101
|
Muth D, Corman VM, Roth H, Binger T, Dijkman R, Gottula LT, Gloza-Rausch F, Balboni A, Battilani M, Rihtarič D, Toplak I, Ameneiros RS, Pfeifer A, Thiel V, Drexler JF, Müller MA, Drosten C. Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus acquired during the early stages of human-to-human transmission. Sci Rep 2018; 8:15177. [PMID: 30310104 PMCID: PMC6181990 DOI: 10.1038/s41598-018-33487-8] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/27/2018] [Indexed: 12/03/2022] Open
Abstract
A 29 nucleotide deletion in open reading frame 8 (ORF8) is the most obvious genetic change in severe acute respiratory syndrome coronavirus (SARS-CoV) during its emergence in humans. In spite of intense study, it remains unclear whether the deletion actually reflects adaptation to humans. Here we engineered full, partially deleted (-29 nt), and fully deleted ORF8 into a SARS-CoV infectious cDNA clone, strain Frankfurt-1. Replication of the resulting viruses was compared in primate cell cultures as well as Rhinolophus bat cells made permissive for SARS-CoV replication by lentiviral transduction of the human angiotensin-converting enzyme 2 receptor. Cells from cotton rat, goat, and sheep provided control scenarios that represent host systems in which SARS-CoV is neither endemic nor epidemic. Independent of the cell system, the truncation of ORF8 (29 nt deletion) decreased replication up to 23-fold. The effect was independent of the type I interferon response. The 29 nt deletion in SARS-CoV is a deleterious mutation acquired along the initial human-to-human transmission chain. The resulting loss of fitness may be due to a founder effect, which has rarely been documented in processes of viral emergence. These results have important implications for the retrospective assessment of the threat posed by SARS.
Collapse
Affiliation(s)
- Doreen Muth
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Charitéplatz 1, 10117, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
- Institute of Virology, University of Bonn Medical Centre, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Victor Max Corman
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Charitéplatz 1, 10117, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
- Institute of Virology, University of Bonn Medical Centre, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Hanna Roth
- Institute of Virology, University of Bonn Medical Centre, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Tabea Binger
- Institute of Virology, University of Bonn Medical Centre, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Ronald Dijkman
- Federal Department of Home Affairs, Institute of Virology and Immunology IVI, Bern and Mittelhäusern, Sensemattstrasse 293, 3147, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012, Bern, Switzerland
| | - Lina Theresa Gottula
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Charitéplatz 1, 10117, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
- Institute of Virology, University of Bonn Medical Centre, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Florian Gloza-Rausch
- Noctalis, Centre for Bat Protection and Information, Oberbergstraße 27, 23795, Bad Segeberg, Germany
| | - Andrea Balboni
- Dipartimento di Scienze Mediche Veterinarie, Facoltà di Medicina Veterinaria, Alma Mater Studiorum-Università di Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, (BO), Italy
| | - Mara Battilani
- Dipartimento di Scienze Mediche Veterinarie, Facoltà di Medicina Veterinaria, Alma Mater Studiorum-Università di Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, (BO), Italy
| | - Danijela Rihtarič
- Virology Unit, Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000, Ljubljana, Slovenia
| | - Ivan Toplak
- Virology Unit, Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000, Ljubljana, Slovenia
| | - Ramón Seage Ameneiros
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein Allee 11, 89069, Ulm, Germany
- Group Morcegos de Galicia, Drosera Society, Pdo. Magdalena, G-2, 2° esq, 15320, As Pontes, Spain
| | - Alexander Pfeifer
- Institute for Pharmacology and Toxicology, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Volker Thiel
- Federal Department of Home Affairs, Institute of Virology and Immunology IVI, Bern and Mittelhäusern, Sensemattstrasse 293, 3147, Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012, Bern, Switzerland
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Charitéplatz 1, 10117, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
- Institute of Virology, University of Bonn Medical Centre, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Marcel Alexander Müller
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Charitéplatz 1, 10117, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
- Institute of Virology, University of Bonn Medical Centre, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Christian Drosten
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Charitéplatz 1, 10117, Berlin, Germany.
- German Center for Infection Research (DZIF), Berlin, Germany.
- Institute of Virology, University of Bonn Medical Centre, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.
| |
Collapse
|
102
|
Structural basis for broad neutralization of ebolaviruses by an antibody targeting the glycoprotein fusion loop. Nat Commun 2018; 9:3934. [PMID: 30258051 PMCID: PMC6158212 DOI: 10.1038/s41467-018-06113-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/17/2018] [Indexed: 11/09/2022] Open
Abstract
The severity of the 2014-2016 ebolavirus outbreak in West Africa expedited clinical development of therapeutics and vaccines though the countermeasures on hand were largely monospecific and lacked efficacy against other ebolavirus species that previously emerged. Recent studies indicate that ebolavirus glycoprotein (GP) fusion loops are targets for cross-protective antibodies. Here we report the 3.72 Å resolution crystal structure of one such cross-protective antibody, CA45, bound to the ectodomain of Ebola virus (EBOV) GP. The CA45 epitope spans multiple faces of the fusion loop stem, across both GP1 and GP2 subunits, with ~68% of residues identical across > 99.5% of known ebolavirus isolates. Extensive antibody interactions within a pan-ebolavirus small-molecule inhibitor binding cavity on GP define this cavity as a novel site of immune vulnerability. The structure elucidates broad ebolavirus neutralization through a highly conserved epitope on GP and further enables rational design and development of broadly protective vaccines and therapeutics.
Collapse
|
103
|
Chabas H, Lion S, Nicot A, Meaden S, van Houte S, Moineau S, Wahl LM, Westra ER, Gandon S. Evolutionary emergence of infectious diseases in heterogeneous host populations. PLoS Biol 2018; 16:e2006738. [PMID: 30248089 PMCID: PMC6171948 DOI: 10.1371/journal.pbio.2006738] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/04/2018] [Accepted: 09/05/2018] [Indexed: 12/26/2022] Open
Abstract
The emergence and re-emergence of pathogens remains a major public health concern. Unfortunately, when and where pathogens will (re-)emerge is notoriously difficult to predict, as the erratic nature of those events is reinforced by the stochastic nature of pathogen evolution during the early phase of an epidemic. For instance, mutations allowing pathogens to escape host resistance may boost pathogen spread and promote emergence. Yet, the ecological factors that govern such evolutionary emergence remain elusive because of the lack of ecological realism of current theoretical frameworks and the difficulty of experimentally testing their predictions. Here, we develop a theoretical model to explore the effects of the heterogeneity of the host population on the probability of pathogen emergence, with or without pathogen evolution. We show that evolutionary emergence and the spread of escape mutations in the pathogen population is more likely to occur when the host population contains an intermediate proportion of resistant hosts. We also show that the probability of pathogen emergence rapidly declines with the diversity of resistance in the host population. Experimental tests using lytic bacteriophages infecting their bacterial hosts containing Clustered Regularly Interspaced Short Palindromic Repeat and CRISPR-associated (CRISPR-Cas) immune defenses confirm these theoretical predictions. These results suggest effective strategies for cross-species spillover and for the management of emerging infectious diseases. The probability that an epidemic will break out is highly dependent on the ability of the pathogen to acquire new adaptive mutations and to induce evolutionary emergence. Forecasting pathogen emergence thus requires a good understanding of the interplay between the epidemiology and evolution taking place at the onset of an outbreak. Here, we provide a comprehensive theoretical framework to analyze the impact of host population heterogeneity on the probability of pathogen evolutionary emergence. We use this model to predict the impact of the fraction of susceptible hosts, the inoculum size of the pathogen, and the diversity of host resistance on pathogen emergence. Our experiments using lytic bacteriophages and CRISPR-resistant bacteria support our theoretical predictions and demonstrate that manipulating the diversity of resistance alleles in a host population may be an effective way to limit the emergence of new pathogens.
Collapse
Affiliation(s)
- Hélène Chabas
- CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier – EPHE, Montpellier, France
| | - Sébastien Lion
- CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier – EPHE, Montpellier, France
| | - Antoine Nicot
- CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier – EPHE, Montpellier, France
| | - Sean Meaden
- ESI and CEC, Biosciences, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| | - Stineke van Houte
- ESI and CEC, Biosciences, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| | - Sylvain Moineau
- Département de biochimie, microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, Canada
| | - Lindi M. Wahl
- Applied Mathematics, Western University, London, Ontario, Canada
| | - Edze R. Westra
- ESI and CEC, Biosciences, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| | - Sylvain Gandon
- CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier – EPHE, Montpellier, France
- * E-mail:
| |
Collapse
|
104
|
Morgan MD, Marioni JC. CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness. Genome Biol 2018; 19:81. [PMID: 29945659 PMCID: PMC6020341 DOI: 10.1186/s13059-018-1461-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/04/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Population phenotypic variation can arise from genetic differences between individuals, or from cellular heterogeneity in an isogenic group of cells or organisms. The emergence of gene expression differences between genetically identical cells is referred to as gene expression noise, the sources of which are not well understood. RESULTS In this work, by studying gene expression noise between multiple cell lineages and mammalian species, we find consistent evidence of a role for CpG islands as sources of gene expression noise. Variation in noise among CpG island promoters can be partially attributed to differences in island size, in which short islands have noisier gene expression. Building on these findings, we investigate the potential for short CpG islands to act as fast response elements to environmental stimuli. Specifically, we find that these islands are enriched amongst primary response genes in SWI/SNF-independent stimuli, suggesting that expression noise is an indicator of promoter responsiveness. CONCLUSIONS Thus, through the integration of single-cell RNA expression profiling, chromatin landscape and temporal gene expression dynamics, we have uncovered a role for short CpG island promoters as fast response elements.
Collapse
Affiliation(s)
- Michael D Morgan
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - John C Marioni
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| |
Collapse
|
105
|
Geoghegan JL, Holmes EC. Predicting virus emergence amid evolutionary noise. Open Biol 2018; 7:rsob.170189. [PMID: 29070612 PMCID: PMC5666085 DOI: 10.1098/rsob.170189] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/24/2017] [Indexed: 12/27/2022] Open
Abstract
The study of virus disease emergence, whether it can be predicted and how it might be prevented, has become a major research topic in biomedicine. Here we show that efforts to predict disease emergence commonly conflate fundamentally different evolutionary and epidemiological time scales, and are likely to fail because of the enormous number of unsampled viruses that could conceivably emerge in humans. Although we know much about the patterns and processes of virus evolution on evolutionary time scales as depicted in family-scale phylogenetic trees, these data have little predictive power to reveal the short-term microevolutionary processes that underpin cross-species transmission and emergence. Truly understanding disease emergence therefore requires a new mechanistic and integrated view of the factors that allow or prevent viruses spreading in novel hosts. We present such a view, suggesting that both ecological and genetic aspects of virus emergence can be placed within a simple population genetic framework, which in turn highlights the importance of host population size and density in determining whether emergence will be successful. Despite this framework, we conclude that a more practical solution to preventing and containing the successful emergence of new diseases entails ongoing virological surveillance at the human–animal interface and regions of ecological disturbance.
Collapse
Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| |
Collapse
|
106
|
Identification of H209 as Essential for pH 8-Triggered Receptor-Independent Syncytium Formation by S Protein of Mouse Hepatitis Virus A59. J Virol 2018. [PMID: 29514915 DOI: 10.1128/jvi.00209-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The spike glycoprotein (S) of murine coronavirus mouse hepatitis virus (MHV) strain A59 uses murine carcinoembryonic antigen-related cell adhesion molecule 1a as its receptor for cell entry, but S protein can also be triggered in the absence of receptor by pH 8.0 alone at 37°C. The mechanism by which conformational changes of this S glycoprotein can be triggered by pH 8.0 has not yet been determined. Here, we show that MHV-A59 S protein is triggered by pH 8.0 at 37°C to induce receptor-independent syncytium (RIS) formation on 293T cells, and that the conformational changes in S proteins triggered by pH 8.0 are very similar to those triggered by receptor binding. We systemically mutated each of 15 histidine residues in S protein and found that H209 is essential for pH 8.0-triggered RIS formation, while H179, H441, H643, and H759 also play important roles in this process. Replacement of H209 with Ala had no effect on receptor binding, but in murine 17Cl.1 cells mutant H209A MHV-A59 showed delayed growth kinetics and was readily outcompeted by wild-type virus when mixed together, indicating that the H209A mutation caused a defect in virus fitness. Finally, the H209A mutation significantly increased the thermostability of S protein in its prefusion conformation, which may raise the energy barrier for conformational change of S protein required for membrane fusion and lead to a decrease in virus fitness in cell culture. Thus, MHV-A59 may have evolved to lower the stability of its S protein in order to increase virus fitness.IMPORTANCE Enveloped viruses enter cells through fusion of viral and cellular membranes, and the process is mediated by interactions between viral envelope proteins and their host receptors. In the prefusion conformation, viral envelope proteins are metastable, and activation to the fusion conformation is tightly regulated, since premature activation would lead to loss of viral infectivity. The stability of viral envelope proteins greatly influences their activation and virus fitness. Here, we report that, similar to the A82V mutation in Ebola glycoprotein, in the S glycoprotein of murine coronavirus MHV-A59, the histidine residue at position of 209 significantly affects the thermal stability of the S protein, determines whether S protein can be activated at 37°C by either pH 8.0 alone or by receptor binding, and affects viral fitness in cell culture. Thus, the spike glycoprotein of MHV-A59 has evolved to retain histidine at position 209 to optimize virus fitness.
Collapse
|
107
|
McMahon DP, Wilfert L, Paxton RJ, Brown MJF. Emerging Viruses in Bees: From Molecules to Ecology. Adv Virus Res 2018; 101:251-291. [PMID: 29908591 DOI: 10.1016/bs.aivir.2018.02.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Emerging infectious diseases arise as a result of novel interactions between populations of hosts and pathogens, and can threaten the health and wellbeing of the entire spectrum of biodiversity. Bees and their viruses are a case in point. However, detailed knowledge of the ecological factors and evolutionary forces that drive disease emergence in bees and other host-pathogen communities is surprisingly lacking. In this review, we build on the fundamental insight that viruses evolve and adapt over timescales that overlap with host ecology. At the same time, we integrate the role of host community ecology, including community structure and composition, biodiversity loss, and human-driven disturbance, all of which represent significant factors in bee virus ecology. Both of these evolutionary and ecological perspectives represent major advances but, in most cases, it remains unclear how evolutionary forces actually operate across different biological scales (e.g., from cell to ecosystem). We present a molecule-to-ecology framework to help address these issues, emphasizing the role of molecular mechanisms as key bottom-up drivers of change at higher ecological scales. We consider the bee-virus system to be an ideal one in which to apply this framework. Unlike many other animal models, bees constitute a well characterized and accessible multispecies assemblage, whose populations and interspecific interactions can be experimentally manipulated and monitored in high resolution across space and time to provide robust tests of prevailing theory.
Collapse
Affiliation(s)
- Dino P McMahon
- Institute of Biology, Freie Universität Berlin, Berlin, Germany; Department for Materials and Environment, BAM Federal Institute for Materials Research and Testing, Berlin, Germany.
| | - Lena Wilfert
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Robert J Paxton
- Institute for Biology, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany; German Centre for integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Mark J F Brown
- School of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
| |
Collapse
|
108
|
Abstract
In 2014, the world witnessed the largest Ebolavirus outbreak in recorded history. The subsequent humanitarian effort spurred extensive research, significantly enhancing our understanding of ebolavirus replication and pathogenicity. The main functions of each ebolavirus protein have been studied extensively since the discovery of the virus in 1976; however, the recent expansion of ebolavirus research has led to the discovery of new protein functions. These newly discovered roles are revealing new mechanisms of virus replication and pathogenicity, whilst enhancing our understanding of the broad functions of each ebolavirus viral protein (VP). Many of these new functions appear to be unrelated to the protein's primary function during virus replication. Such new functions range from bystander T-lymphocyte death caused by VP40-secreted exosomes to new roles for VP24 in viral particle formation. This review highlights the newly discovered roles of ebolavirus proteins in order to provide a more encompassing view of ebolavirus replication and pathogenicity.
Collapse
Affiliation(s)
- Diego Cantoni
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Jeremy S. Rossman
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| |
Collapse
|
109
|
Li Q, Ma L, Yi D, Wang H, Wang J, Zhang Y, Guo Y, Li X, Zhou J, Shi Y, Gao GF, Cen S. Novel cyclo-peptides inhibit Ebola pseudotyped virus entry by targeting primed GP protein. Antiviral Res 2018; 155:1-11. [PMID: 29709562 DOI: 10.1016/j.antiviral.2018.04.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/24/2018] [Accepted: 04/26/2018] [Indexed: 12/19/2022]
Abstract
Ebola virus (EBOV) causes fatal hemorrhagic fever with high death rates in human. Currently, there are no available clinically-approved prophylactic or therapeutic treatments. The recently solved crystal structure of cleavage-primed EBOV glycoprotein (GPcl) in complex with the C domain of endosomal protein Niemann-Pick C1 (NPC1) provides a new target for the development of EBOV entry inhibitors. In this work, a computational approach using docking and molecular dynamic simulations is carried out for the rational design of peptide inhibitors. A novel cyclo-peptide (Pep-3.3) was identified to target at the late stage of EBOV entry and exhibit specific inhibitory activity against EBOV-GP pseudotyped viruses, with 50% inhibitory concentration (IC50) of 5.1 μM. In vitro binding assay and molecular simulations revealed that Pep-3.3 binds to GPcl with a KD value of 69.7 μM, through interacting with predicted residues in the hydrophobic binding pocket of GPcl. Mutation of predicted residues T83 caused resistance to Pep-3.3 inhibition in viral infectivity, providing preliminary support for the model of the peptide binding to GPcl. This study demonstrates the feasibility of inhibiting EBOV entry by targeting GPcl with peptides.
Collapse
Affiliation(s)
- Quanjie Li
- Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Ling Ma
- Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Dongrong Yi
- Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Han Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Wang
- Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Yongxin Zhang
- Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Ying Guo
- Institute of Materia Medica, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Xiaoyu Li
- Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Jinming Zhou
- Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing 100050, China.
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan Cen
- Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing 100050, China.
| |
Collapse
|
110
|
Host shifts result in parallel genetic changes when viruses evolve in closely related species. PLoS Pathog 2018; 14:e1006951. [PMID: 29649296 PMCID: PMC5897010 DOI: 10.1371/journal.ppat.1006951] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 02/27/2018] [Indexed: 01/23/2023] Open
Abstract
Host shifts, where a pathogen invades and establishes in a new host species, are a major source of emerging infectious diseases. They frequently occur between related host species and often rely on the pathogen evolving adaptations that increase their fitness in the novel host species. To investigate genetic changes in novel hosts, we experimentally evolved replicate lineages of an RNA virus (Drosophila C Virus) in 19 different species of Drosophilidae and deep sequenced the viral genomes. We found a strong pattern of parallel evolution, where viral lineages from the same host were genetically more similar to each other than to lineages from other host species. When we compared viruses that had evolved in different host species, we found that parallel genetic changes were more likely to occur if the two host species were closely related. This suggests that when a virus adapts to one host it might also become better adapted to closely related host species. This may explain in part why host shifts tend to occur between related species, and may mean that when a new pathogen appears in a given species, closely related species may become vulnerable to the new disease. Host shifts, where a pathogen jumps from one host species to another, are a major source of infectious disease. Hosts shifts are more likely to occur between related host species and often rely on the pathogen evolving adaptations that increase their fitness in the novel host. Here we have investigated how viruses evolve in different host species, by experimentally evolving replicate lineages of an RNA virus in 19 different host species that shared a common ancestor 40 million years ago. We then deep sequenced the genomes of these viruses to examine the genetic changes that have occurred in different host species that vary in their relatedness. We found that parallel mutations–that are indicative of selection–were significantly more likely to occur within viral lineages from the same host, and between viruses evolved in closely related species. This suggests that a mutation that may adapt a virus to a given host, may also adapt it to closely related host species.
Collapse
|
111
|
Abstract
The deterministic force of natural selection and stochastic influence of drift shape RNA virus evolution. New deep-sequencing and microfluidics technologies allow us to quantify the effect of mutations and trace the evolution of viral populations with single-genome and single-nucleotide resolution. Such experiments can reveal the topography of the genotype-fitness landscapes that shape the path of viral evolution. By combining historical analyses, like phylogenetic approaches, with high-throughput and high-resolution evolutionary experiments, we can observe parallel patterns of evolution that drive important phenotypic transitions. These developments provide a framework for quantifying and anticipating potential evolutionary events. Here, we examine emerging technologies that can map the selective landscapes of viruses, focusing on their application to pathogenic viruses. We identify areas where these technologies can bolster our ability to study the evolution of viruses and to anticipate and possibly intervene in evolutionary events and prevent viral disease.
Collapse
Affiliation(s)
- Patrick T Dolan
- Department of Biology, Stanford University, E200 Clark Center, 318 Campus Drive, Stanford, CA 94305, USA; Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA
| | - Zachary J Whitfield
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA.
| |
Collapse
|
112
|
Gale P. Using thermodynamic parameters to calibrate a mechanistic dose-response for infection of a host by a virus. MICROBIAL RISK ANALYSIS 2018; 8:1-13. [PMID: 32289059 PMCID: PMC7103988 DOI: 10.1016/j.mran.2018.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/29/2017] [Accepted: 01/03/2018] [Indexed: 05/21/2023]
Abstract
Assessing the risk of infection from emerging viruses or of existing viruses jumping the species barrier into novel hosts is limited by the lack of dose response data. The initial stages of the infection of a host by a virus involve a series of specific contact interactions between molecules in the host and on the virus surface. The strength of the interaction is quantified in the literature by the dissociation constant (Kd) which is determined experimentally and is specific for a given virus molecule/host molecule combination. Here, two stages of the initial infection process of host intestinal cells are modelled, namely escape of the virus in the oral challenge dose from the innate host defenses (e.g. mucin proteins in mucus) and the subsequent binding of any surviving virus to receptor molecules on the surface of the host epithelial cells. The strength of virus binding to host cells and to mucins may be quantified by the association constants, Ka and Kmucin, respectively. Here, a mechanistic dose-response model for the probability of infection of a host by a given virus dose is constructed using Ka and Kmucin which may be derived from published Kd values taking into account the number of specific molecular interactions. It is shown that the effectiveness of the mucus barrier is determined not only by the amount of mucin but also by the magnitude of Kmucin. At very high Kmucin values, slight excesses of mucin over virus are sufficient to remove all the virus according to the model. At lower Kmucin values, high numbers of virus may escape even with large excesses of mucin. The output from the mechanistic model is the probability (p1) of infection by a single virion which is the parameter used in conventional dose-response models to predict the risk of infection of the host from the ingested dose. It is shown here how differences in Ka (due to molecular differences in an emerging virus strain or new host) affect p1, and how these differences in Ka may be quantified in terms of two thermodynamic parameters, namely enthalpy and entropy. This provides the theoretical link between sequencing data and risk of infection. Lack of data on entropy is a limitation at present and may also affect our interpretation of Kd in terms of infectivity. It is concluded that thermodynamic approaches have a major contribution to make in developing dose-response models for emerging viruses.
Collapse
Key Words
- Asp, aspartate
- CRD, carbohydrate-recognition domain
- Cr, host cell receptor
- Dose-response
- EBOV, Zaire ebolavirus
- Enthalpy
- Entropy
- G, Gibbs free energy
- GI, gastrointestinal
- GP, glycoprotein
- H, enthalpy
- HA, haemagglutinin
- HBGA, histoblood group antigen
- HeV, Hendra virus
- Ka, Kmucin, association constants
- Kd, dissociation constant for two molecules bound to each other
- L, Avogadro number
- M, molar (moles dm−3)
- MBP, mannose binding protein
- MERS-CoV, MERS coronavirus
- MRA, microbiological risk assessment
- Mucin
- NPC1, Niemann-Pick C1 protein
- NiV, Nipah virus
- NoV, norovirus
- PL, phospholipid
- PRR, pathogen recognition receptor
- Phe, phenylalanine
- R, ideal gas constant
- S, entropy
- SPR, surface plasmon resonance
- T, temperature
- TIM-1, T-cell immunoglobulin and mucin domain protein 1
- VSV, vesicular stomatitis virus
- Virus
- k, on/off rate constant
- n, number of GP/Cr molecular contacts per virus/host cell binding
- pfu, plaque-forming unit
- ΔGa, change in Gibbs free energy on association of virus and cell
- ΔHa, change in enthalpy on association of virus and cell
- ΔSa, change in entropy on association of virus and cell
- ΔΔHa, change in ΔHa
Collapse
|
113
|
Ji Y, Lu Y, Yan Y, Liu X, Su N, Zhang C, Bi S, Xing XH. Design of Fusion Proteins for Efficient and Soluble Production of Immunogenic Ebola Virus Glycoprotein in Escherichia coli. Biotechnol J 2018; 13:e1700627. [PMID: 29500882 DOI: 10.1002/biot.201700627] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/30/2018] [Indexed: 11/08/2022]
Abstract
The Ebola hemorrhagic fever caused by Ebola virus is an extremely dangerous disease, and effective therapeutic agents are still lacking. Platforms for the efficient production of vaccines are crucial to ensure quick response against an Ebola virus outbreak. Ebola virus glycoprotein (EbolaGP) on the virion surface is responsible for membrane binding and virus entry, thus becoming the key target for vaccine development. However, heterologous expression of this protein still faces engineering challenges such as low production levels and insoluble aggregation. Here, the authors design and compare various fusion strategies, attaching great importance to the solubility-enhancing effect, and tag removal process. It is found that a C-terminal intein-based tag greatly enhances the solubility of EbolaGP and allows one-step chromatographic purification of the untagged EbolaGP through thiol-catalyzed self-cleavage. The purified untagged EbolaGP alone or with Freund's adjuvant are highly immunogenic, as confirmed in a mouse model. Consequently, the present study puts forward a new strategy for the efficient and soluble expression of untagged immunogenic EbolaGP. The intein-based protein fusion approach may be of importance for the large-scale production of Ebola virus subunit vaccine.
Collapse
Affiliation(s)
- Yang Ji
- MOE Key Laboratory of Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Yuan Lu
- MOE Key Laboratory of Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Yishu Yan
- MOE Key Laboratory of Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Xinxin Liu
- Bio-Cell Co. Ltd., Beijing, 100085, P. R. China
| | - Nan Su
- Bio-Cell Co. Ltd., Beijing, 100085, P. R. China
| | - Chong Zhang
- MOE Key Laboratory of Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, P. R. China.,Centre for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, P. R. China
| | - Shengli Bi
- Institute of Virology Disease Control, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xin-Hui Xing
- MOE Key Laboratory of Industrial Biocatalysis, Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, P. R. China.,Centre for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, P. R. China
| |
Collapse
|
114
|
Mobula LM, Nathalie MacDermott, Clive Hoggart, Brantly K, Plyler W, Brown J, Kauffeldt B, Eisenhut D, Cooper LA, Fankhauser J. Clinical Manifestations and Modes of Death among Patients with Ebola Virus Disease, Monrovia, Liberia, 2014. Am J Trop Med Hyg 2018; 98:1186-1193. [PMID: 29405115 PMCID: PMC5928808 DOI: 10.4269/ajtmh.17-0090] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Although the high case fatality rate (CFR) associated with Ebola virus disease (EVD) is well documented, there are limited data on the actual modes of death. We conducted a retrospective, observational cohort study among patients with laboratory-confirmed EVD. The patients were all seen at the Eternal Love Winning Africa Ebola Treatment Unit in Monrovia, Liberia, from June to August 2014. Our primary objective was to describe the modes of death of our patients and to determine predictors of mortality. Data were available for 53 patients with laboratory-confirmed EVD, with a median age of 35 years. The most frequent presenting symptoms were weakness (91%), fever (81%), and diarrhea (78%). Visible hemorrhage was noted in 25% of the cases. The CFR was 79%. Odds of death were higher in patients with diarrhea (odds ratio = 26.1, P < 0.01). All patients with hemorrhagic signs died (P < 0.01). Among the 18 fatal cases for which clinical information was available, three distinct modes of death were observed: sudden death after a moderate disease process (44%), profuse hemorrhage (33%), and encephalopathy (22%). We found that these modes of death varied by age (P = 0.04), maximum temperature (P = 0.43), heart rate on admission (P = 0.04), time to death from symptom onset (P = 0.13), and duration of hospitalization (P = 0.04). Although further study is required, our findings provide a foundation for developing treatment strategies that factor in patients with specific disease phenotypes (which often require the use of aggressive hydration). These findings provide insights into underlying pathogenic mechanisms resulting in severe EVD and suggest direction for future research and development of effective treatment options.
Collapse
Affiliation(s)
- Linda M Mobula
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland.,Disaster Response Unit, Samaritan's Purse, Boone, North Carolina.,Division of General Internal Medicine, Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Nathalie MacDermott
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom.,Disaster Response Unit, Samaritan's Purse, Boone, North Carolina
| | - Clive Hoggart
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, United Kingdom
| | - Kent Brantly
- Disaster Response Unit, Samaritan's Purse, Boone, North Carolina
| | - William Plyler
- Disaster Response Unit, Samaritan's Purse, Boone, North Carolina
| | - Jerry Brown
- Eternal Love Winning Africa (ELWA) Hospital, Monrovia, Liberia
| | - Bev Kauffeldt
- Disaster Response Unit, Samaritan's Purse, Boone, North Carolina
| | | | - Lisa A Cooper
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland.,Division of General Internal Medicine, Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - John Fankhauser
- SIM, Monrovia, Liberia.,Disaster Response Unit, Samaritan's Purse, Boone, North Carolina
| |
Collapse
|
115
|
Abstract
The Filoviridae are a family of negative-strand RNA viruses that include several important human pathogens. Ebola virus (EBOV) and Marburg virus are well-known filoviruses which cause life-threatening viral hemorrhagic fever in human and nonhuman primates. In addition to severe pathogenesis, filoviruses also exhibit a propensity for human-to-human transmission by close contact, posing challenges to containment and crisis management. Past outbreaks, in particular the recent West African EBOV epidemic, have been responsible for thousands of deaths and vaulted the filoviruses into public consciousness. Both national and international health agencies continue to regard potential filovirus outbreaks as critical threats to global public health. To develop effective countermeasures, a basic understanding of filovirus biology is needed. This review encompasses the epidemiology, ecology, molecular biology, and evolution of the filoviruses.
Collapse
Affiliation(s)
- Jackson Emanuel
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Andrea Marzi
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Heinz Feldmann
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States.
| |
Collapse
|
116
|
Abstract
The continual emergence of new pathogens and the increased spread of antibiotic resistance in bacterial populations remind us that microbes are living entities that evolve at rates that impact public health interventions. Following the historical thread of the works of Pasteur and Darwin shows how reconciling clinical microbiology, ecology, and evolution can be instrumental to understanding pathology, developing new therapies, and prolonging the efficiency of existing ones.
Collapse
Affiliation(s)
- Samuel Alizon
- Laboratoire MIVEGEC (UMR CNRS 5290, UR IRD 224, UM), Montpellier, France
- * E-mail:
| | | |
Collapse
|
117
|
Kurosaki Y, Ueda MT, Nakano Y, Yasuda J, Koyanagi Y, Sato K, Nakagawa S. Different effects of two mutations on the infectivity of Ebola virus glycoprotein in nine mammalian species. J Gen Virol 2018; 99:181-186. [PMID: 29300152 PMCID: PMC5882082 DOI: 10.1099/jgv.0.000999] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Ebola virus (EBOV), which belongs to the genus Ebolavirus, causes a severe and often fatal infection in primates, including humans, whereas Reston virus (RESTV) only causes lethal disease in non-human primates. Two amino acids (aa) at positions 82 and 544 of the EBOV glycoprotein (GP) are involved in determining viral infectivity. However, it remains unclear how these two aa residues affect the infectivity of Ebolavirus species in various hosts. Here we performed viral pseudotyping experiments with EBOV and RESTV GP derivatives in 10 cell lines from 9 mammalian species. We demonstrated that isoleucine at position 544/545 increases viral infectivity in all host species, whereas valine at position 82/83 modulates viral infectivity, depending on the viral and host species. Structural modelling suggested that the former residue affects viral fusion, whereas the latter residue influences the interaction with the viral entry receptor, Niemann–Pick C1.
Collapse
Affiliation(s)
- Yohei Kurosaki
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Mahoko Takahashi Ueda
- Micro/Nano Technology Center, Tokai University, 411 Kitakaname, Hiratsuka, Kanagawa 259-1292, Japan
| | - Yusuke Nakano
- Laboratory of Systems Virology, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.,Graduate School of Biomedical Sciences and Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Yoshio Koyanagi
- Laboratory of Systems Virology, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kei Sato
- Laboratory of Systems Virology, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.,CREST, Japan Science and Technology Agency, Saitama 322-0012, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan.,Micro/Nano Technology Center, Tokai University, 411 Kitakaname, Hiratsuka, Kanagawa 259-1292, Japan
| |
Collapse
|
118
|
Ewer K, Sebastian S, Spencer AJ, Gilbert S, Hill AVS, Lambe T. Chimpanzee adenoviral vectors as vaccines for outbreak pathogens. Hum Vaccin Immunother 2017; 13:3020-3032. [PMID: 29083948 PMCID: PMC5718829 DOI: 10.1080/21645515.2017.1383575] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/15/2017] [Accepted: 09/19/2017] [Indexed: 12/27/2022] Open
Abstract
The 2014-15 Ebola outbreak in West Africa highlighted the potential for large disease outbreaks caused by emerging pathogens and has generated considerable focus on preparedness for future epidemics. Here we discuss drivers, strategies and practical considerations for developing vaccines against outbreak pathogens. Chimpanzee adenoviral (ChAd) vectors have been developed as vaccine candidates for multiple infectious diseases and prostate cancer. ChAd vectors are safe and induce antigen-specific cellular and humoral immunity in all age groups, as well as circumventing the problem of pre-existing immunity encountered with human Ad vectors. For these reasons, such viral vectors provide an attractive platform for stockpiling vaccines for emergency deployment in response to a threatened outbreak of an emerging pathogen. Work is already underway to develop vaccines against a number of other outbreak pathogens and we will also review progress on these approaches here, particularly for Lassa fever, Nipah and MERS.
Collapse
Affiliation(s)
- Katie Ewer
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Headington, Oxford, UK
| | - Sarah Sebastian
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Headington, Oxford, UK
| | - Alexandra J. Spencer
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Headington, Oxford, UK
| | - Sarah Gilbert
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Headington, Oxford, UK
| | - Adrian V. S. Hill
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Headington, Oxford, UK
| | - Teresa Lambe
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Headington, Oxford, UK
| |
Collapse
|
119
|
Dehghani B, Ghasabi F, Hashempoor T, Joulaei H, Hasanshahi Z, Halaji M, Chatrabnous N, Mousavi Z, Moayedi J. Functional and structural characterization of Ebola virus glycoprotein (1976–2015) — Anin silicostudy. INT J BIOMATH 2017. [DOI: 10.1142/s179352451750108x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ebola virus (EBOV) is the causative agent of a severe hemorrhagic fever disease associated with high mortality rates in humans. This virus has five strains of which Zaire Ebola virus (ZEBOV) is the first and most important strain. It can be transmitted through contact with contaminated surfaces and objects. The genome of EBOV codes one non-structural and seven structural proteins consisting of two forms of glycoprotein (GP): soluble glycoprotein (sGP) and GP (spike). In this paper, we attempted to characterize and predict physicochemical properties, B-cell epitopes, mutation sites, phosphorylation sites, glycosylation sites, and different protein structures of EBOV GP to provide comprehensive data about changes of this GP during a 40-years course (1976–2015). GP sequences were obtained from NCBI gene bank from 1976–2015. Expasy’sProtParam, PROTSCALE, immuneepitope, Bepipred, BcePred, ABCpred, VaxiJen, DISPHOS, NetPhos, and numerous programs were used to predict and analyze all sequences. More variety of mutations were found in 2015 sequences and mutations were related to huge changes in B-cell epitopes, phosphorylation and glycosylation sites. In addition, our results determined different sites of disulfide bonds and an important mutation related to IgE epitope as well as four potent B-cell epitopes (380–387, 318–338, 405–438 and 434–475). In this study, we suggested the effect of mutations on GP properties, six positions for disulfide bonds and four phosphorylation sites for protein kinase C enzyme. Selected sequences were shown different sites for O-link and N-link glycosylation. A mutation that changed GP to an allergen protein and has a significant role in vaccine designing as well as four potent B-cell epitopes in GP protein were found.
Collapse
Affiliation(s)
- Behzad Dehghani
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farzane Ghasabi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Tayebeh Hashempoor
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Joulaei
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Hasanshahi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehrdad Halaji
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Nazanin Chatrabnous
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Mousavi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Javad Moayedi
- Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| |
Collapse
|
120
|
Abstract
The study of virus disease emergence, whether it can be predicted and how it might be prevented, has become a major research topic in biomedicine. Here we show that efforts to predict disease emergence commonly conflate fundamentally different evolutionary and epidemiological time scales, and are likely to fail because of the enormous number of unsampled viruses that could conceivably emerge in humans. Although we know much about the patterns and processes of virus evolution on evolutionary time scales as depicted in family-scale phylogenetic trees, these data have little predictive power to reveal the short-term microevolutionary processes that underpin cross-species transmission and emergence. Truly understanding disease emergence therefore requires a new mechanistic and integrated view of the factors that allow or prevent viruses spreading in novel hosts. We present such a view, suggesting that both ecological and genetic aspects of virus emergence can be placed within a simple population genetic framework, which in turn highlights the importance of host population size and density in determining whether emergence will be successful. Despite this framework, we conclude that a more practical solution to preventing and containing the successful emergence of new diseases entails ongoing virological surveillance at the human-animal interface and regions of ecological disturbance.
Collapse
Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| |
Collapse
|
121
|
Abstract
Recent studies demonstrate that the Ebola virus glycoprotein (GP) acquired an A82V change during the West Africa epidemic and that this change altered the capacity of GP to be activated by host factors, enhancing infection of human cells. How this may alter the outcome of disease remains to be determined.
Collapse
Affiliation(s)
- Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA.
| |
Collapse
|
122
|
Hedrick SM. Understanding Immunity through the Lens of Disease Ecology. Trends Immunol 2017; 38:888-903. [PMID: 28882454 DOI: 10.1016/j.it.2017.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/26/2017] [Accepted: 08/01/2017] [Indexed: 10/25/2022]
Abstract
As we describe the immune system in ever more exquisite detail, we might find that no matter how successful, this approach will not be sufficient to understand the spread of infectious agents, their susceptibility to vaccine therapy, and human disease resistance. Compared with the strict reductionism practiced as a means of characterizing most biological processes, I propose that the progression and outcome of disease-causing host-parasite interactions will be more clearly understood through a focus on disease ecology.
Collapse
Affiliation(s)
- Stephen M Hedrick
- Departments of Molecular Biology and Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| |
Collapse
|
123
|
Infection with the Makona variant results in a delayed and distinct host immune response compared to previous Ebola virus variants. Sci Rep 2017; 7:9730. [PMID: 28852031 PMCID: PMC5574898 DOI: 10.1038/s41598-017-09963-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/01/2017] [Indexed: 11/23/2022] Open
Abstract
Zaire Ebolavirus (ZEBOV) continues to pose a significant threat to human health as highlighted by the recent epidemic that originated in West Africa and the ongoing outbreak in the Democratic Republic of the Congo. Although the ZEBOV variant responsible for this epidemic (Makona) shares significant genetic similarity with previously identified variants (Kikwit and Mayinga), recent reports suggest slower disease progression in nonhuman primates. However, the pathogenesis caused by the new variant is not fully understood. We present the first comprehensive approach in understanding ZEBOV-Makona pathogenesis in cynomolgus macaques by measuring changes in immune cell frequencies, plasma levels of immune mediators, and differentially expressed genes (DEGs) within whole blood (WB) and peripheral blood mononuclear cells (PBMC). Our combined approach revealed a link between: 1) increased interferon-stimulated gene expression, IFNα levels, and activated plasmacytoid dendritic cells; 2) higher proinflammatory gene expression, cytokine and chemokine levels, and non-classical monocytes; 3) gene signature of leukocyte activation and increased granulocytes; and 4) decreased expression of lymphocyte related genes and lymphopenia. In addition, our data strongly indicate delayed disease progression as well as limited overlap (~30%) in host transcriptome changes following ZEBOV-Makona infection compared to ZEBOV-Kikwit. These observations provide novel insight into the molecular mechanisms of ZEBOV-Makona pathogenesis.
Collapse
|
124
|
Next step in the ongoing arms race between myxoma virus and wild rabbits in Australia is a novel disease phenotype. Proc Natl Acad Sci U S A 2017; 114:9397-9402. [PMID: 28808019 DOI: 10.1073/pnas.1710336114] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In host-pathogen arms races, increases in host resistance prompt counteradaptation by pathogens, but the nature of that counteradaptation is seldom directly observed outside of laboratory models. The best-documented field example is the coevolution of myxoma virus (MYXV) in European rabbits. To understand how MYXV in Australia has continued to evolve in wild rabbits under intense selection for genetic resistance to myxomatosis, we compared the phenotypes of the progenitor MYXV and viral isolates from the 1950s and the 1990s in laboratory rabbits with no resistance. Strikingly, and unlike their 1950s counterparts, most virus isolates from the 1990s induced a highly lethal immune collapse syndrome similar to septic shock. Thus, the next step in this canonical case of coevolution after a species jump has been further escalation by the virus in the face of widespread host resistance.
Collapse
|
125
|
Ruedas JB, Ladner JT, Ettinger CR, Gummuluru S, Palacios G, Connor JH. Spontaneous Mutation at Amino Acid 544 of the Ebola Virus Glycoprotein Potentiates Virus Entry and Selection in Tissue Culture. J Virol 2017; 91:e00392-17. [PMID: 28539437 PMCID: PMC5651722 DOI: 10.1128/jvi.00392-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/11/2017] [Indexed: 11/20/2022] Open
Abstract
Ebolaviruses have a surface glycoprotein (GP1,2) that is required for virus attachment and entry into cells. Mutations affecting GP1,2 functions can alter virus growth properties. We generated a recombinant vesicular stomatitis virus encoding Ebola virus Makona variant GP1,2 (rVSV-MAK-GP) and observed emergence of a T544I mutation in the Makona GP1,2 gene during tissue culture passage in certain cell lines. The T544I mutation emerged within two passages when VSV-MAK-GP was grown on Vero E6, Vero, and BS-C-1 cells but not when it was passaged on Huh7 and HepG2 cells. The mutation led to a marked increase in virus growth kinetics and conferred a robust growth advantage over wild-type rVSV-MAK-GP on Vero E6 cells. Analysis of complete viral genomes collected from patients in western Africa indicated that this mutation was not found in Ebola virus clinical samples. However, we observed the emergence of T544I during serial passage of various Ebola Makona isolates on Vero E6 cells. Three independent isolates showed emergence of T544I from undetectable levels in nonpassaged virus or virus passaged once to frequencies of greater than 60% within a single passage, consistent with it being a tissue culture adaptation. Intriguingly, T544I is not found in any Sudan, Bundibugyo, or Tai Forest ebolavirus sequences. Furthermore, T544I did not emerge when we serially passaged recombinant VSV encoding GP1,2 from these ebolaviruses. This report provides experimental evidence that the spontaneous mutation T544I is a tissue culture adaptation in certain cell lines and that it may be unique for the species Zaire ebolavirusIMPORTANCE The Ebola virus (Zaire) species is the most lethal species of all ebolaviruses in terms of mortality rate and number of deaths. Understanding how the Ebola virus surface glycoprotein functions to facilitate entry in cells is an area of intense research. Recently, three groups independently identified a polymorphism in the Ebola glycoprotein (I544) that enhanced virus entry, but they did not agree in their conclusions regarding its impact on pathogenesis. Our findings here address the origins of this polymorphism and provide experimental evidence showing that it is the result of a spontaneous mutation (T544I) specific to tissue culture conditions, suggesting that it has no role in pathogenesis. We further show that this mutation may be unique to the species Zaire ebolavirus, as it does not occur in Sudan, Bundibugyo, and Tai Forest ebolaviruses. Understanding the mechanism behind this mutation can provide insight into functional differences that exist in culture conditions and among ebolavirus glycoproteins.
Collapse
Affiliation(s)
- John B Ruedas
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston, Massachusetts, USA
| | - Jason T Ladner
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
| | - Chelsea R Ettinger
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Suryaram Gummuluru
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Gustavo Palacios
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, USA
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- National Emerging Infectious Diseases Laboratories, Boston, Massachusetts, USA
| |
Collapse
|
126
|
Nikiforuk AM, Cutts TA, Theriault SS, Cook BWM. Challenge of Liquid Stressed Protective Materials and Environmental Persistence of Ebola Virus. Sci Rep 2017; 7:4388. [PMID: 28663587 PMCID: PMC5491502 DOI: 10.1038/s41598-017-04137-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/19/2017] [Indexed: 11/16/2022] Open
Abstract
After the largest Ebola virus outbreak in history, experts have attempted to answer how the Zaire ebolavirus species emerged in West Africa and caused chains of human-to-human transmission. The widespread and untimely infection of Health Care Workers (HCW) in the affected countries accelerated spread of the virus within the community. Among the reasons attributed to this trend, it must be considered that HCW were exposed to the virus in their occupational environment. The contribution of environmental conditions to the spread of Ebola in West Africa was examined by investigating the effect of temperature/humidity on the virus’s environmental persistence and by modeling if saturation (liquid stress) allows for penetration of Ebola virus through personal protective equipment (PPE). Ebola-Makona virus persisted on PPE and materials found in outbreak settings for less than 72 hours at 27 °C and 80% relative humidity (RH). A difference in virus penetration was observed between dry (5%, 1/21 tests) and saturated (33%, 7/21 tests) samples of PPE. Infectious virus particles penetrated through saturated coupons of Tyvek Micro Clean, Tychem QC, whole surgical masks and N95 respirators. These findings suggest inclusion of saturation or similar liquid stress simulation in protective equipment testing standards.
Collapse
Affiliation(s)
- Aidan M Nikiforuk
- Applied Biosafety Research Program, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB, R3E 3P6, Canada.,J. C. Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, 745 Logan Street, Winnipeg, MB, R3E 3L5, Canada.,Department of Microbiology, The University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Todd A Cutts
- Applied Biosafety Research Program, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB, R3E 3P6, Canada.,J. C. Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, 745 Logan Street, Winnipeg, MB, R3E 3L5, Canada
| | - Steven S Theriault
- Applied Biosafety Research Program, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB, R3E 3P6, Canada. .,J. C. Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, 745 Logan Street, Winnipeg, MB, R3E 3L5, Canada. .,Department of Microbiology, The University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
| | - Bradley W M Cook
- Applied Biosafety Research Program, Canadian Science Centre for Human and Animal Health, 1015 Arlington Street, Winnipeg, MB, R3E 3P6, Canada.,J. C. Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, 745 Logan Street, Winnipeg, MB, R3E 3L5, Canada.,Department of Microbiology, The University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| |
Collapse
|
127
|
Abstract
Understanding how viruses adapt to new environments and acquire new phenotypes is critical for developing comprehensive responses to outbreaks. By studying the emergence of vaccine-derived poliovirus outbreaks, Stern et al. describe how a combination of sequence analysis and experimental evolution can be used to reveal adaptive pathways.
Collapse
Affiliation(s)
- Nathan D Grubaugh
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Kristian G Andersen
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Scripps Translational Science Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
128
|
The Major Envelope Glycoprotein of Murid Herpesvirus 4 Promotes Sexual Transmission. J Virol 2017; 91:JVI.00235-17. [PMID: 28424280 DOI: 10.1128/jvi.00235-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/10/2017] [Indexed: 12/25/2022] Open
Abstract
Gammaherpesviruses are important human and animal pathogens. Infection control has proven difficult because the key process of transmission is ill understood. Murid herpesvirus 4 (MuHV-4), a gammaherpesvirus of mice, is transmitted sexually. We show that this depends on the major virion envelope glycoprotein gp150. gp150 is redundant for host entry, and in vitro, it regulates rather than promotes cell binding. We show that gp150-deficient MuHV-4 reaches and replicates normally in the female genital tract after nasal infection but is poorly released from vaginal epithelial cells and fails to pass from the female to the male genital tract during sexual contact. Thus, we show that the regulation of virion binding is a key component of spontaneous gammaherpesvirus transmission.IMPORTANCE Gammaherpesviruses are responsible for many important diseases in both animals and humans. Some important aspects of their life cycle are still poorly understood. Key among these is viral transmission. Here we show that the major envelope glycoprotein of murid herpesvirus 4 functions not in entry or dissemination but in virion release to allow sexual transmission to new hosts.
Collapse
|
129
|
Zhao X, Howell KA, He S, Brannan JM, Wec AZ, Davidson E, Turner HL, Chiang CI, Lei L, Fels JM, Vu H, Shulenin S, Turonis AN, Kuehne AI, Liu G, Ta M, Wang Y, Sundling C, Xiao Y, Spence JS, Doranz BJ, Holtsberg FW, Ward AB, Chandran K, Dye JM, Qiu X, Li Y, Aman MJ. Immunization-Elicited Broadly Protective Antibody Reveals Ebolavirus Fusion Loop as a Site of Vulnerability. Cell 2017; 169:891-904.e15. [PMID: 28525756 PMCID: PMC5803079 DOI: 10.1016/j.cell.2017.04.038] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/20/2017] [Accepted: 04/27/2017] [Indexed: 12/30/2022]
Abstract
While neutralizing antibodies are highly effective against ebolavirus infections, current experimental ebolavirus vaccines primarily elicit species-specific antibody responses. Here, we describe an immunization-elicited macaque antibody (CA45) that clamps the internal fusion loop with the N terminus of the ebolavirus glycoproteins (GPs) and potently neutralizes Ebola, Sudan, Bundibugyo, and Reston viruses. CA45, alone or in combination with an antibody that blocks receptor binding, provided full protection against all pathogenic ebolaviruses in mice, guinea pigs, and ferrets. Analysis of memory B cells from the immunized macaque suggests that elicitation of broadly neutralizing antibodies (bNAbs) for ebolaviruses is possible but difficult, potentially due to the rarity of bNAb clones and their precursors. Unexpectedly, germline-reverted CA45, while exhibiting negligible binding to full-length GP, bound a proteolytically remodeled GP with picomolar affinity, suggesting that engineered ebolavirus vaccines could trigger rare bNAb precursors more robustly. These findings have important implications for developing pan-ebolavirus vaccine and immunotherapeutic cocktails.
Collapse
MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/isolation & purification
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibodies, Viral/isolation & purification
- Complementarity Determining Regions
- Cross Reactions
- Ebola Vaccines/immunology
- Ebolavirus/immunology
- Epitope Mapping
- Epitopes, B-Lymphocyte/immunology
- Female
- Ferrets
- Guinea Pigs
- Hemorrhagic Fever, Ebola/immunology
- Immunoglobulin Fab Fragments/ultrastructure
- Macaca fascicularis
- Male
- Mice
- Mice, Inbred BALB C
- Models, Molecular
Collapse
Affiliation(s)
- Xuelian Zhao
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20878, USA
| | | | - Shihua He
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; Deparment of Medical Microbiology, University of Manitoba, MB R3E 0J9, Canada
| | - Jennifer M Brannan
- US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21701, USA
| | - Anna Z Wec
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chi-I Chiang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20878, USA
| | - Lin Lei
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20878, USA
| | - J Maximilian Fels
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hong Vu
- Integrated BioTherapeutics, Rockville, MD 20850, USA
| | | | | | - Ana I Kuehne
- US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21701, USA
| | - Guodong Liu
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; Deparment of Medical Microbiology, University of Manitoba, MB R3E 0J9, Canada
| | - Mi Ta
- Integral Molecular, Philadelphia, PA 19104, USA
| | - Yimeng Wang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20878, USA
| | - Christopher Sundling
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Yongli Xiao
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Jennifer S Spence
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | | | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - John M Dye
- US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21701, USA
| | - Xiangguo Qiu
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; Deparment of Medical Microbiology, University of Manitoba, MB R3E 0J9, Canada
| | - Yuxing Li
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20878, USA; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - M Javad Aman
- Integrated BioTherapeutics, Rockville, MD 20850, USA.
| |
Collapse
|
130
|
Puschnik AS, Majzoub K, Ooi YS, Carette JE. A CRISPR toolbox to study virus-host interactions. Nat Rev Microbiol 2017; 15:351-364. [PMID: 28420884 PMCID: PMC5800792 DOI: 10.1038/nrmicro.2017.29] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Viruses are obligate intracellular pathogens that depend on host cellular components for replication. Genetic screens are an unbiased and comprehensive method to uncover host cellular components that are critical for the infection with viruses. Loss-of-function screens result in the genome-wide disruption of gene expression, whereas gain-of-function screens rely on large-scale overexpression of host genes. Genetic knockout screens can be conducted using haploid insertional mutagenesis or the CRISPR–Cas system. Genetic screens using the CRISPR–Cas system have provided crucial insights in the host determinants of infections with important human pathogens such as dengue virus, West Nile virus, Zika virus and hepatitis C virus. CRISPR–Cas-based techniques additionally provide ways to generate both in vitro and in vivo models to study viral pathogenesis, to manipulate viral genomes, to eradicate viral disease vectors using gene drive systems and to advance the development of antiviral therapeutics.
In this Review, Puschnik and colleagues discuss the technical aspects of using CRISPR–Cas technology in genome-scale knockout screens to study virus–host interactions, and they compare these screens with alternative genetic screening technologies. Viruses depend on their hosts to complete their replication cycles; they exploit cellular receptors for entry and hijack cellular functions to replicate their genome, assemble progeny virions and spread. Recently, genome-scale CRISPR–Cas screens have been used to identify host factors that are required for virus replication, including the replication of clinically relevant viruses such as Zika virus, West Nile virus, dengue virus and hepatitis C virus. In this Review, we discuss the technical aspects of genome-scale knockout screens using CRISPR–Cas technology, and we compare these screens with alternative genetic screening technologies. The relative ease of use and reproducibility of CRISPR–Cas make it a powerful tool for probing virus–host interactions and for identifying new antiviral targets.
Collapse
Affiliation(s)
- Andreas S Puschnik
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
| | - Karim Majzoub
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
| | - Yaw Shin Ooi
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
131
|
A Polymorphism within the Internal Fusion Loop of the Ebola Virus Glycoprotein Modulates Host Cell Entry. J Virol 2017; 91:JVI.00177-17. [PMID: 28228590 DOI: 10.1128/jvi.00177-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/15/2017] [Indexed: 12/12/2022] Open
Abstract
The large scale of the Ebola virus disease (EVD) outbreak in West Africa in 2013-2016 raised the question whether the host cell interactions of the responsible Ebola virus (EBOV) strain differed from those of other ebolaviruses. We previously reported that the glycoprotein (GP) of the virus circulating in West Africa in 2014 (EBOV2014) exhibited reduced ability to mediate entry into two nonhuman primate (NHP)-derived cell lines relative to the GP of EBOV1976. Here, we investigated the molecular determinants underlying the differential entry efficiency. We found that EBOV2014-GP-driven entry into diverse NHP-derived cell lines, as well as human monocyte-derived macrophages and dendritic cells, was reduced compared to EBOV1976-GP, although entry into most human- and all bat-derived cell lines tested was comparable. Moreover, EBOV2014 replication in NHP but not human cells was diminished relative to EBOV1976, suggesting that reduced cell entry translated into reduced viral spread. Mutagenic analysis of EBOV2014-GP and EBOV1976-GP revealed that an amino acid polymorphism in the receptor-binding domain, A82V, modulated entry efficiency in a cell line-independent manner and did not account for the reduced EBOV2014-GP-driven entry into NHP cells. In contrast, polymorphism T544I, located in the internal fusion loop in the GP2 subunit, was found to be responsible for the entry phenotype. These results suggest that position 544 is an important determinant of EBOV infectivity for both NHP and certain human target cells.IMPORTANCE The Ebola virus disease outbreak in West Africa in 2013 entailed more than 10,000 deaths. The scale of the outbreak and its dramatic impact on human health raised the question whether the responsible virus was particularly adept at infecting human cells. Our study shows that an amino acid exchange, A82V, that was acquired during the epidemic and that was not observed in previously circulating viruses, increases viral entry into diverse target cells. In contrast, the epidemic virus showed a reduced ability to enter cells of nonhuman primates compared to the virus circulating in 1976, and a single amino acid exchange in the internal fusion loop of the viral glycoprotein was found to account for this phenotype.
Collapse
|
132
|
Duraffour S, Malvy D, Sissoko D. How to treat Ebola virus infections? A lesson from the field. Curr Opin Virol 2017; 24:9-15. [PMID: 28410486 DOI: 10.1016/j.coviro.2017.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 02/13/2017] [Accepted: 03/09/2017] [Indexed: 01/11/2023]
Abstract
The reported case fatality ratios (CFR) of Ebola virus disease (EVD) have been as high as 90% in previous outbreaks. While the cumulative CFR among patients medically evacuated and treated in Western countries was inferior to 20%, it peaked to approximately 75% between September and December 2014 in West Africa, thereafter decreasing to less than 40% (May 2015) without current evidence of major virus mutations capable to alter virus pathogenicity over the course of the epidemic. Therefore, the observed diminution of CFR is likely to reflect improvement of EVD patient care. Here, we summarize major lessons learned, that is, progresses and knowledge gaps, about the clinical management of patients in West African settings during the 2014-2016 outbreak.
Collapse
Affiliation(s)
- Sophie Duraffour
- Bernhard Nocht Institute for Tropical Medicine, Department of Virology, Hamburg, Germany.
| | - Denis Malvy
- Bordeaux University Hospital, Department for Infectious Diseases and Tropical Medicine, and INSERM U 1219, Bordeaux University, Bordeaux, France
| | - Daouda Sissoko
- Bordeaux University Hospital, Department for Infectious Diseases and Tropical Medicine, and INSERM U 1219, Bordeaux University, Bordeaux, France.
| |
Collapse
|
133
|
Urbanowicz RA, McClure CP, Sakuntabhai A, Sall AA, Kobinger G, Müller MA, Holmes EC, Rey FA, Simon-Loriere E, Ball JK. Human Adaptation of Ebola Virus during the West African Outbreak. Cell 2017; 167:1079-1087.e5. [PMID: 27814505 PMCID: PMC5101188 DOI: 10.1016/j.cell.2016.10.013] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/23/2016] [Accepted: 10/06/2016] [Indexed: 12/02/2022]
Abstract
The 2013–2016 outbreak of Ebola virus (EBOV) in West Africa was the largest recorded. It began following the cross-species transmission of EBOV from an animal reservoir, most likely bats, into humans, with phylogenetic analysis revealing the co-circulation of several viral lineages. We hypothesized that this prolonged human circulation led to genomic changes that increased viral transmissibility in humans. We generated a synthetic glycoprotein (GP) construct based on the earliest reported isolate and introduced amino acid substitutions that defined viral lineages. Mutant GPs were used to generate a panel of pseudoviruses, which were used to infect different human and bat cell lines. These data revealed that specific amino acid substitutions in the EBOV GP have increased tropism for human cells, while reducing tropism for bat cells. Such increased infectivity may have enhanced the ability of EBOV to transmit among humans and contributed to the wide geographic distribution of some viral lineages. EBOV adapted to humans during the West African outbreak Amino acid substitutions in the EBOV glycoprotein increase human cell tropism The same glycoprotein amino acid substitutions decrease tropism for bat cells
Collapse
Affiliation(s)
- Richard A Urbanowicz
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2RD, UK; NIHR Nottingham Digestive Diseases Biomedical Research Unit, The University of Nottingham, Nottingham University Hospitals NHS Trust, Nottingham NG7 2UH, UK
| | - C Patrick McClure
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2RD, UK; NIHR Nottingham Digestive Diseases Biomedical Research Unit, The University of Nottingham, Nottingham University Hospitals NHS Trust, Nottingham NG7 2UH, UK
| | - Anavaj Sakuntabhai
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, 75724 Paris Cedex 15, France; Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, 75015 Paris, France
| | - Amadou A Sall
- Arbovirus and Viral Hemorrhagic Fever Unit, Institut Pasteur de Dakar, BP 220 Dakar, Senegal
| | - Gary Kobinger
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, ON K1A 0K9, Canada; Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, MB R32T 2N2, Canada
| | - Marcel A Müller
- Institute of Virology, University of Bonn Medical Center, 53127 Bonn, Germany
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2050, Australia
| | - Félix A Rey
- Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France; Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3569, 75724 Paris Cedex 15, France
| | - Etienne Simon-Loriere
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, 75724 Paris Cedex 15, France; Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, 75015 Paris, France.
| | - Jonathan K Ball
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2RD, UK; NIHR Nottingham Digestive Diseases Biomedical Research Unit, The University of Nottingham, Nottingham University Hospitals NHS Trust, Nottingham NG7 2UH, UK.
| |
Collapse
|
134
|
Abstract
A mutation in the Ebola virus glycoprotein arose early during the 2013-2016 epidemic and dominated the viral population. Two studies by Diehl et al. and Urbanowicz et al. now reveal that this mutation is associated with higher infectivity to human cells, representing the clearest example of Ebola's functional adaptation to human hosts.
Collapse
Affiliation(s)
- Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Harmit S Malik
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| |
Collapse
|
135
|
Wang MK, Lim SY, Lee SM, Cunningham JM. Biochemical Basis for Increased Activity of Ebola Glycoprotein in the 2013-16 Epidemic. Cell Host Microbe 2017; 21:367-375. [PMID: 28238624 DOI: 10.1016/j.chom.2017.02.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/12/2017] [Accepted: 02/03/2017] [Indexed: 11/28/2022]
Abstract
Ebola virus (EBOV) infection is characterized by sporadic outbreaks caused by zoonotic transmission. Fixed changes in amino acid sequence, such as A82V in the EBOV glycoprotein (GP) that occurred early in the 2013-16 epidemic, are suspected to confer a selective advantage to the virus. We used biochemical assays of GP function to show that A82V, as well as a polymorphism in residue 544 identified in other outbreaks, enhances infection by decreasing the threshold for activation of membrane fusion activity triggered by the host factors cathepsin B and Niemann-Pick C1. Importantly, the increase in infectivity comes with the cost of decreased virus stability. Thus, emergence of a virus GP with altered properties that can affect transmission and virulence may have contributed to the severity and scope of the 2013-16 EBOV epidemic.
Collapse
Affiliation(s)
- May K Wang
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Sun-Young Lim
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Soo Mi Lee
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - James M Cunningham
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
136
|
Ueda MT, Kurosaki Y, Izumi T, Nakano Y, Oloniniyi OK, Yasuda J, Koyanagi Y, Sato K, Nakagawa S. Functional mutations in spike glycoprotein of Zaire ebolavirus associated with an increase in infection efficiency. Genes Cells 2017; 22:148-159. [PMID: 28084671 DOI: 10.1111/gtc.12463] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 11/29/2016] [Indexed: 01/23/2023]
Abstract
Ebola virus (EBOV) is extremely virulent, and its glycoprotein is necessary for viral entry. EBOV may adapt to its new host humans during outbreaks by acquiring mutations especially in glycoprotein, which allows EBOV to spread more efficiently. To identify these evolutionary selected mutations and examine their effects on viral infectivity, we used experimental-phylogenetic-structural interdisciplinary approaches. In evolutionary analysis of all available Zaire ebolavirus glycoprotein sequences, we detected two codon sites under positive selection, which are located near/within the region critical for the host-viral membrane fusion, namely alanine-to-valine and threonine-to-isoleucine mutations at 82 (A82V) and 544 (T544I), respectively. The fine-scale transmission dynamics of EBOV Makona variants that caused the 2014-2015 outbreak showed that A82V mutant was fixed in the population, whereas T544I was not. Furthermore, pseudotype assays for the Makona glycoprotein showed that the A82V mutation caused a small increase in viral infectivity compared with the T544I mutation. These findings suggest that mutation fixation in EBOV glycoprotein may be associated with their increased infectivity levels; the mutant with a moderate increase in infectivity will fix. Our findings showed that a driving force for Ebola virus evolution via glycoprotein may be a balance between costs and benefits of its virulence.
Collapse
Affiliation(s)
- Mahoko Takahashi Ueda
- Micro/Nano Technology Center, Tokai University, 411 Kitakaname, Hiratsuka, Kanagawa, 259-1193, Japan
| | - Yohei Kurosaki
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Taisuke Izumi
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan.,CREST, Japan Science and Technology Agency, Saitama, 322-0012, Japan
| | - Yusuke Nakano
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Olamide K Oloniniyi
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.,Graduate School of Biomedical Sciences and Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.,Graduate School of Biomedical Sciences and Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Yoshio Koyanagi
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Kei Sato
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan.,CREST, Japan Science and Technology Agency, Saitama, 322-0012, Japan
| | - So Nakagawa
- Micro/Nano Technology Center, Tokai University, 411 Kitakaname, Hiratsuka, Kanagawa, 259-1193, Japan.,Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| |
Collapse
|
137
|
Lawrence P, Danet N, Reynard O, Volchkova V, Volchkov V. Human transmission of Ebola virus. Curr Opin Virol 2016; 22:51-58. [PMID: 28012412 DOI: 10.1016/j.coviro.2016.11.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/25/2016] [Accepted: 11/29/2016] [Indexed: 12/11/2022]
Abstract
Ever since the first recognised outbreak of Ebolavirus in 1976, retrospective epidemiological analyses and extensive studies with animal models have given us insight into the nature of the pathology and transmission mechanisms of this virus. In this review focusing on Ebolavirus, we present an outline of our current understanding of filovirus human-to-human transmission and of our knowledge concerning the molecular basis of viral transmission and potential for adaptation, with particular focus on what we have learnt from the 2014 outbreak in West Africa. We identify knowledge gaps relating to transmission and pathogenicity mechanisms, molecular adaptation and filovirus ecology.
Collapse
Affiliation(s)
- Philip Lawrence
- Molecular Basis of Viral Pathogenicity, International Centre for Research in Infectiology (CIRI), INSERM U1111 - CNRS UMR5308, Université Lyon 1, Ecole Normale Supérieure de Lyon, Lyon 69007, France; Université de Lyon, UMRS 449, Laboratoire de Biologie Générale, Université Catholique de Lyon - EPHE, Lyon 69288, France
| | - Nicolas Danet
- Molecular Basis of Viral Pathogenicity, International Centre for Research in Infectiology (CIRI), INSERM U1111 - CNRS UMR5308, Université Lyon 1, Ecole Normale Supérieure de Lyon, Lyon 69007, France
| | - Olivier Reynard
- Molecular Basis of Viral Pathogenicity, International Centre for Research in Infectiology (CIRI), INSERM U1111 - CNRS UMR5308, Université Lyon 1, Ecole Normale Supérieure de Lyon, Lyon 69007, France
| | - Valentina Volchkova
- Molecular Basis of Viral Pathogenicity, International Centre for Research in Infectiology (CIRI), INSERM U1111 - CNRS UMR5308, Université Lyon 1, Ecole Normale Supérieure de Lyon, Lyon 69007, France
| | - Viktor Volchkov
- Molecular Basis of Viral Pathogenicity, International Centre for Research in Infectiology (CIRI), INSERM U1111 - CNRS UMR5308, Université Lyon 1, Ecole Normale Supérieure de Lyon, Lyon 69007, France.
| |
Collapse
|
138
|
|