Kushagra Khanna
- Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur 56000, Malaysia.
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India.
| | - Khalid Raza
- Computational Intelligence and Bioinformatics Lab, Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India.
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Vu Manh TP, Gouin C, De Wolf J, Jouneau L, Pascale F, Bevilacqua C, Ar Gouilh M, Da Costa B, Chevalier C, Glorion M, Hannouche L, Urien C, Estephan J, Magnan A, Le Guen M, Marquant Q, Descamps D, Dalod M, Schwartz-Cornil I, Sage E. SARS-CoV2 infection in whole lung primarily targets macrophages that display subset-specific responses. Cell Mol Life Sci 2024; 81:351. [PMID: 39147987 PMCID: PMC11335275 DOI: 10.1007/s00018-024-05322-z] [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: 11/09/2023] [Revised: 05/22/2024] [Accepted: 06/05/2024] [Indexed: 08/17/2024]
Abstract
Deciphering the initial steps of SARS-CoV-2 infection, that influence COVID-19 outcomes, is challenging because animal models do not always reproduce human biological processes and in vitro systems do not recapitulate the histoarchitecture and cellular composition of respiratory tissues. To address this, we developed an innovative ex vivo model of whole human lung infection with SARS-CoV-2, leveraging a lung transplantation technique. Through single-cell RNA-seq, we identified that alveolar and monocyte-derived macrophages (AMs and MoMacs) were initial targets of the virus. Exposure of isolated lung AMs, MoMacs, classical monocytes and non-classical monocytes (ncMos) to SARS-CoV-2 variants revealed that while all subsets responded, MoMacs produced higher levels of inflammatory cytokines than AMs, and ncMos contributed the least. A Wuhan lineage appeared to be more potent than a D614G virus, in a dose-dependent manner. Amidst the ambiguity in the literature regarding the initial SARS-CoV-2 cell target, our study reveals that AMs and MoMacs are dominant primary entry points for the virus, and suggests that their responses may conduct subsequent injury, depending on their abundance, the viral strain and dose. Interfering on virus interaction with lung macrophages should be considered in prophylactic strategies.
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Affiliation(s)
- Thien-Phong Vu Manh
- Aix-Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, 13009, Marseille, France.
| | - Carla Gouin
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Julien De Wolf
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
- Department of Thoracic Surgery and Lung Transplantation, Foch Hospital, 92150, Suresnes, France
| | - Luc Jouneau
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
- Université Paris-Saclay, INRAE, UVSQ, BREED, 78350, Jouy-en-Josas, France
| | - Florentina Pascale
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
- Department of Thoracic Surgery and Lung Transplantation, Foch Hospital, 92150, Suresnes, France
| | - Claudia Bevilacqua
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Meriadeg Ar Gouilh
- Department of Virology, Univ Caen Normandie, Dynamicure INSERM UMR 1311, CHU Caen, 14000, Caen, France
| | - Bruno Da Costa
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | | | - Matthieu Glorion
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
- Department of Thoracic Surgery and Lung Transplantation, Foch Hospital, 92150, Suresnes, France
| | - Laurent Hannouche
- Aix-Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, 13009, Marseille, France
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Céline Urien
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Jérôme Estephan
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Antoine Magnan
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
- Department of Pulmonology, Foch Hospital, 92150, Suresnes, France
| | - Morgan Le Guen
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
- Department of Anesthesiology, Foch Hospital, 92150, Suresnes, France
| | - Quentin Marquant
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
- Department of Pulmonology, Foch Hospital, 92150, Suresnes, France
- Delegation to Clinical Research and Innovation, Foch Hospital, 92150, Suresnes, France
| | - Delphyne Descamps
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Marc Dalod
- Aix-Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Turing Center for Living Systems, 13009, Marseille, France
| | | | - Edouard Sage
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
- Department of Thoracic Surgery and Lung Transplantation, Foch Hospital, 92150, Suresnes, France
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Barroso-Arévalo S, Sánchez-Morales L, Porras N, Díaz-Frutos M, Barasona JA, Isla J, López D, Gortázar C, Domínguez L, Sánchez-Vizcaíno JM. Comparative SARS-CoV-2 Omicron BA.5 variant and D614G-Wuhan strain infections in ferrets: insights into attenuation and disease progression during subclinical to mild COVID-19. Front Vet Sci 2024; 11:1435464. [PMID: 39211479 PMCID: PMC11358085 DOI: 10.3389/fvets.2024.1435464] [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: 05/20/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024] Open
Abstract
Introduction As the SARS-CoV-2 virus continues to evolve and new variants emerge, it becomes crucial to understand the comparative pathological and immunological responses elicited by different strains. This study focuses on the original Wuhan strain and the Omicron variant, which have demonstrated significant differences in clinical outcomes and immune responses. Methods We employed ferrets as an experimental model to assess the D614G variant (a derivative of the Wuhan strain) and the Omicron BA.5 variant. Each variant was inoculated into separate groups of ferrets to compare disease severity, viral dissemination, and immune responses. Results The D614G variant induced more severe disease and greater viral spread than the Omicron variant. Notably, ferrets infected with the D614G variant exhibited a robust neutralizing antibody response, whereas those infected with the Omicron variant failed to produce a detectable neutralizing antibody response. Despite the clearance of the virus from nearly all tissues by 7 days post-infection, an increase in pathological lesions was observed from 14 to 21 days, particularly in those infected with the D614G variant, suggesting a sustained immune response even after viral clearance. Discussion These findings underscore the adaptability of SARS-CoV-2 and illuminate how susceptibility and clinical manifestations vary across different strains and species. The results emphasize the necessity of considering both the direct effects of viral infection and the indirect, often prolonged, impacts of the immune response in evaluating the outcomes of SARS-CoV-2 infections.
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Affiliation(s)
- Sandra Barroso-Arévalo
- Department of Animal Health, Faculty of Veterinary, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - Lidia Sánchez-Morales
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - Néstor Porras
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - Marta Díaz-Frutos
- Department of Animal Health, Faculty of Veterinary, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - Jose A. Barasona
- Department of Animal Health, Faculty of Veterinary, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Débora López
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - Christian Gortázar
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Lucas Domínguez
- Department of Animal Health, Faculty of Veterinary, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
| | - Jose M. Sánchez-Vizcaíno
- Department of Animal Health, Faculty of Veterinary, Universidad Complutense de Madrid, Madrid, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid, Spain
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Liu Y, Guo Y, Zhan H, Liu X, Li X, Cui J, Li H, Feng S, Cheng L, Li X, Guo S, Li Y. Immune and inflammation features of severe and critical Omicron infected patients during Omicron wave in China. BMC Infect Dis 2024; 24:809. [PMID: 39123106 PMCID: PMC11316362 DOI: 10.1186/s12879-024-09652-y] [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: 08/31/2023] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
OBJECTIVE The current study aimed to investigate the baseline immune and inflammatory features and in-hospital outcomes of patients infected with the Omicron variant (PIWO) who presented with different disease severities during the first wave of mass Omicron infections in the Chinese population has occurred. METHOD A cross-sectional study was conducted on 140 hospitalized PIWO between December 11, 2022, and February 16, 2023. The clinical features, antibodies against SARS-CoV-2, immune cells, and inflammatory cytokines among mildly, severely, and critically ill PIWO at baseline and during follow-up period were compared. RESULT Patients with severe (n = 49) and critical (n = 35) disease were primarily male, needed invasive mechanical ventilation treatment, and exhibited higher mortality than those with mild disease (n = 56). During acute infection, SARS-CoV-2-specific antibody levels fluctuated with disease severity, serum antibodies increased and the incidence of severe cases decreased in critically ill PIWO over time. Antibody titers in severe or critical PIWO with no antibody responses at baseline did not increase significantly over time. Meanwhile, CD4+T cell, CD8+T cell, and natural killer cell counts were negatively correlated with disease severity, whereas interleukin (IL)-6 and IL-10 levels were positively correlated. In addition, combined diabetes, immunosuppressive therapy before infection, serum amyloid A, IL-10 and neutrophil counts were independently associated with severe and critical illness in PIWO. Among the 11 nonsurvivors, 8, 2, 1 died of respiratory failure, sudden cardiac death, and renal failure, respectively. Compared with survivors, nonsurvivors exhibited lower seropositivity of SARS-CoV-2-specific antibody, reduced CD3+T and CD4+T cell counts, and higher IL-2R, IL-6, IL-8, and IL-10 levels. Of note, lactate dehydrogenase was a significant risk factor of death in severe or critically ill PIWO. CONCLUSION This present study assessed the dynamic changes of SARS-CoV-2-specific antibodies, immune cells and inflammatory indexes between severely and critically ill PIWO. Critical and dead PIWO featured compromised humoral immune response and excessive inflammation, which broadened the understanding of the pathophysiology of Omicron infection and provides warning markers for severe disease and poor prognosis.
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Affiliation(s)
- Yongmei Liu
- Department of Clinical Laboratory, State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100010, China
| | - Yaping Guo
- Department of Clinical Laboratory, Baoding First Central HospitalBaoding NO.1 Central Hospital, No. 320, Great Wall North Street, Baoding, Hebei, 071000, China
| | - Haoting Zhan
- Department of Clinical Laboratory, State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100010, China
| | - Xin Liu
- Department of Clinical Laboratory, Baoding First Central HospitalBaoding NO.1 Central Hospital, No. 320, Great Wall North Street, Baoding, Hebei, 071000, China
| | - Xiaomeng Li
- Department of Clinical Laboratory, State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100010, China
- Department of Clinical Laboratory, Peking University People's Hospital, NO.11, Xizhimen South Street, Beijing, 100035, China
| | - Jingjing Cui
- Department of Clinical Laboratory, Baoding First Central HospitalBaoding NO.1 Central Hospital, No. 320, Great Wall North Street, Baoding, Hebei, 071000, China
| | - Haolong Li
- Department of Clinical Laboratory, State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100010, China
| | - Sha Feng
- Department of Clinical Laboratory, Baoding First Central HospitalBaoding NO.1 Central Hospital, No. 320, Great Wall North Street, Baoding, Hebei, 071000, China
| | - Linlin Cheng
- Department of Clinical Laboratory, State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100010, China
| | - Xiaoyan Li
- Department of Clinical Laboratory, Baoding First Central HospitalBaoding NO.1 Central Hospital, No. 320, Great Wall North Street, Baoding, Hebei, 071000, China
| | - Shuqin Guo
- Department of Endocrinology, Baoding NO.1 Central Hospital, No. 320, Great Wall North Street, Baoding, Hebei, 071000, China.
| | - Yongzhe Li
- Department of Clinical Laboratory, State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 No. 1, Shuaifuyuan, Dongcheng District, Beijing, 100010, China.
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Kircheis R. In Silico Analyses Indicate a Lower Potency for Dimerization of TLR4/MD-2 as the Reason for the Lower Pathogenicity of Omicron Compared to Wild-Type Virus and Earlier SARS-CoV-2 Variants. Int J Mol Sci 2024; 25:5451. [PMID: 38791489 PMCID: PMC11121871 DOI: 10.3390/ijms25105451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
The SARS-CoV-2 Omicron variants have replaced all earlier variants, due to increased infectivity and effective evasion from infection- and vaccination-induced neutralizing antibodies. Compared to earlier variants of concern (VoCs), the Omicron variants show high TMPRSS2-independent replication in the upper airway organs, but lower replication in the lungs and lower mortality rates. The shift in cellular tropism and towards lower pathogenicity of Omicron was hypothesized to correlate with a lower toll-like receptor (TLR) activation, although the underlying molecular mechanisms remained undefined. In silico analyses presented here indicate that the Omicron spike protein has a lower potency to induce dimerization of TLR4/MD-2 compared to wild type virus despite a comparable binding activity to TLR4. A model illustrating the molecular consequences of the different potencies of the Omicron spike protein vs. wild-type spike protein for TLR4 activation is presented. Further analyses indicate a clear tendency for decreasing TLR4 dimerization potential during SARS-CoV-2 evolution via Alpha to Gamma to Delta to Omicron variants.
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Alsalmi O, Mashraqi MM, Alshamrani S, Almasoudi HH, Alharthi AA, Gharib AF. Variolin B from sea sponge against lung cancer: a multitargeted molecular docking with fingerprinting and molecular dynamics simulation study. J Biomol Struct Dyn 2024; 42:3507-3519. [PMID: 37855303 DOI: 10.1080/07391102.2023.2272204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/07/2023] [Indexed: 10/20/2023]
Abstract
Lung Cancer is the one that causes more fatalities in the world compared to other cancers, and its uniqueness is that it can be found in both males and females. However, recent data has shown that males are more affected due to lifestyle habits like smoking, tobacco consumption and inhaling polluted air. The World Health Organization has kept lung cancer on its priority list as it causes 1.8 million deaths worldwide each year, and the predictions show that the cases are going to increase year by year, and by 2050, there can be 3.8 million new cases and 3.2 million deaths, and the global health system is not prepared for it. Also, finding drug candidates that can help shrink cancerous cells and lead to their death is essential to reduce global mortality. The system needs drug compounds that can inhibit multiple paths together not to enter drug resistance quickly and to reduce costs. Our study identified a compound named Variolin B (DB08694) that belongs to the organic compounds class of pyrrolopyridines. The identified compound can inhibit multiple proteins, drastically reducing the global burden. Variolin B was identified as a potential candidate against lung cancer using the multisampling algorithm such as HTVS, SP, and XP, followed by MM\GBSA calculations showing the docking score of -9.245 Kcal/mol to -5.92 Kcal/mol. Also, we have validated it with ADMET predictions and molecular fingerprinting to analyse the interaction patterns. Further, the study was extended to molecular dynamics simulations for 100 ns to understand the complex stability and simulative interactions. The complex's overall molecular dynamics simulation helped us understand that the identified candidate is stable with the lowest deviation and fluctuations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ohud Alsalmi
- Department of Clinical laboratory sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Mutaib M Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Saleh Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Hassan H Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Afaf Awwadh Alharthi
- Department of Clinical laboratory sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Amal F Gharib
- Department of Clinical laboratory sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
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9
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Cummings MJ, Bakamutumaho B, Lutwama JJ, Owor N, Che X, Astorkia M, Postler TS, Kayiwa J, Kiconco J, Muwanga M, Nsereko C, Rwamutwe E, Nayiga I, Kyebambe S, Haumba M, Bosa HK, Ocom F, Watyaba B, Kikaire B, Tomoiaga AS, Kisaka S, Kiwanuka N, Lipkin WI, O'Donnell MR. COVID-19 immune signatures in Uganda persist in HIV co-infection and diverge by pandemic phase. Nat Commun 2024; 15:1475. [PMID: 38368384 PMCID: PMC10874401 DOI: 10.1038/s41467-024-45204-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 01/17/2024] [Indexed: 02/19/2024] Open
Abstract
Little is known about the pathobiology of SARS-CoV-2 infection in sub-Saharan Africa, where severe COVID-19 fatality rates are among the highest in the world and the immunological landscape is unique. In a prospective cohort study of 306 adults encompassing the entire clinical spectrum of SARS-CoV-2 infection in Uganda, we profile the peripheral blood proteome and transcriptome to characterize the immunopathology of COVID-19 across multiple phases of the pandemic. Beyond the prognostic importance of myeloid cell-driven immune activation and lymphopenia, we show that multifaceted impairment of host protein synthesis and redox imbalance define core biological signatures of severe COVID-19, with central roles for IL-7, IL-15, and lymphotoxin-α in COVID-19 respiratory failure. While prognostic signatures are generally consistent in SARS-CoV-2/HIV-coinfection, type I interferon responses uniquely scale with COVID-19 severity in persons living with HIV. Throughout the pandemic, COVID-19 severity peaked during phases dominated by A.23/A.23.1 and Delta B.1.617.2/AY variants. Independent of clinical severity, Delta phase COVID-19 is distinguished by exaggerated pro-inflammatory myeloid cell and inflammasome activation, NK and CD8+ T cell depletion, and impaired host protein synthesis. Combining these analyses with a contemporary Ugandan cohort of adults hospitalized with influenza and other severe acute respiratory infections, we show that activation of epidermal and platelet-derived growth factor pathways are distinct features of COVID-19, deepening translational understanding of mechanisms potentially underlying SARS-CoV-2-associated pulmonary fibrosis. Collectively, our findings provide biological rationale for use of broad and targeted immunotherapies for severe COVID-19 in sub-Saharan Africa, illustrate the relevance of local viral and host factors to SARS-CoV-2 immunopathology, and highlight underemphasized yet therapeutically exploitable immune pathways driving COVID-19 severity.
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Affiliation(s)
- Matthew J Cummings
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA.
| | - Barnabas Bakamutumaho
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Julius J Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Nicholas Owor
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Maider Astorkia
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Thomas S Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - John Kayiwa
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Jocelyn Kiconco
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | | | | | | | - Irene Nayiga
- Entebbe Regional Referral Hospital, Entebbe, Uganda
| | | | - Mercy Haumba
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Henry Kyobe Bosa
- Uganda Peoples' Defence Forces, Kampala, Uganda
- Ministry of Health, Kampala, Uganda
| | | | - Benjamin Watyaba
- European and Developing Countries Clinical Trials Partnership-Eastern Africa Consortium for Clinical Research, Uganda Virus Research Institute, Entebbe, Uganda
| | - Bernard Kikaire
- European and Developing Countries Clinical Trials Partnership-Eastern Africa Consortium for Clinical Research, Uganda Virus Research Institute, Entebbe, Uganda
- Department of Pediatrics, Makerere University College of Health Sciences, Kampala, Uganda
| | - Alin S Tomoiaga
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Accounting, Business Analytics, Computer Information Systems, and Law, Manhattan College, New York, NY, USA
| | - Stevens Kisaka
- Department of Epidemiology and Biostatistics, Makerere University School of Public Health, Kampala, Uganda
- Institute of Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | - Noah Kiwanuka
- Department of Epidemiology and Biostatistics, Makerere University School of Public Health, Kampala, Uganda
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Max R O'Donnell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
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10
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Yang ZS, Li TS, Huang YS, Chang CC, Chien CM. Targeting the receptor binding domain and heparan sulfate binding for antiviral drug development against SARS-CoV-2 variants. Sci Rep 2024; 14:2753. [PMID: 38307890 PMCID: PMC10837157 DOI: 10.1038/s41598-024-53111-2] [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: 06/28/2023] [Accepted: 01/27/2024] [Indexed: 02/04/2024] Open
Abstract
The emergence of SARS-CoV-2 variants diminished the efficacy of current antiviral drugs and vaccines. Hence, identifying highly conserved sequences and potentially druggable pockets for drug development was a promising strategy against SARS-CoV-2 variants. In viral infection, the receptor-binding domain (RBD) proteins are essential in binding to the host receptor. Others, Heparan sulfate (HS), widely distributed on the surface of host cells, is thought to play a central role in the viral infection cycle of SARS-CoV-2. Therefore, it might be a reasonable strategy for antiviral drug design to interfere with the RBD in the HS binding site. In this study, we used computational approaches to analyze multiple sequences of coronaviruses and reveal important information about the binding of HS to RBD in the SARS-CoV-2 spike protein. Our results showed that the potential hot-spots, including R454 and E471, in RBD, exhibited strong interactions in the HS-RBD binding region. Therefore, we screened different compounds in the natural product database towards these hot-spots to find potential antiviral candidates using LibDock, Autodock vina and furthermore applying the MD simulation in AMBER20. The results showed three potential natural compounds, including Acetoside (ACE), Hyperoside (HYP), and Isoquercitrin (ISO), had a strong affinity to the RBD. Our results demonstrate a feasible approach to identify potential antiviral agents by evaluating the binding interaction between viral glycoproteins and host receptors. The present study provided the applications of the structure-based computational approach for designing and developing of new antiviral drugs against SARS-CoV-2 variants.
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Affiliation(s)
- Zi-Sin Yang
- Department of Medical Sciences Industry, College of Health Sciences, Chang Jung Christian University, Tainan, 711, Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Tzong-Shiun Li
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, Taichung, 402, Taiwan
- Department of Plastic Surgery, Chang Bing Show Chwan Memorial Hospital, Changhua, 500, Taiwan
| | - Yu-Sung Huang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Cheng-Chung Chang
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, Taichung, 402, Taiwan
| | - Ching-Ming Chien
- Department of Medical Sciences Industry, College of Health Sciences, Chang Jung Christian University, Tainan, 711, Taiwan.
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11
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Rafeeq MM, Nahhas AF, Binothman N, Habib AH, Aljadani M, Sain ZM, Tuwaijri AA, Alshehri MA, Alzahrani OR. PheroxyPyrabenz and Carbopyrropyridin against major proteins of SARS CoV-2: a comprehensive in-silico molecular docking and dynamics simulation studies. J Biomol Struct Dyn 2023; 41:9121-9133. [PMID: 36318617 DOI: 10.1080/07391102.2022.2140202] [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: 08/08/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
The pandemic that started in 2020 left us with so much information about viruses and respiratory diseases, and the cause behind it was severe acute respiratory syndrome coronavirus-2 (SARS CoV-2). The world is still recovering, which costs so many economic and other indirect disasters; despite that, no medications are available on the market. Although the WHO approved a few vaccines on an emergency basis, the remarks and the reinfection chances are still under investigation, and a few pharmaceutical companies are also claiming that a few medications can be effective. However, there is no situation in control. SARS CoV-2 mutates and comes in different forms, making the situation unpredictable. In this study, we have screened the complete Asinex's BioDesign library, which contains 170,269 compounds, and shorted the data against the docking score that helps in the identification of 4-[5-(3-Ethoxy-4-hydroxyphenyl)-1-(2-hydroxyethyl)-1H-pyrazol-3-yl]-1, 2-benzenediol (PheroxyPyrabenz) and 1-[(3R,4R)-1-(5-Aminopentanoyl)-4-hydroxy-3-pyrrolidinyl]-1H-pyrrolo[2,3-b]pyridine-4-carboxamide (Carbopyrropyridin) as a significant drug candidate that can work against the multiple proteins of the SARS CoV-2 resulting in seizing the complete biological process of the virus. Further, the study extended to Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and molecular dynamics (MD) simulation of both the compounds with their complexity. The complete workflow of the study has shown satisfactory results, and both drug candidates can potentially stop the hunt for drugs against this virus after its experimental validation. Further, we checked both compounds' absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties, showing case-proof validatory results.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Misbahuddin M Rafeeq
- Department of Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Alaa F Nahhas
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Najat Binothman
- Department of Chemistry, College of Sciences & Arts, King Abdulaziz University, Rabigh, Kingdom of Saudi Arabia
| | - Alaa Hamed Habib
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Majidah Aljadani
- Department of Chemistry, College of Sciences & Arts, King Abdulaziz University, Rabigh, Kingdom of Saudi Arabia
| | - Ziaullah M Sain
- Department of Microbiology, Faculty of Medicine, King Abdulaziz University, Rabigh, Kingdom of Saudi Arabia
| | - Abeer Al Tuwaijri
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), Kingdom of Saudi Arabia
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed Ali Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Kingdom of Saudi Arabia
| | - Othman R Alzahrani
- Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia
- Genome and Biotechnology Unit, Faculty of Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia
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12
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Karageorgou V, Papaioannou AI, Kallieri M, Blizou M, Lampadakis S, Sfika M, Krouskos A, Papavasileiou V, Strakosha F, Vandorou KT, Siozos P, Moustaka Christodoulou M, Kontonasiou G, Apollonatou V, Antonogiannaki EM, Kyriakopoulos C, Aggelopoulou C, Chronis C, Kostikas K, Koukaki E, Sotiropoulou Z, Athanasopoulou A, Bakakos P, Schoini P, Alevrakis E, Poupos S, Chondrou E, Tsoukalas D, Chronaiou A, Tsoukalas G, Koukidou S, Hillas G, Dimakou K, Roukas K, Nakou I, Chloros D, Fouka E, Papiris SA, Loukides S. Patients Hospitalized for COVID-19 in the Periods of Delta and Omicron Variant Dominance in Greece: Determinants of Severity and Mortality. J Clin Med 2023; 12:5904. [PMID: 37762846 PMCID: PMC10531654 DOI: 10.3390/jcm12185904] [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: 08/15/2023] [Revised: 09/03/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) has been a pandemic since 2020, and depending on the SARS-CoV-2 mutation, different pandemic waves have been observed. The aim of this study was to compare the baseline characteristics of patients in two phases of the pandemic and evaluate possible predictors of mortality. METHODS This is a retrospective multicenter observational study that included patients with COVID-19 in 4 different centers in Greece. Patients were divided into two groups depending on the period during which they were infected during the Delta and Omicron variant predominance. RESULTS A total of 979 patients (433 Delta, 546 Omicron) were included in the study (median age 67 years (54, 81); 452 [46.2%] female). Compared to the Omicron period, the patients during the Delta period were younger (median age [IQR] 65 [51, 77] vs. 70 [55, 83] years, p < 0.001) and required a longer duration of hospitalization (8 [6, 13] vs. 7 [5, 12] days, p = 0.001), had higher procalcitonin levels (ng/mL): 0.08 [0.05, 0.17] vs. 0.06 [0.02, 0.16], p = 0.005, ferritin levels (ng/mL): 301 [159, 644] vs. 239 [128, 473], p = 0.002, C- reactive protein levels (mg/L): 40.4 [16.7, 98.5] vs. 31.8 [11.9, 81.7], p = 0.003, and lactate dehydrogenase levels (U/L): 277 [221, 375] vs. 255 [205, 329], p < 0.001. The Charlson Comorbidity Index was lower (3 [0, 5] vs. 4 [1, 6], p < 0.001), and the extent of disease on computed tomography (CT) was greater during the Delta wave (p < 0.001). No evidence of a difference in risk of death or admission to the intensive care unit was found between the two groups. Age, cardiovascular events, acute kidney injury during hospitalization, extent of disease on chest CT, D-dimer, and neutrophil/lymphocyte ratio values were identified as independent predictors of mortality for patients in the Delta period. Cardiovascular events and acute liver injury during hospitalization and the PaO2/FiO2 ratio on admission were identified as independent predictors of mortality for patients in the Omicron period. CONCLUSIONS In the Omicron wave, patients were older with a higher number of comorbidities, but patients with the Delta variant had more severe disease and a longer duration of hospitalization.
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Affiliation(s)
- Vagia Karageorgou
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, Athens Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (V.K.); (M.K.); (M.B.); (S.L.); (M.S.); (F.S.); (V.A.)
| | - Andriana I. Papaioannou
- 1st Respiratory Medicine Department, “Sotiria” Chest Hospital, Athens Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (A.I.P.); (Z.S.); (P.B.)
| | - Maria Kallieri
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, Athens Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (V.K.); (M.K.); (M.B.); (S.L.); (M.S.); (F.S.); (V.A.)
| | - Myrto Blizou
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, Athens Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (V.K.); (M.K.); (M.B.); (S.L.); (M.S.); (F.S.); (V.A.)
| | - Stefanos Lampadakis
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, Athens Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (V.K.); (M.K.); (M.B.); (S.L.); (M.S.); (F.S.); (V.A.)
| | - Maria Sfika
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, Athens Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (V.K.); (M.K.); (M.B.); (S.L.); (M.S.); (F.S.); (V.A.)
| | - Antonios Krouskos
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, Athens Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (V.K.); (M.K.); (M.B.); (S.L.); (M.S.); (F.S.); (V.A.)
| | - Vasileios Papavasileiou
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, Athens Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (V.K.); (M.K.); (M.B.); (S.L.); (M.S.); (F.S.); (V.A.)
| | - Franceska Strakosha
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, Athens Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (V.K.); (M.K.); (M.B.); (S.L.); (M.S.); (F.S.); (V.A.)
| | - Kalliopi Theoni Vandorou
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, Athens Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (V.K.); (M.K.); (M.B.); (S.L.); (M.S.); (F.S.); (V.A.)
| | - Pavlos Siozos
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, Athens Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (V.K.); (M.K.); (M.B.); (S.L.); (M.S.); (F.S.); (V.A.)
| | - Marina Moustaka Christodoulou
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, Athens Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (V.K.); (M.K.); (M.B.); (S.L.); (M.S.); (F.S.); (V.A.)
| | - Georgia Kontonasiou
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, Athens Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (V.K.); (M.K.); (M.B.); (S.L.); (M.S.); (F.S.); (V.A.)
| | - Vasiliki Apollonatou
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, Athens Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (V.K.); (M.K.); (M.B.); (S.L.); (M.S.); (F.S.); (V.A.)
| | - Elvira Markella Antonogiannaki
- 4th Respiratory Medicine Department, “Sotiria” Chest Hospital, 11527 Athens, Greece; (E.M.A.); (P.S.); (E.A.); (S.P.); (E.C.); (A.C.)
| | - Christos Kyriakopoulos
- Respiratory Medicine Department, University Hospital of Ioannina, 45500 Ioannina, Greece; (C.K.); (C.C.); (K.K.)
| | - Christina Aggelopoulou
- Respiratory Medicine Department, University Hospital of Ioannina, 45500 Ioannina, Greece; (C.K.); (C.C.); (K.K.)
| | - Christos Chronis
- Respiratory Medicine Department, University Hospital of Ioannina, 45500 Ioannina, Greece; (C.K.); (C.C.); (K.K.)
| | - Konstantinos Kostikas
- Respiratory Medicine Department, University Hospital of Ioannina, 45500 Ioannina, Greece; (C.K.); (C.C.); (K.K.)
| | - Evangelia Koukaki
- 1st Respiratory Medicine Department, “Sotiria” Chest Hospital, Athens Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (A.I.P.); (Z.S.); (P.B.)
| | - Zoi Sotiropoulou
- 1st Respiratory Medicine Department, “Sotiria” Chest Hospital, Athens Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (A.I.P.); (Z.S.); (P.B.)
| | - Athanasia Athanasopoulou
- 1st Respiratory Medicine Department, “Sotiria” Chest Hospital, Athens Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (A.I.P.); (Z.S.); (P.B.)
| | - Petros Bakakos
- 1st Respiratory Medicine Department, “Sotiria” Chest Hospital, Athens Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (A.I.P.); (Z.S.); (P.B.)
| | - Pinelopi Schoini
- 4th Respiratory Medicine Department, “Sotiria” Chest Hospital, 11527 Athens, Greece; (E.M.A.); (P.S.); (E.A.); (S.P.); (E.C.); (A.C.)
| | - Emmanouil Alevrakis
- 4th Respiratory Medicine Department, “Sotiria” Chest Hospital, 11527 Athens, Greece; (E.M.A.); (P.S.); (E.A.); (S.P.); (E.C.); (A.C.)
| | - Sotirios Poupos
- 4th Respiratory Medicine Department, “Sotiria” Chest Hospital, 11527 Athens, Greece; (E.M.A.); (P.S.); (E.A.); (S.P.); (E.C.); (A.C.)
| | - Evangelia Chondrou
- 4th Respiratory Medicine Department, “Sotiria” Chest Hospital, 11527 Athens, Greece; (E.M.A.); (P.S.); (E.A.); (S.P.); (E.C.); (A.C.)
| | - Dionisios Tsoukalas
- 4th Respiratory Medicine Department, “Sotiria” Chest Hospital, 11527 Athens, Greece; (E.M.A.); (P.S.); (E.A.); (S.P.); (E.C.); (A.C.)
| | - Alexia Chronaiou
- 4th Respiratory Medicine Department, “Sotiria” Chest Hospital, 11527 Athens, Greece; (E.M.A.); (P.S.); (E.A.); (S.P.); (E.C.); (A.C.)
| | - George Tsoukalas
- 4th Respiratory Medicine Department, “Sotiria” Chest Hospital, 11527 Athens, Greece; (E.M.A.); (P.S.); (E.A.); (S.P.); (E.C.); (A.C.)
| | - Sofia Koukidou
- 5th Respiratory Medicine Department, “Sotiria” Chest Hospital, 11527 Athens, Greece; (S.K.); (G.H.); (K.D.)
| | - Georgios Hillas
- 5th Respiratory Medicine Department, “Sotiria” Chest Hospital, 11527 Athens, Greece; (S.K.); (G.H.); (K.D.)
| | - Katerina Dimakou
- 5th Respiratory Medicine Department, “Sotiria” Chest Hospital, 11527 Athens, Greece; (S.K.); (G.H.); (K.D.)
| | - Konstantinos Roukas
- COVID-19 Clinic, General Hospital G. Papanikolaou, Aristotle University of Thessaloniki, 57010 Thessaloniki, Greece (I.N.); (D.C.); (E.F.)
| | - Ifigeneia Nakou
- COVID-19 Clinic, General Hospital G. Papanikolaou, Aristotle University of Thessaloniki, 57010 Thessaloniki, Greece (I.N.); (D.C.); (E.F.)
| | - Diamantis Chloros
- COVID-19 Clinic, General Hospital G. Papanikolaou, Aristotle University of Thessaloniki, 57010 Thessaloniki, Greece (I.N.); (D.C.); (E.F.)
| | - Evangelia Fouka
- COVID-19 Clinic, General Hospital G. Papanikolaou, Aristotle University of Thessaloniki, 57010 Thessaloniki, Greece (I.N.); (D.C.); (E.F.)
| | - Spyros A. Papiris
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, Athens Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (V.K.); (M.K.); (M.B.); (S.L.); (M.S.); (F.S.); (V.A.)
| | - Stelios Loukides
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, Athens Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (V.K.); (M.K.); (M.B.); (S.L.); (M.S.); (F.S.); (V.A.)
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13
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Cohen-Hagai K, Hornik-Lurie T, Benchetrit S, Nacasch N, Grupper A, Einbinder Y, Wand O, Shashar M. Clinical efficacy of the fourth dose of the BNT162b2 vaccine in maintenance dialysis patients. J Nephrol 2023; 36:1957-1964. [PMID: 37326951 DOI: 10.1007/s40620-023-01667-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/29/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND OBJECTIVES Highly effective vaccines against severe acute respiratory syndrome virus 2 have been developed and administered worldwide. However, protection from coronavirus disease 2019 is not absolute and an optimal vaccination regimen needs to be established. This study assessed the clinical efficacy of the coronavirus disease 2019 vaccine among dialysis patients receiving 3 or 4 doses of vaccine. DESIGN, SETTING, PARTICIPANTS, AND MEASUREMENTS This retrospective study was conducted using the electronic database of Clalit Health Maintenance Organization in Israel. Chronic dialysis patients treated with either hemodialysis or peritoneal dialysis during the coronavirus disease 2019 pandemic were included. We compared clinical outcomes of patients who had received three or four doses of the severe acute respiratory syndrome virus 2 vaccine. RESULTS This study included 1,030 patients on chronic dialysis, with a mean age of 68 ± 13 years. Among them, 502 patients had received 3 doses of the vaccine and 528 received 4 doses. Severe acute respiratory syndrome virus 2 infection rates, severe COVID-19 that resulted in hospitalizations, COVID-19-related mortality and all-cause mortality rates were lower among chronic dialysis patients who received a fourth dose of vaccine as compared to those who received only 3 doses (after controlling for age, sex and comorbidities). Despite lower mortality rates observed with the Omicron variant, the fourth dose was significantly associated with reduced COVID-19-related mortality (1.7% vs. 3.8%, p = 0.04). Odds ratio for COVID-19-related mortality was 0.44 with 95% CI 0.2-0.98. CONCLUSIONS As seen in the general population and with previous vaccine boosters, the fourth dose of the BNT162b2 vaccine reduced rates of severe COVID-19-related hospitalization and mortality among chronic dialysis patients. Further studies are needed to establish the optimal regimens of vaccination for patients on chronic dialysis.
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Affiliation(s)
- Keren Cohen-Hagai
- Department of Nephrology and Hypertension, Meir Medical Center, Kfar Saba, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Sydney Benchetrit
- Department of Nephrology and Hypertension, Meir Medical Center, Kfar Saba, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Naomi Nacasch
- Department of Nephrology and Hypertension, Meir Medical Center, Kfar Saba, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ayelet Grupper
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Nephrology and Hypertension, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Yael Einbinder
- Department of Nephrology and Hypertension, Meir Medical Center, Kfar Saba, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ori Wand
- Department of Pulmonology, Barzilai University Medical Center, Ashkelon, Israel
- Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Moshe Shashar
- Department of Nephrology and Hypertension, Laniado Hospital, Netanya, Israel.
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
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14
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Lomoio U, Puccio B, Tradigo G, Guzzi PH, Veltri P. SARS-CoV-2 protein structure and sequence mutations: Evolutionary analysis and effects on virus variants. PLoS One 2023; 18:e0283400. [PMID: 37471335 PMCID: PMC10358949 DOI: 10.1371/journal.pone.0283400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/04/2023] [Indexed: 07/22/2023] Open
Abstract
The structure and sequence of proteins strongly influence their biological functions. New models and algorithms can help researchers in understanding how the evolution of sequences and structures is related to changes in functions. Recently, studies of SARS-CoV-2 Spike (S) protein structures have been performed to predict binding receptors and infection activity in COVID-19, hence the scientific interest in the effects of virus mutations due to sequence, structure and vaccination arises. However, there is the need for models and tools to study the links between the evolution of S protein sequence, structure and functions, and virus transmissibility and the effects of vaccination. As studies on S protein have been generated a large amount of relevant information, we propose in this work to use Protein Contact Networks (PCNs) to relate protein structures with biological properties by means of network topology properties. Topological properties are used to compare the structural changes with sequence changes. We find that both node centrality and community extraction analysis can be used to relate protein stability and functionality with sequence mutations. Starting from this we compare structural evolution to sequence changes and study mutations from a temporal perspective focusing on virus variants. Finally by applying our model to the Omicron variant we report a timeline correlation between Omicron and the vaccination campaign.
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Affiliation(s)
- Ugo Lomoio
- Department of Surgical and Medical Sciences, University of Catanzaro, Catanzaro, Italy
| | - Barbara Puccio
- Department of Surgical and Medical Sciences, University of Catanzaro, Catanzaro, Italy
| | | | - Pietro Hiram Guzzi
- Department of Surgical and Medical Sciences, University of Catanzaro, Catanzaro, Italy
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15
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Al-Kubati AAG, Kandeel M, Hussen J, Hemida MG, Al-Mubarak AIA. Immunoinformatic prediction of the pathogenicity of bovine viral diarrhea virus genotypes: implications for viral virulence determinants, designing novel diagnostic assays and vaccines development. Front Vet Sci 2023; 10:1130147. [PMID: 37483297 PMCID: PMC10359904 DOI: 10.3389/fvets.2023.1130147] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/31/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction Bovine viral diarrhea virus (BVDV) significantly impacts the bovine industries, both dairy and beef sectors. BVDV can infect various domestic and wild animals, most notably cattle. The dynamic variations among BVDV serotypes due to the continuous genetic diversity, especially in BVDV1 (BVDV1), reduce the effectiveness of the currently available vaccines and reduce the specificity/sensitivity of the diagnostic assays. The development of novel, safe, and effective vaccines against BVDV requires deep knowledge of the antigenicity and virulence of the virus. Previous studies on the antigenicity and the virulence of BVDV serotypes have been mainly focused on one or a few BVDV proteins. While however, little is known about the orchestration of all BVDV in the context of viral virulence and immunogenicity. The main aim of the current study was to do a comparative computational evaluation of the immunogenicity, and virulence for all the encoded proteins of both BVDV1 and BVDV2 and their sub-genotypes. Methods To achieve this goal, 11,737 protein sequences were retrieved from Virus Pathogen Resource. The analysis involved a total of 4,583 sequences after the removal of short sequences and those with unknown collection time. We used the MP3 tool to map the pathogenic proteins across different BVDV strains. The potential protective and the epitope motifs were predicted using the VaxiJen and EMBOSS antigen tools, respectively. Results and discussion The virulence prediction revealed that the NS4B proteins of both BVDV1 and BVDV2 likely have essential roles in BVDV virulence. Similarly, both the capsid (C) and the NS4-A proteins of BVDV1 and the Npro and P7 proteins of BVDV2 are likely important virulent factors. There was a clear trend of increasing predicted virulence with the progression of time in the case of BVDV1 proteins, but that was not the case for the BVDV2 proteins. Most of the proteins of the two BVDV serotypes possess antigens predicted immunogens except Npro, P7, and NS4B. However, the predicted antigenicity of the BVDV1 was significantly higher than that of BVDV2. Meanwhile, the predicted immunogenicity of the immunodominant-E2 protein has been decreasing over time. Based on our predicted antigenicity and pathogenicity studies of the two BVDV serotypes, the sub-genotypes (1a, 1f, 1k, 2a, and 2b) may represent ideal candidates for the development of future vaccines against BVDV infection in cattle. In summary, we identified some common differences between the two BVDV genotypes (BVDV1 and BVDV2) and their sub-genotypes regarding their protein antigenicity and pathogenicity. The data presented here will increase our understanding of the molecular pathogenesis of BVDV infection in cattle. It will also pave the way for developing some novel diagnostic assays and novel vaccines against BVDV in the near future.
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Affiliation(s)
- Anwar A. G. Al-Kubati
- Department of Veterinary Medicine, Faculty of Agriculture and Veterinary Medicine, Thamar University, Thamar, Yemen
| | - Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Hofuf, Saudi Arabia
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Jamal Hussen
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Al-Hofuf, Saudi Arabia
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, New York, NY, United States
| | - Maged Gomaa Hemida
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Al-Hofuf, Saudi Arabia
| | - Abdullah I. A. Al-Mubarak
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Al-Hofuf, Saudi Arabia
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, New York, NY, United States
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16
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Vettori M, Dima F, Henry BM, Carpenè G, Gelati M, Celegon G, Salvagno GL, Lippi G. Effects of Different Types of Recombinant SARS-CoV-2 Spike Protein on Circulating Monocytes' Structure. Int J Mol Sci 2023; 24:ijms24119373. [PMID: 37298324 DOI: 10.3390/ijms24119373] [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: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
This study investigated the biological effects on circulating monocytes after challenge with SARS-CoV-2 recombinant spike protein. Whole blood collected from seven ostensibly healthy healthcare workers was incubated for 15 min with 2 and 20 ng/mL final concentration of recombinant spike protein of Ancestral, Alpha, Delta, and Omicron variants. Samples were analyzed with Sysmex XN and DI-60 analyzers. Cellular complexity (i.e., the presence of granules, vacuoles and other cytoplasmic inclusions) increased in all samples challenged with the recombinant spike protein of the Ancestral, Alpha, and Delta variants, but not in those containing Omicron. The cellular content of nucleic acids was constantly decreased in most samples, achieving statistical significance in those containing 20 ng/mL of Alpha and Delta recombinant spike proteins. The heterogeneity of monocyte volumes significantly increased in all samples, achieving statistical significance in those containing 20 ng/mL of recombinant spike protein of the Ancestral, Alpha and Delta variants. The monocyte morphological abnormalities after spike protein challenge included dysmorphia, granulation, intense vacuolization, platelet phagocytosis, development of aberrant nuclei, and cytoplasmic extrusions. The SARS-CoV-2 spike protein triggers important monocyte morphological abnormalities, more evident in cells challenged with recombinant spike protein of the more clinically severe Alpha and Delta variants.
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Affiliation(s)
- Marco Vettori
- Section of Clinical Biochemistry, University of Verona, 37129 Verona, Italy
| | - Francesco Dima
- Section of Clinical Biochemistry, University of Verona, 37129 Verona, Italy
| | - Brandon Michael Henry
- Clinical Laboratory, Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Giovanni Carpenè
- Section of Clinical Biochemistry, University of Verona, 37129 Verona, Italy
| | - Matteo Gelati
- Section of Clinical Biochemistry, University of Verona, 37129 Verona, Italy
| | - Giovanni Celegon
- Section of Clinical Biochemistry, University of Verona, 37129 Verona, Italy
| | - Gian Luca Salvagno
- Section of Clinical Biochemistry, University of Verona, 37129 Verona, Italy
| | - Giuseppe Lippi
- Section of Clinical Biochemistry, University of Verona, 37129 Verona, Italy
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