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Okoh OS, Nii-Trebi NI, Jakkari A, Olaniran TT, Senbadejo TY, Kafintu-kwashie AA, Dairo EO, Ganiyu TO, Akaninyene IE, Ezediuno LO, Adeosun IJ, Ockiya MA, Jimah EM, Spiro DJ, Oladipo EK, Trovão NS. Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.05.17.21257341. [PMID: 34031660 PMCID: PMC8142660 DOI: 10.1101/2021.05.17.21257341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
COVID-19 disease dynamics have been widely studied in different settings around the globe, but little is known about these patterns in the African continent. To investigate the epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa, more than 2400 complete genomes from 33 African countries were retrieved from the GISAID database and analyzed. We investigated their diversity using various clade and lineage nomenclature systems, reconstructed their evolutionary divergence and history using maximum likelihood inference methods, and studied the case and death trends in the continent. We also examined potential repeat patterns and motifs across the sequences. In this study, we show that after almost one year of the COVID-19 pandemic, only 143 out of the 782 Pango lineages found worldwide circulated in Africa, with five different lineages dominating in distinct periods of the pandemic. Analysis of the number of reported deaths in Africa also revealed large heterogeneity across the continent. Phylogenetic analysis revealed that African viruses cluster closely with those from all continents but more notably with viruses from Europe. However, the extent of viral diversity observed among African genomes is closest to that of the Oceania outbreak, most likely due to genomic under-surveillance in Africa. We also identified two motifs that could function as integrin-binding sites and N-glycosylation domains. These results shed light on the evolutionary dynamics of the circulating viral strains in Africa, elucidate the functions of protein motifs present in the genome sequences, and emphasize the need to expand genomic surveillance efforts in the continent to better understand the molecular, evolutionary, epidemiological, and spatiotemporal dynamics of the COVID-19 pandemic in Africa.
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Affiliation(s)
| | - Nicholas Israel Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra, Ghana
| | - Abdulrokeeb Jakkari
- Department of Microbiology, Faculty of Science, Lagos State University, Ojo, Lagos, Nigeria
| | - Tosin Titus Olaniran
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Helix Biogen Institute, Ogbomoso, Nigeria
| | - Tosin Yetunde Senbadejo
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Anna Aba Kafintu-kwashie
- Department of Medical Microbiology Clinical Virology unit, University of Ghana Medical School, Accra, Ghana
| | - Emmanuel Oluwatobi Dairo
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Tajudeen Oladunni Ganiyu
- Department of Biological Sciences, College of Natural and Applied Sciences, Fountain University, Osogbo, Nigeria
| | - Ifiokakaninyene Ekpo Akaninyene
- Department of Pure and Applied Biology (Microbiology Unit), Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Helix Biogen Institute, Ogbomoso, Nigeria
| | | | - Idowu Jesulayomi Adeosun
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
| | - Michael Asebake Ockiya
- Department of Animal Science, Niger Delta University, Wilberforce Island, Bayelsa State, Nigeria
| | - Esther Moradeyo Jimah
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, University of Ilorin, Nigeria
| | - David J. Spiro
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Elijah Kolawole Oladipo
- Helix Biogen Institute, Ogbomoso, Nigeria
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
| | - Nídia S. Trovão
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
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Chung MK, Zidar DA, Bristow MR, Cameron SJ, Chan T, Harding CV, Kwon DH, Singh T, Tilton JC, Tsai EJ, Tucker NR, Barnard J, Loscalzo J. COVID-19 and Cardiovascular Disease: From Bench to Bedside. Circ Res 2021; 128:1214-1236. [PMID: 33856918 PMCID: PMC8048382 DOI: 10.1161/circresaha.121.317997] [Citation(s) in RCA: 200] [Impact Index Per Article: 66.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A pandemic of historic impact, coronavirus disease 2019 (COVID-19) has potential consequences on the cardiovascular health of millions of people who survive infection worldwide. Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), the etiologic agent of COVID-19, can infect the heart, vascular tissues, and circulating cells through ACE2 (angiotensin-converting enzyme 2), the host cell receptor for the viral spike protein. Acute cardiac injury is a common extrapulmonary manifestation of COVID-19 with potential chronic consequences. This update provides a review of the clinical manifestations of cardiovascular involvement, potential direct SARS-CoV-2 and indirect immune response mechanisms impacting the cardiovascular system, and implications for the management of patients after recovery from acute COVID-19 infection.
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Affiliation(s)
- Mina K. Chung
- Cleveland Clinic (M.K.C., S.J.C., T.C., D.H.K., T.S., J.B.), OH
- Cleveland Clinic Lerner College of Medicine (M.K.C., S.J.C., T.C., D.H.K., T.S., J.B.), OH
- Case Western Reserve University School of Medicine (M.K.C., D.A.Z., S.J.C., T.C., C.V.H., D.H.K., T.S., J.C.T.), OH
| | - David A. Zidar
- Case Western Reserve University School of Medicine (M.K.C., D.A.Z., S.J.C., T.C., C.V.H., D.H.K., T.S., J.C.T.), OH
- Louis Stokes Cleveland Veterans Affairs Medical Center, OH (D.A.Z.)
| | | | - Scott J. Cameron
- Cleveland Clinic (M.K.C., S.J.C., T.C., D.H.K., T.S., J.B.), OH
- Cleveland Clinic Lerner College of Medicine (M.K.C., S.J.C., T.C., D.H.K., T.S., J.B.), OH
- Case Western Reserve University School of Medicine (M.K.C., D.A.Z., S.J.C., T.C., C.V.H., D.H.K., T.S., J.C.T.), OH
| | - Timothy Chan
- Cleveland Clinic (M.K.C., S.J.C., T.C., D.H.K., T.S., J.B.), OH
- Cleveland Clinic Lerner College of Medicine (M.K.C., S.J.C., T.C., D.H.K., T.S., J.B.), OH
- Case Western Reserve University School of Medicine (M.K.C., D.A.Z., S.J.C., T.C., C.V.H., D.H.K., T.S., J.C.T.), OH
| | - Clifford V. Harding
- Case Western Reserve University School of Medicine (M.K.C., D.A.Z., S.J.C., T.C., C.V.H., D.H.K., T.S., J.C.T.), OH
| | - Deborah H. Kwon
- Cleveland Clinic (M.K.C., S.J.C., T.C., D.H.K., T.S., J.B.), OH
- Cleveland Clinic Lerner College of Medicine (M.K.C., S.J.C., T.C., D.H.K., T.S., J.B.), OH
- Case Western Reserve University School of Medicine (M.K.C., D.A.Z., S.J.C., T.C., C.V.H., D.H.K., T.S., J.C.T.), OH
| | - Tamanna Singh
- Cleveland Clinic (M.K.C., S.J.C., T.C., D.H.K., T.S., J.B.), OH
- Cleveland Clinic Lerner College of Medicine (M.K.C., S.J.C., T.C., D.H.K., T.S., J.B.), OH
- Case Western Reserve University School of Medicine (M.K.C., D.A.Z., S.J.C., T.C., C.V.H., D.H.K., T.S., J.C.T.), OH
| | - John C. Tilton
- Case Western Reserve University School of Medicine (M.K.C., D.A.Z., S.J.C., T.C., C.V.H., D.H.K., T.S., J.C.T.), OH
| | - Emily J. Tsai
- Columbia University Vagelos College of Physicians and Surgeons, New York (E.J.T.)
| | - Nathan R. Tucker
- Masonic Medical Research Institute, Utica, NY (N.R.T.)
- Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Boston, MA (N.R.T.)
| | - John Barnard
- Cleveland Clinic (M.K.C., S.J.C., T.C., D.H.K., T.S., J.B.), OH
- Cleveland Clinic Lerner College of Medicine (M.K.C., S.J.C., T.C., D.H.K., T.S., J.B.), OH
| | - Joseph Loscalzo
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA (J.L.)
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The Spike Glycoprotein of SARS-CoV-2 Binds to β1 Integrins Expressed on the Surface of Lung Epithelial Cells. Viruses 2021; 13:v13040645. [PMID: 33918599 PMCID: PMC8069079 DOI: 10.3390/v13040645] [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: 03/24/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 01/12/2023] Open
Abstract
The spike glycoprotein attached to the envelope of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds to and exploits angiotensin-converting enzyme 2 (ACE2) as an entry receptor to infect pulmonary epithelial cells. A subset of integrins that recognize the arginyl–glycyl–aspartic acid (RGD) sequence in the cognate ligands has been predicted in silico to bind the spike glycoprotein and, thereby, to be exploited for viral infection. Here, we show experimental evidence that the β1 integrins predominantly expressed on human pulmonary epithelial cell lines and primary mouse alveolar epithelial cells bind to this spike protein. The cellular β1 integrins support adhesive interactions with the spike protein independently of ACE2, suggesting the possibility that the β1 integrins may function as an alternative receptor for SARS-CoV-2, which could be targeted for the prevention of viral infections.
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Ludwig BS, Kessler H, Kossatz S, Reuning U. RGD-Binding Integrins Revisited: How Recently Discovered Functions and Novel Synthetic Ligands (Re-)Shape an Ever-Evolving Field. Cancers (Basel) 2021; 13:1711. [PMID: 33916607 PMCID: PMC8038522 DOI: 10.3390/cancers13071711] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 12/19/2022] Open
Abstract
Integrins have been extensively investigated as therapeutic targets over the last decades, which has been inspired by their multiple functions in cancer progression, metastasis, and angiogenesis as well as a continuously expanding number of other diseases, e.g., sepsis, fibrosis, and viral infections, possibly also Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2). Although integrin-targeted (cancer) therapy trials did not meet the high expectations yet, integrins are still valid and promising targets due to their elevated expression and surface accessibility on diseased cells. Thus, for the future successful clinical translation of integrin-targeted compounds, revisited and innovative treatment strategies have to be explored based on accumulated knowledge of integrin biology. For this, refined approaches are demanded aiming at alternative and improved preclinical models, optimized selectivity and pharmacological properties of integrin ligands, as well as more sophisticated treatment protocols considering dose fine-tuning of compounds. Moreover, integrin ligands exert high accuracy in disease monitoring as diagnostic molecular imaging tools, enabling patient selection for individualized integrin-targeted therapy. The present review comprehensively analyzes the state-of-the-art knowledge on the roles of RGD-binding integrin subtypes in cancer and non-cancerous diseases and outlines the latest achievements in the design and development of synthetic ligands and their application in biomedical, translational, and molecular imaging approaches. Indeed, substantial progress has already been made, including advanced ligand designs, numerous elaborated pre-clinical and first-in-human studies, while the discovery of novel applications for integrin ligands remains to be explored.
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Affiliation(s)
- Beatrice S. Ludwig
- Department of Nuclear Medicine, University Hospital Klinikum Rechts der Isar and Central Institute for Translational Cancer Research (TranslaTUM), Technical University Munich, 81675 Munich, Germany;
| | - Horst Kessler
- Department of Chemistry, Institute for Advanced Study, Technical University Munich, 85748 Garching, Germany;
| | - Susanne Kossatz
- Department of Nuclear Medicine, University Hospital Klinikum Rechts der Isar and Central Institute for Translational Cancer Research (TranslaTUM), Technical University Munich, 81675 Munich, Germany;
- Department of Chemistry, Institute for Advanced Study, Technical University Munich, 85748 Garching, Germany;
| | - Ute Reuning
- Clinical Research Unit, Department of Obstetrics and Gynecology, University Hospital Klinikum Rechts der Isar, Technical University Munich, 81675 Munich, Germany
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Oz M, Lorke DE. Multifunctional angiotensin converting enzyme 2, the SARS-CoV-2 entry receptor, and critical appraisal of its role in acute lung injury. Biomed Pharmacother 2021; 136:111193. [PMID: 33461019 PMCID: PMC7836742 DOI: 10.1016/j.biopha.2020.111193] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/15/2020] [Accepted: 12/26/2020] [Indexed: 12/11/2022] Open
Abstract
The recent emergence of coronavirus disease-2019 (COVID-19) as a pandemic affecting millions of individuals has raised great concern throughout the world, and the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was identified as the causative agent for COVID-19. The multifunctional protein angiotensin converting enzyme 2 (ACE2) is accepted as its primary target for entry into host cells. In its enzymatic function, ACE2, like its homologue ACE, regulates the renin-angiotensin system (RAS) critical for cardiovascular and renal homeostasis in mammals. Unlike ACE, however, ACE2 drives an alternative RAS pathway by degrading Ang-II and thus operates to balance RAS homeostasis in the context of hypertension, heart failure, and cardiovascular as well as renal complications of diabetes. Outside the RAS, ACE2 hydrolyzes key peptides, such as amyloid-β, apelin, and [des-Arg9]-bradykinin. In addition to its enzymatic functions, ACE2 is found to regulate intestinal amino acid homeostasis and the gut microbiome. Although the non-enzymatic function of ACE2 as the entry receptor for SARS-CoV-2 has been well established, the contribution of enzymatic functions of ACE2 to the pathogenesis of COVID-19-related lung injury has been a matter of debate. A complete understanding of this central enzyme may begin to explain the various symptoms and pathologies seen in SARS-CoV-2 infected individuals, and may aid in the development of novel treatments for COVID-19.
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Affiliation(s)
- Murat Oz
- Department of Pharmacology and Therapeutics, Faculty of Pharmacy, Kuwait University, Safat 13110, Kuwait.
| | - Dietrich Ernst Lorke
- Department of Anatomy and Cellular Biology, Khalifa University, Abu Dhabi, United Arab Emirates; Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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56
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Carvacho I, Piesche M. RGD-binding integrins and TGF-β in SARS-CoV-2 infections - novel targets to treat COVID-19 patients? Clin Transl Immunology 2021; 10:e1240. [PMID: 33747508 PMCID: PMC7971943 DOI: 10.1002/cti2.1240] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 02/06/2023] Open
Abstract
The new coronavirus SARS-CoV-2 is a global pandemic and a severe public health crisis. SARS-CoV-2 is highly contagious and shows high mortality rates, especially in elderly and patients with pre-existing medical conditions. At the current stage, no effective drugs are available to treat these patients. In this review, we analyse the rationale of targeting RGD-binding integrins to potentially inhibit viral cell infection and to block TGF-β activation, which is involved in the severity of several human pathologies, including the complications of severe COVID-19 cases. Furthermore, we demonstrate the correlation between ACE2 and TGF-β expression and the possible consequences for severe COVID-19 infections. Finally, we list approved drugs or drugs in clinical trials for other diseases that also target the RGD-binding integrins or TGF-β. These drugs have already shown a good safety profile and, therefore, can be faster brought into a trial to treat COVID-19 patients.
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Affiliation(s)
- Ingrid Carvacho
- Department of Biology and ChemistryFaculty of Basic SciencesUniversidad Católica del MauleTalcaChile
| | - Matthias Piesche
- Biomedical Research Laboratories, Medicine FacultyUniversidad Católica del MauleTalcaChile
- Oncology Center, Medicine FacultyUniversidad Católica del MauleTalcaChile
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57
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Biological and Clinical Consequences of Integrin Binding via a Rogue RGD Motif in the SARS CoV-2 Spike Protein. Viruses 2021; 13:v13020146. [PMID: 33498225 PMCID: PMC7909284 DOI: 10.3390/v13020146] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
Although ACE2 (angiotensin converting enzyme 2) is considered the primary receptor for CoV-2 cell entry, recent reports suggest that alternative pathways may contribute. This paper considers the hypothesis that viral binding to cell-surface integrins may contribute to the high infectivity and widespread extra-pulmonary impacts of the SARS-CoV-2 virus. This potential is suggested on the basis of the emergence of an RGD (arginine-glycine-aspartate) sequence in the receptor-binding domain of the spike protein. RGD is a motif commonly used by viruses to bind cell-surface integrins. Numerous signaling pathways are mediated by integrins and virion binding could lead to dysregulation of these pathways, with consequent tissue damage. Integrins on the surfaces of pneumocytes, endothelial cells and platelets may be vulnerable to CoV-2 virion binding. For instance, binding of intact virions to integrins on alveolar cells could enhance viral entry. Binding of virions to integrins on endothelial cells could activate angiogenic cell signaling pathways; dysregulate integrin-mediated signaling pathways controlling developmental processes; and precipitate endothelial activation to initiate blood clotting. Such a procoagulant state, perhaps together with enhancement of platelet aggregation through virions binding to integrins on platelets, could amplify the production of microthrombi that pose the threat of pulmonary thrombosis and embolism, strokes and other thrombotic consequences. The susceptibility of different tissues to virion–integrin interactions may be modulated by a host of factors, including the conformation of relevant integrins and the impact of the tissue microenvironment on spike protein conformation. Patient-specific differences in these factors may contribute to the high variability of clinical presentation. There is danger that the emergence of receptor-binding domain mutations that increase infectivity may also enhance access of the RGD motif for integrin binding, resulting in viral strains with ACE2 independent routes of cell entry and novel integrin-mediated biological and clinical impacts. The highly infectious variant, B.1.1.7 (or VUI 202012/01), includes a receptor-binding domain amino acid replacement, N501Y, that could potentially provide the RGD motif with enhanced access to cell-surface integrins, with consequent clinical impacts.
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58
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Schütz D, Ruiz-Blanco YB, Münch J, Kirchhoff F, Sanchez-Garcia E, Müller JA. Peptide and peptide-based inhibitors of SARS-CoV-2 entry. Adv Drug Deliv Rev 2020; 167:47-65. [PMID: 33189768 PMCID: PMC7665879 DOI: 10.1016/j.addr.2020.11.007] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 12/18/2022]
Abstract
To date, no effective vaccines or therapies are available against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative pandemic agent of the coronavirus disease 2019 (COVID-19). Due to their safety, efficacy and specificity, peptide inhibitors hold great promise for the treatment of newly emerging viral pathogens. Based on the known structures of viral proteins and their cellular targets, antiviral peptides can be rationally designed and optimized. The resulting peptides may be highly specific for their respective targets and particular viral pathogens or exert broad antiviral activity. Here, we summarize the current status of peptides inhibiting SARS-CoV-2 entry and outline the strategies used to design peptides targeting the ACE2 receptor or the viral spike protein and its activating proteases furin, transmembrane serine protease 2 (TMPRSS2), or cathepsin L. In addition, we present approaches used against related viruses such as SARS-CoV-1 that might be implemented for inhibition of SARS-CoV-2 infection.
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Affiliation(s)
- Desiree Schütz
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, 45117 Essen, Germany.
| | - Janis A Müller
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany.
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