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Gruber CEM, Tucci FG, Rueca M, Mazzotta V, Gramigna G, Vergori A, Fabeni L, Berno G, Giombini E, Butera O, Focosi D, Prandi IG, Chillemi G, Nicastri E, Vaia F, Girardi E, Antinori A, Maggi F. Treatment-Emergent Cilgavimab Resistance Was Uncommon in Vaccinated Omicron BA.4/5 Outpatients. Biomolecules 2023; 13:1538. [PMID: 37892220 PMCID: PMC10605390 DOI: 10.3390/biom13101538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/03/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Mutations in the SARS-CoV-2 Spike glycoprotein can affect monoclonal antibody efficacy. Recent findings report the occurrence of resistant mutations in immunocompromised patients after tixagevimab/cilgavimab treatment. More recently, the Food and Drug Agency revoked the authorization for tixagevimab/cilgavimab, while this monoclonal antibody cocktail is currently recommended by the European Medical Agency. We retrospectively reviewed 22 immunocompetent patients at high risk for disease progression who received intramuscular tixagevimab/cilgavimab as early COVID-19 treatment and presented a prolonged high viral load. Complete SARS-CoV-2 genome sequences were obtained for a deep investigation of mutation frequencies in Spike protein before and during treatment. At seven days, only one patient showed evidence of treatment-emergent cilgavimab resistance. Quasispecies analysis revealed two different deletions on the Spike protein (S:del138-144 or S:del141-145) in combination with the resistance S:K444N mutation. The structural and dynamic impact of the two quasispecies was characterized by using molecular dynamics simulations, showing the conservation of the principal functional movements in the mutated systems and their capabilities to alter the structure and dynamics of the RBD, responsible for the interaction with the ACE2 human receptor. Our study underlines the importance of prompting an early virological investigation to prevent drug resistance or clinical failures in immunocompetent patients.
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Affiliation(s)
- Cesare Ernesto Maria Gruber
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Fabio Giovanni Tucci
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Martina Rueca
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Valentina Mazzotta
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (V.M.); (A.V.); (E.N.); (A.A.)
| | - Giulia Gramigna
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Alessandra Vergori
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (V.M.); (A.V.); (E.N.); (A.A.)
| | - Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Giulia Berno
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Emanuela Giombini
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
| | - Ornella Butera
- Laboratory of Microbiology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy;
| | - Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy;
| | - Ingrid Guarnetti Prandi
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via S. Camillo de Lellis s.n.c, 01100 Viterbo, Italy; (I.G.P.); (G.C.)
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via S. Camillo de Lellis s.n.c, 01100 Viterbo, Italy; (I.G.P.); (G.C.)
| | - Emanuele Nicastri
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (V.M.); (A.V.); (E.N.); (A.A.)
| | - Francesco Vaia
- General Direction, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy;
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy;
| | - Andrea Antinori
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (V.M.); (A.V.); (E.N.); (A.A.)
| | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (C.E.M.G.); (F.G.T.); (M.R.); (G.G.); (G.B.); (E.G.); (F.M.)
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2
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Rescifina A. Progress of the "Molecular Informatics" Section in 2022. Int J Mol Sci 2023; 24:ijms24119442. [PMID: 37298393 DOI: 10.3390/ijms24119442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
This is the first Editorial of the "Molecular Informatics" Section (MIS) of the International Journal of Molecular Sciences (IJMS), which was created towards the end of 2018 (the first article was submitted on 27 September 2018) and has experienced significant growth from 2018 to now [...].
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Affiliation(s)
- Antonio Rescifina
- Department of Drug and Health Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy
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3
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Lamkiewicz K, Esquivel Gomez LR, Kühnert D, Marz M. Genome Structure, Life Cycle, and Taxonomy of Coronaviruses and the Evolution of SARS-CoV-2. Curr Top Microbiol Immunol 2023; 439:305-339. [PMID: 36592250 DOI: 10.1007/978-3-031-15640-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Coronaviruses have a broad host range and exhibit high zoonotic potential. In this chapter, we describe their genomic organization in terms of encoded proteins and provide an introduction to the peculiar discontinuous transcription mechanism. Further, we present evolutionary conserved genomic RNA secondary structure features, which are involved in the complex replication mechanism. With a focus on computational methods, we review the emergence of SARS-CoV-2 starting with the 2019 strains. In that context, we also discuss the debated hypothesis of whether SARS-CoV-2 was created in a laboratory. We focus on the molecular evolution and the epidemiological dynamics of this recently emerged pathogen and we explain how variants of concern are detected and characterised. COVID-19, the disease caused by SARS-CoV-2, can spread through different transmission routes and also depends on a number of risk factors. We describe how current computational models of viral epidemiology, or more specifically, phylodynamics, have facilitated and will continue to enable a better understanding of the epidemic dynamics of SARS-CoV-2.
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Affiliation(s)
- Kevin Lamkiewicz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743, Jena, Germany
- European Virus Bioinformatics Center, Leutragraben 1, 07743, Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103, Leipzig, Germany
| | - Luis Roger Esquivel Gomez
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745, Jena, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745, Jena, Germany
- European Virus Bioinformatics Center, Leutragraben 1, 07743, Jena, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743, Jena, Germany.
- European Virus Bioinformatics Center, Leutragraben 1, 07743, Jena, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103, Leipzig, Germany.
- FLI Leibniz Institute for Age Research, Beutenbergstraße 11, 07745, Jena, Germany.
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4
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Solis O, Beccari AR, Iaconis D, Talarico C, Ruiz-Bedoya CA, Nwachukwu JC, Cimini A, Castelli V, Bertini R, Montopoli M, Cocetta V, Borocci S, Prandi IG, Flavahan K, Bahr M, Napiorkowski A, Chillemi G, Ooka M, Yang X, Zhang S, Xia M, Zheng W, Bonaventura J, Pomper MG, Hooper JE, Morales M, Rosenberg AZ, Nettles KW, Jain SK, Allegretti M, Michaelides M. The SARS-CoV-2 spike protein binds and modulates estrogen receptors. SCIENCE ADVANCES 2022; 8:eadd4150. [PMID: 36449624 PMCID: PMC9710872 DOI: 10.1126/sciadv.add4150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein binds angiotensin-converting enzyme 2 as its primary infection mechanism. Interactions between S and endogenous proteins occur after infection but are not well understood. We profiled binding of S against >9000 human proteins and found an interaction between S and human estrogen receptor α (ERα). Using bioinformatics, supercomputing, and experimental assays, we identified a highly conserved and functional nuclear receptor coregulator (NRC) LXD-like motif on the S2 subunit. In cultured cells, S DNA transfection increased ERα cytoplasmic accumulation, and S treatment induced ER-dependent biological effects. Non-invasive imaging in SARS-CoV-2-infected hamsters localized lung pathology with increased ERα lung levels. Postmortem lung experiments from infected hamsters and humans confirmed an increase in cytoplasmic ERα and its colocalization with S in alveolar macrophages. These findings describe the discovery of a S-ERα interaction, imply a role for S as an NRC, and advance knowledge of SARS-CoV-2 biology and coronavirus disease 2019 pathology.
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Affiliation(s)
- Oscar Solis
- Biobehavioral Imaging and Molecular Neuropsychopharmacology Unit, National Institute on Drug Abuse Intramural Research Program, Baltimore, MD 21224, USA
| | | | | | | | - Camilo A. Ruiz-Bedoya
- Center for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB-II Room 109, Baltimore, MD 21287, USA
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jerome C. Nwachukwu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Annamaria Cimini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Vanessa Castelli
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | | | - Monica Montopoli
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
- VIMM- Veneto Institute of Molecular Medicine, Fondazione per la Ricerca Biomedica Avanzata, Padova, Italy
| | - Veronica Cocetta
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Stefano Borocci
- Department for Innovation in Biological, Agro-Food and Forest Systems, DIBAF, University of Tuscia, Viterbo, Italy
| | - Ingrid G. Prandi
- Department for Innovation in Biological, Agro-Food and Forest Systems, DIBAF, University of Tuscia, Viterbo, Italy
| | - Kelly Flavahan
- Center for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB-II Room 109, Baltimore, MD 21287, USA
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Melissa Bahr
- Center for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB-II Room 109, Baltimore, MD 21287, USA
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Anna Napiorkowski
- Center for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB-II Room 109, Baltimore, MD 21287, USA
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems, DIBAF, University of Tuscia, Viterbo, Italy
| | - Masato Ooka
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850, USA
| | - Xiaoping Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Shiliang Zhang
- Neuronal Networks Section, National Institute on Drug Abuse Intramural Research Program, Baltimore, MD 21224, USA
| | - Menghang Xia
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850, USA
| | - Wei Zheng
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD 20850, USA
| | - Jordi Bonaventura
- Departament de Patologia i Terapèutica Experimental, Institut de Neurociències, Universitat de Barcelona, L’Hospitalet de Llobregat, Catalonia, Spain
| | - Martin G. Pomper
- Department of Radiology and Radiological Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jody E. Hooper
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marisela Morales
- Neuronal Networks Section, National Institute on Drug Abuse Intramural Research Program, Baltimore, MD 21224, USA
| | - Avi Z. Rosenberg
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Kendall W. Nettles
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Sanjay K. Jain
- Center for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB-II Room 109, Baltimore, MD 21287, USA
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Marcello Allegretti
- Dompé farmaceutici S.p.A, L’Aquila, Italy
- Corresponding author. (M.M.); (M.A.)
| | - Michael Michaelides
- Biobehavioral Imaging and Molecular Neuropsychopharmacology Unit, National Institute on Drug Abuse Intramural Research Program, Baltimore, MD 21224, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Corresponding author. (M.M.); (M.A.)
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5
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Romeo I, Prandi IG, Giombini E, Gruber CEM, Pietrucci D, Borocci S, Abid N, Fava A, Beccari AR, Chillemi G, Talarico C. The Spike Mutants Website: A Worldwide Used Resource against SARS-CoV-2. Int J Mol Sci 2022; 23:13082. [PMID: 36361870 PMCID: PMC9654198 DOI: 10.3390/ijms232113082] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 07/22/2023] Open
Abstract
A large number of SARS-CoV-2 mutations in a short period of time has driven scientific research related to vaccines, new drugs, and antibodies to combat the new variants of the virus. Herein, we present a web portal containing the structural information, the tridimensional coordinates, and the molecular dynamics trajectories of the SARS-CoV-2 spike protein and its main variants. The Spike Mutants website can serve as a rapid online tool for investigating the impact of novel mutations on virus fitness. Taking into account the high variability of SARS-CoV-2, this application can help the scientific community when prioritizing molecules for experimental assays, thus, accelerating the identification of promising drug candidates for COVID-19 treatment. Below we describe the main features of the platform and illustrate the possible applications for speeding up the drug discovery process and hypothesize new effective strategies to overcome the recurrent mutations in SARS-CoV-2 genome.
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Affiliation(s)
- Isabella Romeo
- Dipartimento di Scienze della Salute, Università Magna Græcia di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università Magna Graecia di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Ingrid Guarnetti Prandi
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy
| | - Emanuela Giombini
- Laboratory of Virology, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Roma, Italy
| | | | - Daniele Pietrucci
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), CNR, 70126 Bari, Italy
| | - Stefano Borocci
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, Monastir 5000, Tunisia
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, Monastir 5000, Tunisia
- High Institute of Biotechnology of Monastir, Department of Molecular and Cellular Biology, University of Monastir, Monastir 5000, Tunisia
| | - Anna Fava
- Dompé Farmaceutici SpA, Via Tommaso De Amicis, 95, 80131 Napoli, Italy
| | - Andrea R. Beccari
- Dompé Farmaceutici SpA, Via Tommaso De Amicis, 95, 80131 Napoli, Italy
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy
| | - Carmine Talarico
- Dompé Farmaceutici SpA, Via Tommaso De Amicis, 95, 80131 Napoli, Italy
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6
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Beccari AR, Vistoli G. Exscalate4CoV: Innovative High Performing Computing (HPC) Strategies to Tackle Pandemic Crisis. Int J Mol Sci 2022; 23:ijms231911576. [PMID: 36232873 PMCID: PMC9569893 DOI: 10.3390/ijms231911576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022] Open
Affiliation(s)
- Andrea R. Beccari
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis 95, I-80131 Napoli, Italy
| | - Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, I-20133 Milano, Italy
- Correspondence:
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7
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Prandi IG, Mavian C, Giombini E, Gruber CEM, Pietrucci D, Borocci S, Abid N, Beccari AR, Talarico C, Chillemi G. Structural Evolution of Delta (B.1.617.2) and Omicron (BA.1) Spike Glycoproteins. Int J Mol Sci 2022; 23:ijms23158680. [PMID: 35955815 PMCID: PMC9369368 DOI: 10.3390/ijms23158680] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 02/07/2023] Open
Abstract
The vast amount of epidemiologic and genomic data that were gathered as a global response to the COVID-19 pandemic that was caused by SARS-CoV-2 offer a unique opportunity to shed light on the structural evolution of coronaviruses and in particular on the spike (S) glycoprotein, which mediates virus entry into the host cell by binding to the human ACE2 receptor. Herein, we carry out an investigation into the dynamic properties of the S glycoprotein, focusing on the much more transmissible Delta and Omicron variants. Notwithstanding the great number of mutations that have accumulated, particularly in the Omicron S glycoprotein, our data clearly showed the conservation of some structural and dynamic elements, such as the global motion of the receptor binding domain (RBD). However, our studies also revealed structural and dynamic alterations that were concentrated in the aa 627–635 region, on a small region of the receptor binding motif (aa 483–485), and the so-called “fusion-peptide proximal region”. In particular, these last two S regions are known to be involved in the human receptor ACE2 recognition and membrane fusion. Our structural evidence, therefore, is likely involved in the observed different transmissibility of these S mutants. Finally, we highlighted the role of glycans in the increased RBD flexibility of the monomer in the up conformation of Omicron.
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Affiliation(s)
- Ingrid Guarnetti Prandi
- Department for Innovation in Biological, Agro-Food and Forest Systems—DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy
| | - Carla Mavian
- Emerging Pathogen Institute, University of Florida, Gainesville, FL 32608, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Emanuela Giombini
- Laboratory of Virology, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Roma, Italy
| | - Cesare E. M. Gruber
- Laboratory of Virology, INMI Lazzaro Spallanzani IRCCS, Via Portuense 292, 00149 Roma, Italy
| | - Daniele Pietrucci
- Department for Innovation in Biological, Agro-Food and Forest Systems—DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies—IBIOM, CNR, 70126 Bari, Italy
| | - Stefano Borocci
- Department for Innovation in Biological, Agro-Food and Forest Systems—DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy
- Institute for Biological Systems—ISB, CNR, Area della Ricerca di Roma 1, SP35d 9, 00010 Montelibretti, Italy
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, Monastir 5000, Tunisia
- High Institute of Biotechnology of Monastir, Department of Molecular and Cellular Biology, University of Monastir, Monastir 5000, Tunisia
| | | | - Carmine Talarico
- Dompé Farmaceutici SpA, Via Campo di Pile, 67100 L’Aquila, Italy
- Correspondence: (C.T.); (G.C.)
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems—DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy
- Correspondence: (C.T.); (G.C.)
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8
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Otieno JR, Cherry JL, Spiro DJ, Nelson MI, Trovão NS. Origins and Evolution of Seasonal Human Coronaviruses. Viruses 2022; 14:1551. [PMID: 35891531 PMCID: PMC9320361 DOI: 10.3390/v14071551] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
Four seasonal human coronaviruses (sHCoVs) are endemic globally (229E, NL63, OC43, and HKU1), accounting for 5-30% of human respiratory infections. However, the epidemiology and evolution of these CoVs remain understudied due to their association with mild symptomatology. Using a multigene and complete genome analysis approach, we find the evolutionary histories of sHCoVs to be highly complex, owing to frequent recombination of CoVs including within and between sHCoVs, and uncertain, due to the under sampling of non-human viruses. The recombination rate was highest for 229E and OC43 whereas substitutions per recombination event were highest in NL63 and HKU1. Depending on the gene studied, OC43 may have ungulate, canine, or rabbit CoV ancestors. 229E may have origins in a bat, camel, or an unsampled intermediate host. HKU1 had the earliest common ancestor (1809-1899) but fell into two distinct clades (genotypes A and B), possibly representing two independent transmission events from murine-origin CoVs that appear to be a single introduction due to large gaps in the sampling of CoVs in animals. In fact, genotype B was genetically more diverse than all the other sHCoVs. Finally, we found shared amino acid substitutions in multiple proteins along the non-human to sHCoV host-jump branches. The complex evolution of CoVs and their frequent host switches could benefit from continued surveillance of CoVs across non-human hosts.
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Affiliation(s)
- James R. Otieno
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Joshua L. Cherry
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - David J. Spiro
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Martha I. Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
| | - Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; (J.L.C.); (D.J.S.); (M.I.N.)
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9
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Lessons Learned and Yet-to-Be Learned on the Importance of RNA Structure in SARS-CoV-2 Replication. Microbiol Mol Biol Rev 2022; 86:e0005721. [PMID: 35862724 PMCID: PMC9491204 DOI: 10.1128/mmbr.00057-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
SARS-CoV-2, the etiological agent responsible for the COVID-19 pandemic, is a member of the virus family Coronaviridae, known for relatively extensive (~30-kb) RNA genomes that not only encode for numerous proteins but are also capable of forming elaborate structures. As highlighted in this review, these structures perform critical functions in various steps of the viral life cycle, ultimately impacting pathogenesis and transmissibility. We examine these elements in the context of coronavirus evolutionary history and future directions for curbing the spread of SARS-CoV-2 and other potential human coronaviruses. While we focus on structures supported by a variety of biochemical, biophysical, and/or computational methods, we also touch here on recent evidence for novel structures in both protein-coding and noncoding regions of the genome, including an assessment of the potential role for RNA structure in the controversial finding of SARS-CoV-2 integration in “long COVID” patients. This review aims to serve as a consolidation of previous works on coronavirus and more recent investigation of SARS-CoV-2, emphasizing the need for improved understanding of the role of RNA structure in the evolution and adaptation of these human viruses.
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10
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Solis O, Beccari AR, Iaconis D, Talarico C, Ruiz-Bedoya CA, Nwachukwu JC, Cimini A, Castelli V, Bertini R, Montopoli M, Cocetta V, Borocci S, Prandi IG, Flavahan K, Bahr M, Napiorkowski A, Chillemi G, Ooka M, Yang X, Zhang S, Xia M, Zheng W, Bonaventura J, Pomper MG, Hooper JE, Morales M, Rosenberg AZ, Nettles KW, Jain SK, Allegretti M, Michaelides M. The SARS-CoV-2 spike protein binds and modulates estrogen receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.05.21.492920. [PMID: 35665018 PMCID: PMC9164441 DOI: 10.1101/2022.05.21.492920] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein binds angiotensin-converting enzyme 2 (ACE2) at the cell surface, which constitutes the primary mechanism driving SARS-CoV-2 infection. Molecular interactions between the transduced S and endogenous proteins likely occur post-infection, but such interactions are not well understood. We used an unbiased primary screen to profile the binding of full-length S against >9,000 human proteins and found significant S-host protein interactions, including one between S and human estrogen receptor alpha (ERα). After confirming this interaction in a secondary assay, we used bioinformatics, supercomputing, and experimental assays to identify a highly conserved and functional nuclear receptor coregulator (NRC) LXD-like motif on the S2 subunit and an S-ERα binding mode. In cultured cells, S DNA transfection increased ERα cytoplasmic accumulation, and S treatment induced ER-dependent biological effects and ACE2 expression. Noninvasive multimodal PET/CT imaging in SARS-CoV-2-infected hamsters using [ 18 F]fluoroestradiol (FES) localized lung pathology with increased ERα lung levels. Postmortem experiments in lung tissues from SARS-CoV-2-infected hamsters and humans confirmed an increase in cytoplasmic ERα expression and its colocalization with S protein in alveolar macrophages. These findings describe the discovery and characterization of a novel S-ERα interaction, imply a role for S as an NRC, and are poised to advance knowledge of SARS-CoV-2 biology, COVID-19 pathology, and mechanisms of sex differences in the pathology of infectious disease.
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Affiliation(s)
- Oscar Solis
- Biobehavioral Imaging and Molecular Neuropsychopharmacology Unit, National Institute on Drug Abuse Intramural Research Program, Baltimore, 21224, MD, USA
| | | | | | | | - Camilo A. Ruiz-Bedoya
- Center for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB-II Room 109, Baltimore, MD, USA
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jerome C. Nwachukwu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Annamaria Cimini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, Temple University, Philadelphia, PA, USA
| | - Vanessa Castelli
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | | | - Monica Montopoli
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
- VIMM- Veneto Institute of Molecular Medicine, Fondazione per la Ricerca Biomedica Avanzata, Padova, Italy
| | - Veronica Cocetta
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Stefano Borocci
- Department for Innovation in Biological, Agro-Food and Forest Systems, DIBAF, University of Tuscia, Viterbo, Italy
| | - Ingrid G. Prandi
- Department for Innovation in Biological, Agro-Food and Forest Systems, DIBAF, University of Tuscia, Viterbo, Italy
| | - Kelly Flavahan
- Center for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB-II Room 109, Baltimore, MD, USA
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Melissa Bahr
- Center for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB-II Room 109, Baltimore, MD, USA
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anna Napiorkowski
- Center for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB-II Room 109, Baltimore, MD, USA
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems, DIBAF, University of Tuscia, Viterbo, Italy
| | - Masato Ooka
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Xiaoping Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shiliang Zhang
- Neuronal Networks Section, National Institute on Drug Abuse Intramural Research Program, Baltimore, 21224, MD, USA
| | - Menghang Xia
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Wei Zheng
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Jordi Bonaventura
- Departament de Patologia i Terapèutica Experimental, Institut de Neurociències, Universitat de Barcelona, L’Hospitalet de Llobregat, Catalonia
| | - Martin G. Pomper
- Department of Radiology and Radiological Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jody E. Hooper
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marisela Morales
- Neuronal Networks Section, National Institute on Drug Abuse Intramural Research Program, Baltimore, 21224, MD, USA
| | - Avi Z. Rosenberg
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kendall W. Nettles
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Sanjay K. Jain
- Center for Infection and Inflammation Imaging Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB-II Room 109, Baltimore, MD, USA
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Michael Michaelides
- Biobehavioral Imaging and Molecular Neuropsychopharmacology Unit, National Institute on Drug Abuse Intramural Research Program, Baltimore, 21224, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
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11
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Chazal N. Coronavirus, the King Who Wanted More Than a Crown: From Common to the Highly Pathogenic SARS-CoV-2, Is the Key in the Accessory Genes? Front Microbiol 2021; 12:682603. [PMID: 34335504 PMCID: PMC8317507 DOI: 10.3389/fmicb.2021.682603] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that emerged in late 2019, is the etiologic agent of the current "coronavirus disease 2019" (COVID-19) pandemic, which has serious health implications and a significant global economic impact. Of the seven human coronaviruses, all of which have a zoonotic origin, the pandemic SARS-CoV-2, is the third emerging coronavirus, in the 21st century, highly pathogenic to the human population. Previous human coronavirus outbreaks (SARS-CoV-1 and MERS-CoV) have already provided several valuable information on some of the common molecular and cellular mechanisms of coronavirus infections as well as their origin. However, to meet the new challenge caused by the SARS-CoV-2, a detailed understanding of the biological specificities, as well as knowledge of the origin are crucial to provide information on viral pathogenicity, transmission and epidemiology, and to enable strategies for therapeutic interventions and drug discovery. Therefore, in this review, we summarize the current advances in SARS-CoV-2 knowledges, in light of pre-existing information of other recently emerging coronaviruses. We depict the specificity of the immune response of wild bats and discuss current knowledge of the genetic diversity of bat-hosted coronaviruses that promotes viral genome expansion (accessory gene acquisition). In addition, we describe the basic virology of coronaviruses with a special focus SARS-CoV-2. Finally, we highlight, in detail, the current knowledge of genes and accessory proteins which we postulate to be the major keys to promote virus adaptation to specific hosts (bat and human), to contribute to the suppression of immune responses, as well as to pathogenicity.
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Affiliation(s)
- Nathalie Chazal
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS, Montpellier, France
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12
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Li X, Zhang L, Chen S, Ouyang H, Ren L. Possible Targets of Pan-Coronavirus Antiviral Strategies for Emerging or Re-Emerging Coronaviruses. Microorganisms 2021; 9:1479. [PMID: 34361915 PMCID: PMC8306356 DOI: 10.3390/microorganisms9071479] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 12/16/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which caused Coronaviruses Disease 2019 (COVID-19) and a worldwide pandemic, is the seventh human coronavirus that has been cross-transmitted from animals to humans. It can be predicted that with continuous contact between humans and animals, more viruses will spread from animals to humans. Therefore, it is imperative to develop universal coronavirus or pan-coronavirus vaccines or drugs against the next coronavirus pandemic. However, a suitable target is critical for developing pan-coronavirus antivirals against emerging or re-emerging coronaviruses. In this review, we discuss the latest progress of possible targets of pan-coronavirus antiviral strategies for emerging or re-emerging coronaviruses, including targets for pan-coronavirus inhibitors and vaccines, which will provide prospects for the current and future research and treatment of the disease.
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Affiliation(s)
| | | | | | | | - Linzhu Ren
- Key Laboratory for Zoonoses Research, College of Animal Sciences, Ministry of Education, Jilin University, 5333 Xi’An Road, Changchun 130062, China; (X.L.); (L.Z.); (S.C.); (H.O.)
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13
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Zella D, Giovanetti M, Cella E, Borsetti A, Ciotti M, Ceccarelli G, D’Ettorre G, Pezzuto A, Tambone V, Campanozzi L, Magheri M, Unali F, Bianchi M, Benedetti F, Pascarella S, Angeletti S, Ciccozzi M. The importance of genomic analysis in cracking the coronavirus pandemic. Expert Rev Mol Diagn 2021; 21:547-562. [PMID: 33849359 PMCID: PMC8095159 DOI: 10.1080/14737159.2021.1917998] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/13/2021] [Indexed: 12/11/2022]
Abstract
Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has pushed the scientific community to undertake intense research efforts. Understanding SARS-CoV-2 biology is necessary to discover therapeutic or preventive strategies capable of containing the pandemic. Knowledge of the structural characteristics of the virus genome and proteins is essential to find targets for therapies and immunological interventions.Areas covered: This review covers different areas of expertise, genomic analysis of circulating strains, structural biology, viral mutations, molecular diagnostics, disease, and vaccines. In particular, the review is focused on the molecular approaches and modern clinical strategies used in these fields.Expert opinion: Molecular approaches to SARS-CoV-2 pandemic have been critical to shorten time for new diagnostic, therapeutic and prevention strategies. In this perspective, the entire scientific community is moving in the same direction. Vaccines, together with the development of new drugs to treat the disease, represent the most important strategy to protect human from viral disease and prevent further spread. In this regard, new molecular technologies have been successfully implemented. The use of a novel strategy of communication is suggested for a better diffusion to the broader public of new data and results.
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Affiliation(s)
- Davide Zella
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, USA
- , Member of the Global Virus Network, Baltimore, USA
| | - Marta Giovanetti
- Flavivirus Laboratory, Oswaldo Cruz Institute Oswaldo Cruz Foundation, Rio De Janeiro, Brazil
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA
| | - Alessandra Borsetti
- Department of infectious diseases, National HIV/AIDS Research Center Istituto Superiore Di Sanità, Rome, Italy
| | - Marco Ciotti
- Virology Unit, Laboratory of Clinical Microbiology and Virology, Polyclinic Tor Vergata Foundation, Rome, Italy
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Gabriella D’Ettorre
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Aldo Pezzuto
- Cardiovascular-Respiratory Science Department, Sant’ Andrea Hospital-Sapienza University, Rome, Italy
| | - Vittoradolfo Tambone
- Institute of Philosophy of Scientific and Technological Practice, Campus Bio-Medico University, Rome, Italy
| | - Laura Campanozzi
- Institute of Philosophy of Scientific and Technological Practice, Campus Bio-Medico University, Rome, Italy
| | - Marco Magheri
- Communication Division, University Campus Bio-Medico of Rome, Rome, Italy
| | - Francesco Unali
- Communication Division, University Campus Bio-Medico of Rome, Rome, Italy
| | - Martina Bianchi
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome “La Sapienza”, Rome, Italy
| | - Francesca Benedetti
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, USA
| | - Stefano Pascarella
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome “La Sapienza”, Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
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14
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Borocci S, Cerchia C, Grottesi A, Sanna N, Prandi IG, Abid N, Beccari AR, Chillemi G, Talarico C. Altered Local Interactions and Long-Range Communications in UK Variant (B.1.1.7) Spike Glycoprotein. Int J Mol Sci 2021; 22:5464. [PMID: 34067272 PMCID: PMC8196891 DOI: 10.3390/ijms22115464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 12/24/2022] Open
Abstract
The COVID-19 pandemic is caused by SARS-CoV-2. Currently, most of the research efforts towards the development of vaccines and antibodies against SARS-CoV-2 were mainly focused on the spike (S) protein, which mediates virus entry into the host cell by binding to ACE2. As the virus SARS-CoV-2 continues to spread globally, variants have emerged, characterized by multiple mutations of the S glycoprotein. Herein, we employed microsecond-long molecular dynamics simulations to study the impact of the mutations of the S glycoprotein in SARS-CoV-2 Variant of Concern 202012/01 (B.1.1.7), termed the "UK variant", in comparison with the wild type, with the aim to decipher the structural basis of the reported increased infectivity and virulence. The simulations provided insights on the different dynamics of UK and wild-type S glycoprotein, regarding in particular the Receptor Binding Domain (RBD). In addition, we investigated the role of glycans in modulating the conformational transitions of the RBD. The overall results showed that the UK mutant experiences higher flexibility in the RBD with respect to wild type; this behavior might be correlated with the increased transmission reported for this variant. Our work also adds useful structural information on antigenic "hotspots" and epitopes targeted by neutralizing antibodies.
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Affiliation(s)
- Stefano Borocci
- Department for Innovation in Biological, Agro-Food and Forest Systems, DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (N.S.)
- Institute for Biological Systems, ISB, CNR, Via Salaria, Km 29.500, Monterotondo, 00015 Rome, Italy
| | - Carmen Cerchia
- Department of Pharmacy, University of Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy;
| | | | - Nico Sanna
- Department for Innovation in Biological, Agro-Food and Forest Systems, DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (N.S.)
| | - Ingrid Guarnetti Prandi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 3, 56124 Pisa, Italy;
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Rue Ibn Sina, Monastir 5000, Tunisia;
- High Institute of Biotechnology of Sidi Thabet, Department of Biotechnology, University of Manouba, BP-66, Ariana-Tunis 2020, Tunisia
| | | | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems, DIBAF, University of Tuscia, Via S. Camillo de Lellis s.n.c., 01100 Viterbo, Italy; (S.B.); (N.S.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM, CNR, Via Giovanni Amendola, 122/O, 70126 Bari, Italy
| | - Carmine Talarico
- Dompé Farmaceutici SpA, Via Campo di Pile, 67100 L’Aquila, Italy;
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15
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Lednicky JA, Tagliamonte MS, White SK, Elbadry MA, Alam MM, Stephenson CJ, Bonny TS, Loeb JC, Telisma T, Chavannes S, Ostrov DA, Mavian C, De Rochars VMB, Salemi M, Morris JG. Emergence of porcine delta-coronavirus pathogenic infections among children in Haiti through independent zoonoses and convergent evolution. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 33791709 PMCID: PMC8010738 DOI: 10.1101/2021.03.19.21253391] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Coronaviruses have caused three major epidemics since 2003, including the ongoing SARS-CoV-2 pandemic. In each case, coronavirus emergence in our species has been associated with zoonotic transmissions from animal reservoirs1,2, underscoring how prone such pathogens are to spill over and adapt to new species. Among the four recognized genera of the family Coronaviridae – Alphacoronavirus, Betacoronavirus, Deltacoronavirus, Gammacoronavirus, – human infections reported to date have been limited to alpha- and betacoronaviruses3. We identify, for the first time, porcine deltacoronavirus (PDCoV) strains in plasma samples of three Haitian children with acute undifferentiated febrile illness. Genomic and evolutionary analyses reveal that human infections were the result of at least two independent zoonoses of distinct viral lineages that acquired the same mutational signature in the nsp15 and the spike glycoprotein genes by convergent evolution. In particular, structural analysis predicts that one of the changes in the Spike S1 subunit, which contains the receptor-binding domain, may affect protein’s flexibility and binding to the host cell receptor. Our findings not only underscore the ability of deltacoronaviruses to adapt and potentially lead to human-to-human transmission, but also raise questions about the role of such transmissions in development of pre-existing immunity to other coronaviruses, such as SARS-CoV-2.
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16
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Montoya V, McLaughlin A, Mordecai GJ, Miller RL, Joy JB. Variable routes to genomic and host adaptation among coronaviruses. J Evol Biol 2021; 34:924-936. [PMID: 33751699 PMCID: PMC8242483 DOI: 10.1111/jeb.13771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/19/2021] [Accepted: 01/25/2021] [Indexed: 12/19/2022]
Abstract
Natural selection operating on the genomes of viral pathogens in different host species strongly contributes to adaptation facilitating host colonization. Here, we analyse, quantify and compare viral adaptation in genomic sequence data derived from seven zoonotic events in the Coronaviridae family among primary, intermediate and human hosts. Rates of nonsynonymous (dN) and synonymous (dS) changes on specific amino acid positions were quantified for each open reading frame (ORF). Purifying selection accounted for 77% of all sites under selection. Diversifying selection was most frequently observed in viruses infecting the primary hosts of each virus and predominantly occurred in the orf1ab genomic region. Within all four intermediate hosts, diversifying selection on the spike gene was observed either solitarily or in combination with orf1ab and other genes. Consistent with previous evidence, pervasive diversifying selection on coronavirus spike genes corroborates the role this protein plays in host cellular entry, adaptation to new hosts and evasion of host cellular immune responses. Structural modelling of spike proteins identified a significantly higher proportion of sites for SARS‐CoV‐2 under positive selection in close proximity to sites of glycosylation relative to the other coronaviruses. Among human coronaviruses, there was a significant inverse correlation between the number of sites under positive selection and the estimated years since the virus was introduced into the human population. Abundant diversifying selection observed in SARS‐CoV‐2 suggests the virus remains in the adaptive phase of the host switch, typical of recent host switches. A mechanistic understanding of where, when and how genomic adaptation occurs in coronaviruses following a host shift is crucial for vaccine design, public health responses and predicting future pandemics.
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Affiliation(s)
- Vincent Montoya
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Angela McLaughlin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada
| | - Gideon J Mordecai
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Rachel L Miller
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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17
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Lednicky JA, Tagliamonte MS, White SK, Elbadry MA, Alam MM, Stephenson CJ, Bonny TS, Loeb JC, Telisma T, Chavannes S, Ostrov DA, Mavian C, Beau De Rochars VM, Salemi M, Morris JG. Independent infections of porcine deltacoronavirus among Haitian children. Nature 2021; 600:133-137. [PMID: 34789872 PMCID: PMC8636265 DOI: 10.1038/s41586-021-04111-z] [Citation(s) in RCA: 152] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/07/2021] [Indexed: 01/07/2023]
Abstract
Coronaviruses have caused three major epidemics since 2003, including the ongoing SARS-CoV-2 pandemic. In each case, the emergence of coronavirus in our species has been associated with zoonotic transmissions from animal reservoirs1,2, underscoring how prone such pathogens are to spill over and adapt to new species. Among the four recognized genera of the family Coronaviridae, human infections reported so far have been limited to alphacoronaviruses and betacoronaviruses3-5. Here we identify porcine deltacoronavirus strains in plasma samples of three Haitian children with acute undifferentiated febrile illness. Genomic and evolutionary analyses reveal that human infections were the result of at least two independent zoonoses of distinct viral lineages that acquired the same mutational signature in the genes encoding Nsp15 and the spike glycoprotein. In particular, structural analysis predicts that one of the changes in the spike S1 subunit, which contains the receptor-binding domain, may affect the flexibility of the protein and its binding to the host cell receptor. Our findings highlight the potential for evolutionary change and adaptation leading to human infections by coronaviruses outside of the previously recognized human-associated coronavirus groups, particularly in settings where there may be close human-animal contact.
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Affiliation(s)
- John A. Lednicky
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL USA
| | - Massimiliano S. Tagliamonte
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL USA
| | - Sarah K. White
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL USA
| | - Maha A. Elbadry
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL USA
| | - Md. Mahbubul Alam
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL USA
| | - Caroline J. Stephenson
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL USA
| | - Tania S. Bonny
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL USA
| | - Julia C. Loeb
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL USA
| | | | | | - David A. Ostrov
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL USA
| | - Carla Mavian
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL USA
| | - Valery Madsen Beau De Rochars
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Health Services Research, Management and Policy, College of Public Health and Health Professions, University of Florida, Gainesville, FL USA
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA. .,Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA.
| | - J. Glenn Morris
- grid.15276.370000 0004 1936 8091Emerging Pathogens Institute, University of Florida, Gainesville, FL USA ,grid.15276.370000 0004 1936 8091Department of Medicine, College of Medicine, University of Florida, Gainesville, FL USA
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