1
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Dupuy LC, Spiropoulou CF, Towner JS, Spengler JR, Sullivan NJ, Montgomery JM. Filoviruses: Scientific Gaps and Prototype Pathogen Recommendation. J Infect Dis 2023; 228:S446-S459. [PMID: 37849404 PMCID: PMC11009505 DOI: 10.1093/infdis/jiad362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023] Open
Abstract
Viruses in the family Filoviridae, including the commonly known Ebola (EBOV) and Marburg (MARV) viruses, can cause severe hemorrhagic fever in humans and nonhuman primates. Sporadic outbreaks of filovirus disease occur in sub-Saharan Africa with reported case fatality rates ranging from 25% to 90%. The high mortality and increasing frequency and magnitude of recent outbreaks along with the increased potential for spread from rural to urban areas highlight the importance of pandemic preparedness for these viruses. Despite their designation as high-priority pathogens, numerous scientific gaps exist in critical areas. In this review, these gaps and an assessment of potential prototype pathogen candidates are presented for this important virus family.
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Affiliation(s)
- Lesley C Dupuy
- Virology Branch, Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Christina F Spiropoulou
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nancy J Sullivan
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA
| | - Joel M Montgomery
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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2
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Rochman ND, Wolf YI, Koonin EV. Molecular adaptations during viral epidemics. EMBO Rep 2022; 23:e55393. [PMID: 35848484 PMCID: PMC9346483 DOI: 10.15252/embr.202255393] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/18/2022] [Accepted: 06/27/2022] [Indexed: 07/20/2023] Open
Abstract
In 1977, the world witnessed both the eradication of smallpox and the beginning of the modern age of genomics. Over the following half-century, 7 epidemic viruses of international concern galvanized virologists across the globe and led to increasingly extensive virus genome sequencing. These sequencing efforts exerted over periods of rapid adaptation of viruses to new hosts, in particular, humans provide insight into the molecular mechanisms underpinning virus evolution. Investment in virus genome sequencing was dramatically increased by the unprecedented support for phylogenomic analyses during the COVID-19 pandemic. In this review, we attempt to piece together comprehensive molecular histories of the adaptation of variola virus, HIV-1 M, SARS, H1N1-SIV, MERS, Ebola, Zika, and SARS-CoV-2 to the human host. Disruption of genes involved in virus-host interaction in animal hosts, recombination including genome segment reassortment, and adaptive mutations leading to amino acid replacements in virus proteins involved in host receptor binding and membrane fusion are identified as the key factors in the evolution of epidemic viruses.
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Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Yuri I Wolf
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Eugene V Koonin
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
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3
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Jacob ST, Crozier I, Fischer WA, Hewlett A, Kraft CS, Vega MADL, Soka MJ, Wahl V, Griffiths A, Bollinger L, Kuhn JH. Ebola virus disease. Nat Rev Dis Primers 2020; 6:13. [PMID: 32080199 PMCID: PMC7223853 DOI: 10.1038/s41572-020-0147-3] [Citation(s) in RCA: 278] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/10/2020] [Indexed: 12/16/2022]
Abstract
Ebola virus disease (EVD) is a severe and frequently lethal disease caused by Ebola virus (EBOV). EVD outbreaks typically start from a single case of probable zoonotic transmission, followed by human-to-human transmission via direct contact or contact with infected bodily fluids or contaminated fomites. EVD has a high case-fatality rate; it is characterized by fever, gastrointestinal signs and multiple organ dysfunction syndrome. Diagnosis requires a combination of case definition and laboratory tests, typically real-time reverse transcription PCR to detect viral RNA or rapid diagnostic tests based on immunoassays to detect EBOV antigens. Recent advances in medical countermeasure research resulted in the recent approval of an EBOV-targeted vaccine by European and US regulatory agencies. The results of a randomized clinical trial of investigational therapeutics for EVD demonstrated survival benefits from two monoclonal antibody products targeting the EBOV membrane glycoprotein. New observations emerging from the unprecedented 2013-2016 Western African EVD outbreak (the largest in history) and the ongoing EVD outbreak in the Democratic Republic of the Congo have substantially improved the understanding of EVD and viral persistence in survivors of EVD, resulting in new strategies toward prevention of infection and optimization of clinical management, acute illness outcomes and attendance to the clinical care needs of patients.
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Affiliation(s)
- Shevin T Jacob
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Global Health Security Department, Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Ian Crozier
- Integrated Research Facility at Fort Detrick, Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research supported by the National Cancer Institute, Frederick, MD, USA
| | - William A Fischer
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, Chapel Hill, NC, USA
| | - Angela Hewlett
- Nebraska Biocontainment Unit, Division of Infectious Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Colleen S Kraft
- Microbiology Section, Emory Medical Laboratory, Emory University School of Medicine, Atlanta, GA, USA
| | - Marc-Antoine de La Vega
- Department of Microbiology, Immunology & Infectious Diseases, Université Laval, Quebec City, QC, Canada
| | - Moses J Soka
- Partnership for Ebola Virus Disease Research in Liberia, Monrovia Medical Units ELWA-2 Hospital, Monrovia, Liberia
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Laura Bollinger
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA.
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4
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Ciccozzi M, Lai A, Zehender G, Borsetti A, Cella E, Ciotti M, Sagnelli E, Sagnelli C, Angeletti S. The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review. J Med Virol 2019; 91:1707-1724. [PMID: 31243773 DOI: 10.1002/jmv.25526] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/24/2019] [Indexed: 12/16/2022]
Abstract
In the last decade, the phylogenetic approach is recurrent in molecular evolutionary analysis. On 12 May, 2019, about 2 296 213 papers are found, but typing "phylogeny" or "epidemiology AND phylogeny" only 199 804 and 20 133 are retrieved, respectively. Molecular epidemiology in infectious diseases is widely used to define the source of infection as so as the ancestral relationships of individuals sampled from a population. Coalescent theory and phylogeographic analysis have had scientific application in several, recent pandemic events, and nosocomial outbreaks. Hepatitis viruses and immunodeficiency virus (human immunodeficiency virus) have been largely studied. Phylogenetic analysis has been recently applied on Polyomaviruses so as in the more recent outbreaks due to different arboviruses type as Zika and chikungunya viruses discovering the source of infection and the geographic spread. Data on sequences isolated by the microorganism are essential to apply the phylogenetic tools and research in the field of infectious disease phylodinamics is growing up. There is the need to apply molecular phylogenetic and evolutionary methods in areas out of infectious diseases, as translational genomics and personalized medicine. Lastly, the application of these tools in vaccine strategy so as in antibiotic and antiviral researchers are encouraged.
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Affiliation(s)
- Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, Roma, Italy
| | - Eleonora Cella
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Marco Ciotti
- Laboratory of Molecular Virology, Polyclinic Tor Vergata Foundation, Rome, Italy
| | - Evangelista Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
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5
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Effects of multiple sources of genetic drift on pathogen variation within hosts. PLoS Biol 2018; 16:e2004444. [PMID: 29590105 PMCID: PMC5891033 DOI: 10.1371/journal.pbio.2004444] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 04/09/2018] [Accepted: 02/26/2018] [Indexed: 12/17/2022] Open
Abstract
Changes in pathogen genetic variation within hosts alter the severity and spread of infectious diseases, with important implications for clinical disease and public health. Genetic drift may play a strong role in shaping pathogen variation, but analyses of drift in pathogens have oversimplified pathogen population dynamics, either by considering dynamics only at a single scale-such as within hosts or between hosts-or by making drastic simplifying assumptions, for example, that host immune systems can be ignored or that transmission bottlenecks are complete. Moreover, previous studies have used genetic data to infer the strength of genetic drift, whereas we test whether the genetic drift imposed by pathogen population processes can be used to explain genetic data. We first constructed and parameterized a mathematical model of gypsy moth baculovirus dynamics that allows genetic drift to act within and between hosts. We then quantified the genome-wide diversity of baculovirus populations within each of 143 field-collected gypsy moth larvae using Illumina sequencing. Finally, we determined whether the genetic drift imposed by host-pathogen population dynamics in our model explains the levels of pathogen diversity in our data. We found that when the model allows drift to act at multiple scales-including within hosts, between hosts, and between years-it can accurately reproduce the data, but when the effects of drift are simplified by neglecting transmission bottlenecks and stochastic variation in virus replication within hosts, the model fails. A de novo mutation model and a purifying selection model similarly fail to explain the data. Our results show that genetic drift can play a strong role in determining pathogen variation and that mathematical models that account for pathogen population growth at multiple scales of biological organization can be used to explain this variation.
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6
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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.
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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.
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7
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Banerjee A, Pal A, Pal D, Mitra P. Ebolavirus interferon antagonists—protein interaction perspectives to combat pathogenesis. Brief Funct Genomics 2017; 17:392-401. [DOI: 10.1093/bfgp/elx034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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8
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Zhou S, Cella E, Zhou W, Kong WH, Liu MQ, Liu PL, Ciccozzi M, Salemi M, Chen X. Population dynamics of hepatitis C virus subtypes in injecting drug users on methadone maintenance treatment in China associated with economic and health reform. J Viral Hepat 2017; 24:551-560. [PMID: 28092412 DOI: 10.1111/jvh.12677] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/19/2016] [Indexed: 12/16/2022]
Abstract
The extensive genetic heterogeneity of hepatitis C virus (HCV) requires in-depth understanding of the population dynamics of different viral subtypes for more effective control of epidemic outbreaks. We analysed HCV sequences data from 125 participants in Wuhan, China. These participants were newly infected by subtype 1b (n=13), 3a (n=15), 3b (n=50) and 6a (n=39) while on methadone maintenance treatment (MMT). Bayesian phylogenies and demographic histories were inferred for these subtypes. Participants infected with HCV-1b and 3a were clustered in well-supported monophyletic clades, indicating local subepidemics. Subtypes 3b and 6a strains were intermixed with other Chinese isolates, as well as isolates from other Asian countries, reflecting ongoing across geographic boundary transmissions. Subtypes 1b and 3a declined continuously during the past ten years, consistent with the health and economic reform in China, while subtype 3b showed ongoing exponential growth and 6a was characterized by several epidemic waves, possibly related to the recently growing number of travellers between China and other Asian countries. In conclusion, results of this study suggest that HCV subtype 3b and 6a subepidemics in China are currently not under control, and new epidemic waves may emerge given the rapid increase in international travelling following substantial economic growth.
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Affiliation(s)
- S Zhou
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.,Wuhan Centers for Disease Prevention and Control, Wuhan, China
| | - E Cella
- Department of Infectious Parasitic and Immunomediated Diseases, Reference Centre on Phylogeny, Molecular Epidemiology and Microbial Evolution (FEMEM)/Epidemiology Unit, Istituto Superiore di Sanità, Rome, Italy.,Public Health and Infectious Diseases, Sapienza University, Rome, Italy.,Department of Pathology, Immunology, and Laboratory Sciences, College of Medicine, University of Florida, Gainesville, FL, USA
| | - W Zhou
- Wuhan Centers for Disease Prevention and Control, Wuhan, China
| | - W-H Kong
- Wuhan Centers for Disease Prevention and Control, Wuhan, China
| | - M-Q Liu
- Wuhan Centers for Disease Prevention and Control, Wuhan, China
| | - P-L Liu
- Wuhan Centers for Disease Prevention and Control, Wuhan, China
| | - M Ciccozzi
- Department of Infectious Parasitic and Immunomediated Diseases, Reference Centre on Phylogeny, Molecular Epidemiology and Microbial Evolution (FEMEM)/Epidemiology Unit, Istituto Superiore di Sanità, Rome, Italy.,University Hospital Campus Bio-Medico, Rome, Italy
| | - M Salemi
- Department of Pathology, Immunology, and Laboratory Sciences, College of Medicine, University of Florida, Gainesville, FL, USA.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - X Chen
- Wuhan Centers for Disease Prevention and Control, Wuhan, China.,Department of Epidemiology, College of Public Health and Health Profession & College of Medicine, University of Florida, Gainesville, FL, USA
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9
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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
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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.
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10
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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.
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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
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11
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Li X, Zai J, Liu H, Feng Y, Li F, Wei J, Zou S, Yuan Z, Shao Y. The 2014 Ebola virus outbreak in West Africa highlights no evidence of rapid evolution or adaptation to humans. Sci Rep 2016; 6:35822. [PMID: 27767073 PMCID: PMC5073338 DOI: 10.1038/srep35822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/05/2016] [Indexed: 11/25/2022] Open
Abstract
Following its immergence in December 2013, the recent Zaire Ebola virus (EBOV) outbreak in West Africa has spread and persisted for more than two years, making it the largest EBOV epidemic in both scale and geographical region to date. In this study, a total of 726 glycoprotein (GP) gene sequences of the EBOV full-length genome obtained from West Africa from the 2014 outbreak, combined with 30 from earlier outbreaks between 1976 and 2008 were used to investigate the genetic divergence, evolutionary history, population dynamics, and selection pressure of EBOV among distinct epidemic waves. Results from our dataset showed that no non-synonymous substitutions occurred on the GP gene coding sequences of EBOV that were likely to have affected protein structure or function in any way. Furthermore, the significantly different dN/dS ratios observed between the 2014 West African outbreak and earlier outbreaks were more likely due to the confounding presence of segregating polymorphisms. Our results highlight no robust evidence that the 2014 EBOV outbreak is fast-evolving and adapting to humans. Therefore, the unprecedented nature of the 2014 EBOV outbreak might be more likely related to non-virological elements, such as environmental and sociological factors.
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Affiliation(s)
- Xingguang Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Junjie Zai
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, University of Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Haizhou Liu
- Centre for Emerging Infectious Diseases, State Key Laboratory of Virology, Wuhan Institute of Virology, University of Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Fan Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Jing Wei
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Sen Zou
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Zhiming Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, University of Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
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12
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Abstract
The recent Ebola epidemic provides a dramatic example of the devastation and fear generated by epidemics, particularly those caused by new emerging or reemerging diseases. A focus on the control and prevention of diseases in living populations dominates most epidemic disease research. However, research on epidemics in the past provides a temporal depth to our understanding of the context and consequences of diseases and is crucial for predicting how diseases might shape human biology and demography in the future. This article reviews recent research on historic epidemics of plague and tuberculosis, both of which have affected human populations for millennia. Research on these diseases demonstrates the range (and differential availability) of various lines of evidence (e.g., burial context, diagnostic skeletal lesions, molecular data) that inform about past disease in general. I highlight how research on past epidemics may be informative in ways that benefit living populations.
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Affiliation(s)
- Sharon N. DeWitte
- Department of Anthropology and Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208
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13
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Angeletti S, Lo Presti A, Giovanetti M, Grifoni A, Amicosante M, Ciotti M, Alcantara LCJ, Cella E, Ciccozzi M. Phylogenesys and homology modeling in Zika virus epidemic: food for thought. Pathog Glob Health 2016; 110:269-274. [PMID: 27670692 DOI: 10.1080/20477724.2016.1235337] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Zika virus (ZIKV) is an emerging Flavivirus that have recently caused an outbreak in Brazil and rapid spread in several countries. In this study, the consequences of ZIKV evolution on protein recognition by the host immune system have been analyzed. Evolutionary analysis was combined with homology modeling and T-B cells epitope predictions. Two separate clades, the African one with the Uganda sequence, as the most probable ancestor, and the second one containing all the most recent sequences from the equatorial belt were identified. Brazilian strains clustered all together and closely related to the French Polynesia isolates. A strong presence of a negatively selected site in the envelope gene (Env) protein was evidenced, suggesting a probable purging of deleterious polymorphisms in functionally important genes. Our results show relative conservancy of ZIKV sequences when envelope and other non-structural proteins (NS3 and NS5) are analyzed by homology modeling. However, some regions within the consensus sequence of NS5 protein and to a lesser extent in the envelope protein, show localized high mutation frequency corresponding to a considerable alteration in protein stability. In terms of viral immune escape, envelope protein is under a higher selective pressure than NS5 and NS3 proteins for HLA class I and II molecules. Moreover, envelope mutations that are not strictly related to T-cell immune responses are mostly located on the surface of the protein in putative B-cell epitopes, suggesting an important contribution of B cells in the immune response as well.
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Affiliation(s)
- Silvia Angeletti
- a Unit of Clinical Pathology and Microbiology , University Campus Bio-Medico , Rome , Italy
| | - Alessandra Lo Presti
- b Department of Infectious, Parasitic, and Immune-Mediated Diseases, Epidemiology Unit, Reference Centre on Phylogeny, Molecular Epidemiology, and Microbial Evolution (FEMEM) , National Institute of Health , Rome , Italy
| | - Marta Giovanetti
- c Oswaldo Cruz Foundation (FIOCRUZ) , Salvador , Brazil.,d Department of Biology , University of Rome 'Tor Vergata' , Rome , Italy
| | | | - Massimo Amicosante
- e ProxAgen Ltd , Sofia , Bulgaria.,f Department of Biomedicine and Prevention , University of Rome "Tor Vergata" , Rome , Italy
| | - Marco Ciotti
- g Laboratory of Molecular Virology , Polyclinic Tor Vergata Foundation , Rome , Italy
| | | | - Eleonora Cella
- b Department of Infectious, Parasitic, and Immune-Mediated Diseases, Epidemiology Unit, Reference Centre on Phylogeny, Molecular Epidemiology, and Microbial Evolution (FEMEM) , National Institute of Health , Rome , Italy.,h Department of Public Health and Infectious Diseases , Sapienza University of Rome , Rome , Italy
| | - Massimo Ciccozzi
- a Unit of Clinical Pathology and Microbiology , University Campus Bio-Medico , Rome , Italy.,b Department of Infectious, Parasitic, and Immune-Mediated Diseases, Epidemiology Unit, Reference Centre on Phylogeny, Molecular Epidemiology, and Microbial Evolution (FEMEM) , National Institute of Health , Rome , Italy
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14
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Affiliation(s)
- Angela L. Rasmussen
- Department of Microbiology, University of Washington, Seattle, Washington 98109;
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15
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Pontremoli C, Forni D, Cagliani R, Filippi G, De Gioia L, Pozzoli U, Clerici M, Sironi M. Positive Selection Drives Evolution at the Host-Filovirus Interaction Surface. Mol Biol Evol 2016; 33:2836-2847. [PMID: 27512112 DOI: 10.1093/molbev/msw158] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Filovirus infection is mediated by engagement of the surface-exposed glycoprotein (GP) by its cellular receptor, NPC1 (Niemann-Pick C1). Two loops in the C domain of NPC1 (NPC1-C) bind filovirus GP. Herein, we show that filovirus GP and NPC1-C evolve under mutual selective pressure. Analysis of a large mammalian phylogeny indicated that strong functional/structural constraints limit the NPC1 sequence space available for adaptive change and most sites at the contact interface with GP are under negative selection. These constraints notwithstanding, we detected positive selection at NPC1-C in all mammalian orders, from Primates to Xenarthra. Different codons evolved adaptively in distinct mammals, and most selected sites are located within the two NPC1-C loops that engage GP, or at their anchor points. In Homininae, NPC1-C was a preferential selection target, and the T419I variant possibly represents a human-specific adaptation to filovirus infection. On the other side of the arms-race, GP evolved adaptively during filovirus speciation. One of the selected sites (S142Q) establishes several atom-to-atom contacts with NPC1-C. Additional selected sites are located within epitopes recognized by neutralizing antibodies, including the 14G7 epitope, where sites selected during the recent EBOV epidemic also map. Finally, pairs of co-evolving sites in Marburgviruses and Ebolaviruses were found to involve antigenic determinants. These findings suggest that the host humoral immune response was a major selective pressure during filovirus speciation. The S142Q variant may contribute to determine Ebolavirus host range in the wild. If this were the case, EBOV/BDBV (S142) and SUDV (Q142) may not share the same reservoir(s).
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Affiliation(s)
- Chiara Pontremoli
- Scientific Institute IRCCS E.MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Diego Forni
- Scientific Institute IRCCS E.MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E.MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Giulia Filippi
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E.MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E.MEDEA, Bioinformatics, Bosisio Parini, Italy
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16
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Angeletti S, Lo Presti A, Cella E, Ciccozzi M. Molecular epidemiology and phylogeny of Nipah virus infection: A mini review. ASIAN PAC J TROP MED 2016; 9:630-4. [PMID: 27393089 PMCID: PMC7105010 DOI: 10.1016/j.apjtm.2016.05.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/16/2016] [Accepted: 05/23/2016] [Indexed: 12/22/2022] Open
Abstract
Nipah virus (NiV) is a member of the genus Henipavirus of the family Paramyxoviridae, characterized by high pathogenicity and endemic in South Asia. It is classified as a Biosafety Level-4 (BSL-4) agent. The case-fatality varies from 40% to 70% depending on the severity of the disease and on the availability of adequate healthcare facilities. At present no antiviral drugs are available for NiV disease and the treatment is just supportive. Phylogenetic and evolutionary analyses can be used to help in understanding the epidemiology and the temporal origin of this virus. This review provides an overview of evolutionary studies performed on Nipah viruses circulating in different countries. Thirty phylogenetic studies have been published from 2000 to 2015 years, searching on pub-med using the key words ‘Nipah virus AND phylogeny’ and twenty-eight molecular epidemiological studies from 2006 to 2015 have been performed, typing the key words ‘Nipah virus AND molecular epidemiology’. Overall data from the published study demonstrated as phylogenetic and evolutionary analysis represent promising tools to evidence NiV epidemics, to study their origin and evolution and finally to act with effective preventive measure.
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Affiliation(s)
- Silvia Angeletti
- Unit of Clinical Pathology and Microbiology, University Campus Bio-Medico of Rome, Italy
| | - Alessandra Lo Presti
- Department of Infectious Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Eleonora Cella
- Department of Infectious Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy; Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Massimo Ciccozzi
- Department of Infectious Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Rome, Italy.
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17
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Grifoni A, Lo Presti A, Giovanetti M, Montesano C, Amicosante M, Colizzi V, Lai A, Zehender G, Cella E, Angeletti S, Ciccozzi M. Genetic diversity in Ebola virus: Phylogenetic and in silico structural studies of Ebola viral proteins. ASIAN PAC J TROP MED 2016; 9:337-343. [PMID: 27086151 DOI: 10.1016/j.apjtm.2016.03.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/20/2016] [Accepted: 03/01/2016] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVE To explore the genetic diversity and the modification of antibody response in the recent outbreak of Ebola Virus. METHODS Sequences retrieved from public databases, the selective pressure analysis and the homology modeling based on the all protein (nucleoprotein, VP35, VP40, soluble glycoprotein, small soluble glycoprotein, VP30, VP24 and polymerase) were used. RESULTS Structural proteins VP24, VP30, VP35 and VP40 showed relative conserved sequences making them suitable target candidates for antiviral treatment. On the contrary, nucleoprotein, polymerase and soluble glycoprotein have high mutation frequency. CONCLUSIONS Data from this study point out important aspects of Ebola virus sequence variability that for epitope and vaccine design should be considered for appropriate targeting of conserved protein regions.
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Affiliation(s)
| | - Alessandra Lo Presti
- Department of Infectious Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy
| | - Marta Giovanetti
- Department of Infectious Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy; Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Carla Montesano
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Massimo Amicosante
- ProxAgen Ltd, Sofia, Bulgaria; Department of Biomedicine and Prevention, University of Rome 'Tor Vergata', Rome, Italy
| | - Vittorio Colizzi
- Department of Biology, University of Rome 'Tor Vergata', Rome, Italy
| | - Alessia Lai
- Laboratory of Infectious Diseases and Tropical Medicine, University of Milan, Italy
| | | | - Eleonora Cella
- Department of Infectious Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy; Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Silvia Angeletti
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Rome, Italy
| | - Massimo Ciccozzi
- Department of Infectious Parasitic and Immunomediated Diseases, National Institute of Health, Rome, Italy; University Campus Bio-Medico, Rome, Italy.
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18
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Canuti M, O’Leary KE, Hunter BD, Spearman G, Ojkic D, Whitney HG, Lang AS. Driving forces behind the evolution of the Aleutian mink disease parvovirus in the context of intensive farming. Virus Evol 2016; 2:vew004. [PMID: 27774297 PMCID: PMC4989880 DOI: 10.1093/ve/vew004] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Aleutian mink disease virus (AMDV) causes plasmacytosis, an immune complex-associated syndrome that affects wild and farmed mink. The virus can also infect other small mammals (e.g., ferrets, skunks, ermines, and raccoons), but the disease in these hosts has been studied less. In 2007, a mink plasmacytosis outbreak began on the Island of Newfoundland, and the virus has been endemic in farms since then. In this study, we evaluated the molecular epidemiology of AMDV in farmed and wild animals of Newfoundland since before the beginning of the outbreak and investigated the epidemic in a global context by studying AMDV worldwide, thereby examining its diffusion and phylogeography. Furthermore, AMDV evolution was examined in the context of intensive farming, where host population dynamics strongly influence viral evolution. Partial NS1 sequences and several complete genomes were obtained from Newfoundland viruses and analyzed along with numerous sequences from other locations worldwide that were either obtained as part of this study or from public databases. We observed very high viral diversity within Newfoundland and within single farms, where high rates of co-infection, recombinant viruses and polymorphisms were observed within single infected individuals. Worldwide, we documented a partial geographic distribution of strains, where viruses from different countries co-exist within clades but form country-specific subclades. Finally, we observed the occurrence of recombination and the predominance of negative selection pressure on AMDV proteins. A surprisingly low number of immunoepitopic sites were under diversifying pressure, possibly because AMDV gains no benefit by escaping the immune response as viral entry into target cells is mediated through interactions with antibodies, which therefore contribute to cell infection. In conclusion, the high prevalence of AMDV in farms facilitates the establishment of co-infections that can favor the occurrence of recombination and enhance viral diversity. Viruses are then exchanged between different farms and countries and can be introduced into the wild, with the rapidly evolving viruses producing many parallel lineages.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, Newfoundland and Labrador, A1B 3X9, Canada
| | - Kimberly E. O’Leary
- Animal Health Division, Forestry and Agrifoods Agency, P.O. Box 7400, St. John’s, Newfoundland and Labrador, A1E 3Y5, Canada
| | - Bruce D. Hunter
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Grant Spearman
- Department of Agriculture, Animal Health Laboratory, 65 River Rd., Truro, Nova Scotia, B2N 5E3, Canada and
| | - Davor Ojkic
- Animal Health Laboratory, 419 Gordon Street, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Hugh G. Whitney
- Animal Health Division, Forestry and Agrifoods Agency, P.O. Box 7400, St. John’s, Newfoundland and Labrador, A1E 3Y5, Canada
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, Newfoundland and Labrador, A1B 3X9, Canada
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19
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Local Mutational Pressures in Genomes of Zaire Ebolavirus and Marburg Virus. Adv Bioinformatics 2015; 2015:678587. [PMID: 26798338 PMCID: PMC4698526 DOI: 10.1155/2015/678587] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/30/2015] [Accepted: 11/03/2015] [Indexed: 11/18/2022] Open
Abstract
Heterogeneities in nucleotide content distribution along the length of Zaire ebolavirus and Marburg virus genomes have been analyzed. Results showed that there is asymmetric mutational A-pressure in the majority of Zaire ebolavirus genes; there is mutational AC-pressure in the coding region of the matrix protein VP40, probably, caused by its high expression at the end of the infection process; there is also AC-pressure in the 3'-part of the nucleoprotein (NP) coding gene associated with low amount of secondary structure formed by the 3'-part of its mRNA; in the middle of the glycoprotein (GP) coding gene that kind of mutational bias is linked with the high amount of secondary structure formed by the corresponding fragment of RNA negative (-) strand; there is relatively symmetric mutational AU-pressure in the polymerase (Pol) coding gene caused by its low expression level. In Marburg virus all genes, including C-rich fragment of GP coding region, demonstrate asymmetric mutational A-bias, while the last gene (Pol) demonstrates more symmetric mutational AU-pressure. The hypothesis of a newly synthesized RNA negative (-) strand shielding by complementary fragments of mRNAs has been described in this work: shielded fragments of RNA negative (-) strand should be better protected from oxidative damage and prone to ADAR-editing.
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20
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Abstract
The past year has marked the most devastating Ebola outbreak the world has ever witnessed, with over 28,000 cases and over 11,000 deaths. Ebola virus (EBOV) has now been around for almost 50 years. In this review, we discuss past and present outbreaks of EBOV and how those variants evolved over time. We explore and discuss selective pressures that drive the evolution of different Ebola variants, and how they may modify the efficacy of therapeutic treatments and vaccines currently being developed. Finally, given the unprecedented size and spread of the outbreak, as well as the extended period of replication in human hosts, specific attention is given to the 2014-2015 West African outbreak variant (Makona).
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Affiliation(s)
- Marc-Antoine de La Vega
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Derek Stein
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Gary P Kobinger
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
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21
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Cheng Y, Prickett MD, Gutowska W, Kuo R, Belov K, Burt DW. Evolution of the avian β-defensin and cathelicidin genes. BMC Evol Biol 2015; 15:188. [PMID: 26373713 PMCID: PMC4571063 DOI: 10.1186/s12862-015-0465-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/21/2015] [Indexed: 11/10/2022] Open
Abstract
Background β-defensins and cathelicidins are two families of cationic antimicrobial peptides (AMPs) with a broad range of antimicrobial activities that are key components of the innate immune system. Due to their important roles in host defense against rapidly evolving pathogens, the two gene families provide an ideal system for studying adaptive gene evolution. In this study we performed phylogenetic and selection analyses on β-defensins and cathelicidins from 53 avian species representing 32 orders to examine the evolutionary dynamics of these peptides in birds. Results and conclusions Avian β-defensins are found in a gene cluster consisting of 13 subfamiles. Nine of these are conserved as one to one orthologs in all birds, while the others (AvBD1, AvBD3, AvBD7 and AvBD14) are more subject to gene duplication or pseudogenisation events in specific avian lineages. Avian cathelicidins are found in a gene cluster consisting of three subfamilies with species-specific duplications and gene loss. Evidence suggested that the propiece and mature peptide domains of avian cathelicidins are possibly co-evolving in such a way that the cationicity of the mature peptide is partially neutralised by the negative charge of the propiece prior to peptide secretion (further evidence obtained by repeating the analyses on primate cathelicidins). Negative selection (overall mean dN < dS) was detected in most of the gene domains examined, conserving certain amino acid residues that may be functionally crucial for the avian β-defensins and cathelicidins, while episodic positive selection was also involved in driving the diversification of specific codon sites of certain AMPs in avian evolutionary history. These findings have greatly improved our understanding of the molecular evolution of avian AMPs and will be useful to understand their role in the avian innate immune response. Additionally, the large dataset of β-defensin and cathelicidin peptides may also provide a valuable resource for translational research and development of novel antimicrobial agents in the future. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0465-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuanyuan Cheng
- RMC Gunn Building B19, Faculty of Veterinary Science, University of Sydney, Camperdown, 2006, NSW, Australia.
| | - Michael Dennis Prickett
- Dipartimento di Scienze della Vita-Edif. C11, Università di Trieste, Via Licio Giorgieri 1, 34127, Trieste, Italy.
| | - Weronika Gutowska
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Richard Kuo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Katherine Belov
- RMC Gunn Building B19, Faculty of Veterinary Science, University of Sydney, Camperdown, 2006, NSW, Australia.
| | - David W Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
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22
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DeWitte SN. Setting the stage for medieval plague: Pre-black death trends in survival and mortality. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 158:441-51. [DOI: 10.1002/ajpa.22806] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/15/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Sharon N. DeWitte
- Department of Anthropology; University of South Carolina; Columbia SC 29208
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