1
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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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2
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Garg A, Dabburu GR, Singhal N, Kumar M. Investigating the disordered regions (MoRFs, SLiMs and LCRs) and functions of mimicry proteins/peptides in silico. PLoS One 2022; 17:e0265657. [PMID: 35421114 PMCID: PMC9009644 DOI: 10.1371/journal.pone.0265657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/04/2022] [Indexed: 11/24/2022] Open
Abstract
Microbial mimicry of the host proteins/peptides can elicit host auto-reactive T- or B-cells resulting in autoimmune disease(s). Since intrinsically disordered protein regions (IDPRs) are involved in several host cell signaling and PPI networks, molecular mimicry of the IDPRs can help the pathogens in substituting their own proteins in the host cell-signaling and PPI networks and, ultimately hijacking the host cellular machinery. Thus, the present study was conducted to discern the structural disorder and intrinsically disordered protein regions (IDPRs) like, molecular recognition features (MoRFs), short linear motifs (SLiMs), and low complexity regions (LCRs) in the experimentally verified mimicry proteins and peptides (mimitopes) of bacteria, viruses and host. Also, functional characteristics of the mimicry proteins were studied in silico. Our results indicated that 78% of the bacterial host mimicry proteins and 45% of the bacterial host mimitopes were moderately/highly disordered while, 73% of the viral host mimicry proteins and 31% of the viral host mimitopes were moderately/highly disordered. Among the pathogens, 27% of the bacterial mimicry proteins and 13% of the bacterial mimitopes were moderately/highly disordered while, 53% of the viral mimicry proteins and 21% of the viral mimitopes were moderately/highly disordered. Though IDPR were frequent in host, bacterial and viral mimicry proteins, only a few mimitopes overlapped with the IDPRs like, MoRFs, SLiMs and LCRs. This suggests that most of the microbes cannot use molecular mimicry to modulate the host PPIs and hijack the host cell machinery. Functional analyses indicated that most of the pathogens exhibited mimicry with the host proteins involved in ion binding and signaling pathways. This is the first report on the disordered regions and functional aspects of experimentally proven host and microbial mimicry proteins.
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Affiliation(s)
- Anjali Garg
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Govinda Rao Dabburu
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Neelja Singhal
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
- * E-mail: (MK); (NS)
| | - Manish Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
- * E-mail: (MK); (NS)
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3
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Villa TG, Abril AG, Sánchez S, de Miguel T, Sánchez-Pérez A. Animal and human RNA viruses: genetic variability and ability to overcome vaccines. Arch Microbiol 2021; 203:443-464. [PMID: 32989475 PMCID: PMC7521576 DOI: 10.1007/s00203-020-02040-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/29/2020] [Accepted: 09/12/2020] [Indexed: 02/06/2023]
Abstract
RNA viruses, in general, exhibit high mutation rates; this is mainly due to the low fidelity displayed by the RNA-dependent polymerases required for their replication that lack the proofreading machinery to correct misincorporated nucleotides and produce high mutation rates. This lack of replication fidelity, together with the fact that RNA viruses can undergo spontaneous mutations, results in genetic variants displaying different viral morphogenesis, as well as variation on their surface glycoproteins that affect viral antigenicity. This diverse viral population, routinely containing a variety of mutants, is known as a viral 'quasispecies'. The mutability of their virions allows for fast evolution of RNA viruses that develop antiviral resistance and overcome vaccines much more rapidly than DNA viruses. This also translates into the fact that pathogenic RNA viruses, that cause many diseases and deaths in humans, represent the major viral group involved in zoonotic disease transmission, and are responsible for worldwide pandemics.
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Affiliation(s)
- T G Villa
- Department of Microbiology, Faculty of Pharmacy, University of Santiago de Compostela, 5706, Santiago de Compostela, Spain.
| | - Ana G Abril
- Department of Microbiology, Faculty of Pharmacy, University of Santiago de Compostela, 5706, Santiago de Compostela, Spain
| | - S Sánchez
- Department of Microbiology, Faculty of Pharmacy, University of Santiago de Compostela, 5706, Santiago de Compostela, Spain
| | - T de Miguel
- Department of Microbiology, Faculty of Pharmacy, University of Santiago de Compostela, 5706, Santiago de Compostela, Spain
| | - A Sánchez-Pérez
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, 2006, Australia
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4
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Powlson J, Wright D, Zeltina A, Giza M, Nielsen M, Rampling T, Venkatrakaman N, Bowden TA, Hill AVS, Ewer KJ. Characterization of Antigenic MHC-Class-I-Restricted T Cell Epitopes in the Glycoprotein of Ebolavirus. Cell Rep 2020; 29:2537-2545.e3. [PMID: 31775024 PMCID: PMC6899439 DOI: 10.1016/j.celrep.2019.10.105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/20/2019] [Accepted: 10/25/2019] [Indexed: 11/05/2022] Open
Abstract
Ebolavirus causes highly lethal hemorrhagic fever in humans. The envelope-displayed viral glycoprotein (GP) is the primary target of humoral immunity induced by natural exposure and vaccination. No T cell epitopes in the GP have been characterized in humans. A phase I clinical trial of a heterologous prime-boost vaccination regime with viral vectors encoding filovirus antigens elicits humoral and T cell responses in vaccinees. The most frequently recognized peptide pools are deconvoluted to identify the minimal epitopes recognized by antigen-specific T cells. We characterize nine immunogenic epitopes on the Ebolavirus GP. Histocompatibility leukocyte antigen (HLA) typing with in silico epitope analysis determines the likely MHC class I restriction elements. Thirteen HLA-A and -B alleles are predicted to present the identified CD8+ T cell epitopes, suggesting promiscuous recognition and a broad immune response. Delivery of the Ebolavirus GP antigen by using a heterologous prime-boost approach is immunogenic in genetically diverse human populations, with responses against multiple epitopes. Vaccination induces high T cell responses to the Ebola virus glycoprotein in humans Eight CD8+ epitopes were defined, recognized through multiple MHC class I alleles Responses match those observed in Ebola survivors and could boost vaccine efficacy
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Affiliation(s)
- Jonathan Powlson
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Daniel Wright
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Antra Zeltina
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Mark Giza
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Morten Nielsen
- Department of Health Technology, The Technical University of Denmark, Anker Engelunds Vej 1 Bygning 101A, 2800 Kgs Lyngby, Denmark
| | - Tommy Rampling
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Navin Venkatrakaman
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Adrian V S Hill
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK
| | - Katie J Ewer
- The Jenner Institute, Old Road Campus Research Building, University of Oxford, Oxford OX3 7DQ, UK.
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5
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Rodríguez-Ruiz HA, Garibay-Cerdenares OL, Illades-Aguiar B, Montaño S, Jiang X, Leyva-Vázquez MA. In silico prediction of structural changes in human papillomavirus type 16 (HPV16) E6 oncoprotein and its variants. BMC Mol Cell Biol 2019; 20:35. [PMID: 31426742 PMCID: PMC6700771 DOI: 10.1186/s12860-019-0217-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/08/2019] [Indexed: 12/11/2022] Open
Abstract
Background HPV16 infection is one of the main risk factors involved in the development of cervical cancer, mainly due to the high oncogenic potential of the viral proteins E6 and E7, which are involved in the different processes of malignant transformation. There is a broad spectrum of intratypical variation of E6, which is reflected in its high diversity, biological behavior, global distribution and risk of causing cervical cancer. Experimental studies have shown that the intratypical variants of the protein E6 from the European variants (E-G350, E-A176/G350, E-C188/G350) and Asian-American variants (AAa and AAc), are capable of inducing the differential expression of genes involved in the development of cervical cancer. Results An in silico analysis was performed to characterize the molecular effects of these variations using the structure of the HPV16 E6 oncoprotein (PDB: 4XR8; chain H) as a template. In particular, we evaluated the 3D structures of the intratypical variants by structural alignment, ERRAT, Ramachandran plots and prediction of protein disorder, which was further validated by molecular dynamics simulations. Our results, in general, showed no significant changes in the protein 3D structure. However, we observed subtle changes in protein physicochemical features and structural disorder in the N- and C-termini. Conclusions Our results showed that mutations in the viral oncogene E6 of six high-risk HPV16 variants are effectively neutral and do not cause significant structural changes except slight variations of structural disorder. As structural disorder is involved in rewiring protein-protein interactions, these results suggest a differential pattern of interaction of E6 with the target protein P53 and possibly different patterns of tumor aggressiveness associated with certain types of variants of the E6 oncoprotein. Electronic supplementary material The online version of this article (10.1186/s12860-019-0217-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hugo Alberto Rodríguez-Ruiz
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo, Mexico
| | - Olga Lilia Garibay-Cerdenares
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo, Mexico.,CONACyT-Autonomous University of Guerrero, Chilpancingo, Mexico
| | - Berenice Illades-Aguiar
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo, Mexico
| | - Sarita Montaño
- Faculty of Chemical and Biological Sciences, Autonomous University of Sinaloa, Culiacan, Mexico
| | - Xiaowei Jiang
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China. .,Guangzhou-Birmingham Joint Research Center for Birth Cohorts and Disease Cohorts, Guangzhou Medical University, Guangzhou, China. .,Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
| | - Marco Antonio Leyva-Vázquez
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo, Mexico.
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6
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Vaughan K, Xu X, Peters B, Sette A. Investigation of Outbreak-Specific Nonsynonymous Mutations on Ebolavirus GP in the Context of Known Immune Reactivity. J Immunol Res 2018; 2018:1846207. [PMID: 30581874 PMCID: PMC6276448 DOI: 10.1155/2018/1846207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/01/2018] [Accepted: 10/22/2018] [Indexed: 11/17/2022] Open
Abstract
The global response to the most recent EBOV outbreak has led to increased generation and availability of data, which can be globally analyzed to increase our understanding of immune responses to EBOV. We analyzed the published antibody epitope data to identify regions immunogenic for humans on the main GP antigenic target and determine sequence variance/nonsynonymous mutations between historical isolates and variants from the 2013-2016 outbreak. Approximately half of the GP sequence has been reported as targeted by antibody responses. Our results show an enrichment of nonsynonymous mutations (NSMs) within epitopic regions on GP (70%, p = 0.0133). Mapping NSMs to human epitope reactivity may be useful for future therapeutic and prophylaxis development as well as for our general understanding of immunity against EBOV.
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Affiliation(s)
- Kerrie Vaughan
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Xiaojun Xu
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
- University of California San Diego, Department of Medicine, La Jolla, CA 92093, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
- University of California San Diego, Department of Medicine, La Jolla, CA 92093, USA
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7
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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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8
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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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9
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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.
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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.
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10
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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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11
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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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12
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Stenger DC, Krugner R, Nouri S, Ferriol I, Falk BW, Sisterson MS. Sequence polymorphism in an insect RNA virus field population: A snapshot from a single point in space and time reveals stochastic differences among and within individual hosts. Virology 2016; 498:209-217. [PMID: 27598532 DOI: 10.1016/j.virol.2016.08.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 08/26/2016] [Accepted: 08/27/2016] [Indexed: 02/02/2023]
Abstract
Population structure of Homalodisca coagulata Virus-1 (HoCV-1) among and within field-collected insects sampled from a single point in space and time was examined. Polymorphism in complete consensus sequences among single-insect isolates was dominated by synonymous substitutions. The mutant spectrum of the C2 helicase region within each single-insect isolate was unique and dominated by nonsynonymous singletons. Bootstrapping was used to correct the within-isolate nonsynonymous:synonymous arithmetic ratio (N:S) for RT-PCR error, yielding an N:S value ~one log-unit greater than that of consensus sequences. Probability of all possible single-base substitutions for the C2 region predicted N:S values within 95% confidence limits of the corrected within-isolate N:S when the only constraint imposed was viral polymerase error bias for transitions over transversions. These results indicate that bottlenecks coupled with strong negative/purifying selection drive consensus sequences toward neutral sequence space, and that most polymorphism within single-insect isolates is composed of newly-minted mutations sampled prior to selection.
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Affiliation(s)
- Drake C Stenger
- USDA, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Ave., Parlier, CA 93648-9757, USA.
| | - Rodrigo Krugner
- USDA, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Ave., Parlier, CA 93648-9757, USA
| | - Shahideh Nouri
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Inmaculada Ferriol
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Bryce W Falk
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Mark S Sisterson
- USDA, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Ave., Parlier, CA 93648-9757, USA
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13
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May M, Relich RF. A Comprehensive Systems Biology Approach to Studying Zika Virus. PLoS One 2016; 11:e0161355. [PMID: 27584813 PMCID: PMC5008700 DOI: 10.1371/journal.pone.0161355] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 08/03/2016] [Indexed: 01/08/2023] Open
Abstract
Zika virus (ZIKV) is responsible for an ongoing and intensifying epidemic in the Western Hemisphere. We examined the complete predicted proteomes, glycomes, and selectomes of 33 ZIKV strains representing temporally diverse members of the African lineage, the Asian lineage, and the current outbreak in the Americas. Derivation of the complete selectome is an 'omics' approach to identify distinct evolutionary pressures acting on different features of an organism. Employment of the M8 model did not show evidence of global diversifying selection acting on the ZIKV polyprotein; however, a mixed effect model of evolution showed strong evidence (P<0.05) for episodic diversifying selection acting on specific sites. Single nucleotide polymorphisms (SNPs) were predictably frequent across strains relative to the derived consensus sequence. None of the 9 published detection procedures utilize targets that share 100% identity across the 33 strains examined, indicating that ZIKV escape from molecular detection is predictable. The predicted O-linked glycome showed marked diversity across strains; however, the N-linked glycome was highly stable. All Asian and American strains examined were predicted to include glycosylation of E protein ASN154, a modification proposed to mediate neurotropism, whereas the modification was not predicted for African strains. SNP diversity, episodic diversifying selection, and differential glycosylation, particularly of ASN154, may have major biological implications for ZIKV disease. Taken together, the systems biology perspective of ZIKV indicates: a.) The recently emergent Asian/American N-glycotype is mediating the new and emerging neuropathogenic potential of ZIKV; and b.) further divergence at specific sites is predictable as endemnicity is established in the Americas.
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Affiliation(s)
- Meghan May
- Department of Biomedical Sciences, University of New England College of Osteopathic Medicine, Biddeford, Maine, United States of America
- Seacoast Biomedical Science Institute, York, Maine, United States of America
| | - Ryan F. Relich
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
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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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Brown CJ, Quates CJ, Mirabzadeh CA, Miller CR, Wichman HA, Miura TA, Ytreberg FM. New Perspectives on Ebola Virus Evolution. PLoS One 2016; 11:e0160410. [PMID: 27479005 PMCID: PMC4968807 DOI: 10.1371/journal.pone.0160410] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/19/2016] [Indexed: 12/01/2022] Open
Abstract
Since the recent devastating outbreak of Ebola virus disease in western Africa, there has been significant effort to understand the evolution of the deadly virus that caused the outbreak. There has been a considerable investment in sequencing Ebola virus (EBOV) isolates, and the results paint an important picture of how the virus has spread in western Africa. EBOV evolution cannot be understood outside the context of previous outbreaks, however. We have focused this study on the evolution of the EBOV glycoprotein gene (GP) because one of its products, the spike glycoprotein (GP1,2), is central to the host immune response and because it contains a large amount of the phylogenetic signal for this virus. We inferred the maximum likelihood phylogeny of 96 nonredundant GP gene sequences representing each of the outbreaks since 1976 up to the end of 2014. We tested for positive selection and considered the placement of adaptive amino acid substitutions along the phylogeny and within the protein structure of GP1,2. We conclude that: 1) the common practice of rooting the phylogeny of EBOV between the first known outbreak in 1976 and the next outbreak in 1995 provides a misleading view of EBOV evolution that ignores the fact that there is a non-human EBOV host between outbreaks; 2) the N-terminus of GP1 may be constrained from evolving in response to the host immune system by the highly expressed, secreted glycoprotein, which is encoded by the same region of the GP gene; 3) although the mucin-like domain of GP1 is essential for EBOV in vivo, it evolves rapidly without losing its twin functions: providing O-linked glycosylation sites and a flexible surface.
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Affiliation(s)
- Celeste J Brown
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America.,Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America.,Center for Modeling Complex Interactions, University of Idaho, Moscow, Idaho, United States of America
| | - Caleb J Quates
- Center for Modeling Complex Interactions, University of Idaho, Moscow, Idaho, United States of America.,Department of Physics, University of Idaho, Moscow, Idaho, United States of America
| | - Christopher A Mirabzadeh
- Center for Modeling Complex Interactions, University of Idaho, Moscow, Idaho, United States of America.,Department of Physics, University of Idaho, Moscow, Idaho, United States of America
| | - Craig R Miller
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America.,Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America.,Center for Modeling Complex Interactions, University of Idaho, Moscow, Idaho, United States of America
| | - Holly A Wichman
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America.,Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America.,Center for Modeling Complex Interactions, University of Idaho, Moscow, Idaho, United States of America
| | - Tanya A Miura
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America.,Center for Modeling Complex Interactions, University of Idaho, Moscow, Idaho, United States of America
| | - F Marty Ytreberg
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America.,Center for Modeling Complex Interactions, University of Idaho, Moscow, Idaho, United States of America.,Department of Physics, University of Idaho, Moscow, Idaho, United States of America
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16
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Vetter P, Dayer JA, Schibler M, Allegranzi B, Brown D, Calmy A, Christie D, Eremin S, Hagon O, Henderson D, Iten A, Kelley E, Marais F, Ndoye B, Pugin J, Robert-Nicoud H, Sterk E, Tapper M, Siegrist CA, Kaiser L, Pittet D. The 2014–2015 Ebola outbreak in West Africa: Hands On. Antimicrob Resist Infect Control 2016. [PMCID: PMC4858848 DOI: 10.1186/s13756-016-0112-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The International Consortium for Prevention and Infection Control (ICPIC) organises a biannual conference (ICPIC) on various subjects related to infection prevention, treatment and control. During ICPIC 2015, held in Geneva in June 2015, a full one-day session focused on the 2014–2015 Ebola virus disease (EVD) outbreak in West Africa. This article is a non-exhaustive compilation of these discussions. It concentrates on lessons learned and imagining a way forward for the communities most affected by the epidemic. The reader can access video recordings of all lectures delivered during this one-day session, as referenced. Topics include the timeline of the international response, linkages between the dynamics of the epidemic and infection prevention and control, the importance of community engagement, and updates on virology, diagnosis, treatment and vaccination issues. The paper also includes discussions from public health, infectious diseases, critical care and infection control experts who cared for patients with EVD in Africa, in Europe, and in the United Sates and were involved in Ebola preparedness in both high- and low-resource settings and countries. This review concludes that too little is known about the pathogenesis and treatment of EVD, therefore basic and applied research in this area are urgently required. Furthermore, it is clear that epidemic preparedness needs to improve globally, in particular through the strengthening of health systems at local and national levels. There is a strong need for culturally sensitive approaches to public health which could be designed and delivered by social scientists and medical professionals working together. As of December 2015, this epidemic killed more than 11,000 people and infected more than 28,000; it has also generated more than 17,000 survivors and orphans, many of whom face somatic and psychological complications. The continued treatment and rehabilitation of these people is a public health priority, which also requires an integration of specific medical and social science approaches, not always available in West Africa.
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17
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Burger VM, Nolasco DO, Stultz CM. Expanding the Range of Protein Function at the Far End of the Order-Structure Continuum. J Biol Chem 2016; 291:6706-13. [PMID: 26851282 PMCID: PMC4807258 DOI: 10.1074/jbc.r115.692590] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The traditional view of the structure-function paradigm is that a protein's function is inextricably linked to a well defined, three-dimensional structure, which is determined by the protein's primary amino acid sequence. However, it is now accepted that a number of proteins do not adopt a unique tertiary structure in solution and that some degree of disorder is required for many proteins to perform their prescribed functions. In this review, we highlight how a number of protein functions are facilitated by intrinsic disorder and introduce a new protein structure taxonomy that is based on quantifiable metrics of a protein's disorder.
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Affiliation(s)
- Virginia M Burger
- From the Research Laboratory for Electronics, Department of Electrical Engineering & Computer Science, and
| | - Diego O Nolasco
- From the Research Laboratory for Electronics, Department of Electrical Engineering & Computer Science, and
| | - Collin M Stultz
- From the Research Laboratory for Electronics, Department of Electrical Engineering & Computer Science, and the Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02138
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18
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Miller CR, Johnson EL, Burke AZ, Martin KP, Miura TA, Wichman HA, Brown CJ, Ytreberg FM. Initiating a watch list for Ebola virus antibody escape mutations. PeerJ 2016; 4:e1674. [PMID: 26925318 PMCID: PMC4768679 DOI: 10.7717/peerj.1674] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 01/18/2016] [Indexed: 12/26/2022] Open
Abstract
The 2014 Ebola virus (EBOV) outbreak in West Africa is the largest in recorded history and resulted in over 11,000 deaths. It is essential that strategies for treatment and containment be developed to avoid future epidemics of this magnitude. With the development of vaccines and antibody-based therapies using the envelope glycoprotein (GP) of the 1976 Mayinga strain, one important strategy is to anticipate how the evolution of EBOV might compromise these efforts. In this study we have initiated a watch list of potential antibody escape mutations of EBOV by modeling interactions between GP and the antibody KZ52. The watch list was generated using molecular modeling to estimate stability changes due to mutation. Every possible mutation of GP was considered and the list was generated from those that are predicted to disrupt GP-KZ52 binding but not to disrupt the ability of GP to fold and to form trimers. The resulting watch list contains 34 mutations (one of which has already been seen in humans) at six sites in the GP2 subunit. Should mutations from the watch list appear and spread during an epidemic, it warrants attention as these mutations may reflect an evolutionary response from the virus that could reduce the effectiveness of interventions such as vaccination. However, this watch list is incomplete and emphasizes the need for more experimental structures of EBOV interacting with antibodies in order to expand the watch list to other epitopes. We hope that this work provokes experimental research on evolutionary escape in both Ebola and other viral pathogens.
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Affiliation(s)
- Craig R Miller
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States; Department of Mathematics, University of Idaho, Moscow, ID, United States; Center for Modeling Complex Interactions, University of Idaho, Moscow, ID, United States; Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - Erin L Johnson
- Center for Modeling Complex Interactions, University of Idaho , Moscow, ID , United States
| | - Aran Z Burke
- Center for Modeling Complex Interactions, University of Idaho, Moscow, ID, United States; Department of Physics, University of Idaho, Moscow, ID, United States
| | - Kyle P Martin
- Center for Modeling Complex Interactions, University of Idaho, Moscow, ID, United States; Department of Physics, University of Idaho, Moscow, ID, United States
| | - Tanya A Miura
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States; Center for Modeling Complex Interactions, University of Idaho, Moscow, ID, United States
| | - Holly A Wichman
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States; Center for Modeling Complex Interactions, University of Idaho, Moscow, ID, United States; Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - Celeste J Brown
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States; Center for Modeling Complex Interactions, University of Idaho, Moscow, ID, United States; Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - F Marty Ytreberg
- Center for Modeling Complex Interactions, University of Idaho, Moscow, ID, United States; Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States; Department of Physics, University of Idaho, Moscow, ID, United States
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19
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Brainard J, Hooper L, Pond K, Edmunds K, Hunter PR. Risk factors for transmission of Ebola or Marburg virus disease: a systematic review and meta-analysis. Int J Epidemiol 2016; 45:102-16. [PMID: 26589246 PMCID: PMC4795563 DOI: 10.1093/ije/dyv307] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2015] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The Ebola virus disease outbreak that started in Western Africa in 2013 was unprecedented because it spread within densely populated urban environments and affected many thousands of people. As a result, previous advice and guidelines need to be critically reviewed, especially with regard to transmission risks in different contexts. METHODS Scientific and grey literature were searched for articles about any African filovirus. Articles were screened for information about transmission (prevalence or odds ratios especially). Data were extracted from eligible articles and summarized narratively with partial meta-analysis. Study quality was also evaluated. RESULTS A total of 31 reports were selected from 6552 found in the initial search. Eight papers gave numerical odds for contracting filovirus illness; 23 further articles provided supporting anecdotal observations about how transmission probably occurred for individuals. Many forms of contact (conversation, sharing a meal, sharing a bed, direct or indirect touching) were unlikely to result in disease transmission during incubation or early illness. Among household contacts who reported directly touching a case, the attack rate was 32% [95% confidence interval (CI) 26-38%]. Risk of disease transmission between household members without direct contact was low (1%; 95% CI 0-5%). Caring for a case in the community, especially until death, and participation in traditional funeral rites were strongly associated with acquiring disease, probably due to a high degree of direct physical contact with case or cadaver. CONCLUSIONS Transmission of filovirus is unlikely except through close contact, especially during the most severe stages of acute illness. More data are needed about the context, intimacy and timing of contact required to raise the odds of disease transmission. Risk factors specific to urban settings may need to be determined.
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Affiliation(s)
- Julii Brainard
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Lee Hooper
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Katherine Pond
- Robens Centre for Public and Environmental Health, University of Surrey, Guildford, UK
| | - Kelly Edmunds
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Paul R Hunter
- Norwich Medical School, University of East Anglia, Norwich, UK
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20
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Petti S, Messano GA, Vingolo EM, Marsella LT, Scully C. The face of Ebola: changing frequency of haemorrhage in the West African compared with Eastern-Central African outbreaks. BMC Infect Dis 2015; 15:564. [PMID: 26653293 PMCID: PMC4676861 DOI: 10.1186/s12879-015-1302-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 12/01/2015] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The West-African (WA) Zaire Ebolavirus disease (EVD) outbreak was characterized by an exceptionally high number of cases and deaths as compared with the Eastern-Central African (ECA) outbreaks. Despite the Zaire Ebolavirus being the most lethal for humans, case-fatality rate, close to 80 % in ECA outbreaks, almost halved to 47 % in Guinea-Liberia-Sierra Leone (WA). Such an improvement was due to the remarkable implementation of international humanitarian aids. Some studies also suggested that the long human-to-human transmission cycle occurred in WA, gave rise to human adaptation and consequent immune escape. Haemorrhage, the main feature in seriously infected EVD patients, is due to the immune system that triggers the infected endothelial cells which expose the spike-like glycoprotein (GP) of the virion on their surface. If the human adaptation hypothesis holds true, the proportion of EVD patients with haemorrhage in the WA outbreak should be lower than in the ECA outbreaks due to immune escape. Therefore, the aim of this meta-analysis was to compare the relative frequencies of three typical haemorrhagic symptoms (conjunctival -CB, nasal -NB, gingival -GB- bleedings) in the ECA and WA outbreaks. METHODS Literature searches were performed through PubMed and Scopus using generic keywords; surveys including at least ten patients reporting CB, NB, GB relative frequencies were extracted and split into ECA and WA. The meta-analytical methods chosen were based on the levels of between-study heterogeneity and publication bias. Pooled CB, NB, GB relative frequencies in ECA and WA were estimated and compared. Subgroup analysis including only studies on Zaire Ebolavirus also was performed. RESULTS Fifteen studies (10 ECA, 5 WA) were located with 4,867 (CB), 3,859 (NB), 4,278 (GB) EVD patients overall. GB pooled relative frequency was 45.3 % (95 % confidence interval -95 CI, 34.7-56.1 %) and 18.0 % (95 CI, 6.0-34.5 %), in ECA and WA; NB was 10.6 % (95 CI, 5.7-16.8 %) and 1.3 % (1.0-1.8 %); GB was 24.2 % (95 CI, 11.9-39.2 %) and 1.9 % (95 CI, 1.4-2.4 %). Subgroup analysis confirmed these results. CONCLUSIONS During the WA outbreak the relative frequency of GB decreased by two thirds, while NB and GB almost disappeared, suggesting that the Zaire Ebolavirus human adaptation hypothesis is plausible.
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Affiliation(s)
- Stefano Petti
- Department of Public Health and Infectious Diseases, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Giuseppe Alessio Messano
- Department of Public Health and Infectious Diseases, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Enzo Maria Vingolo
- Ophthalmology Department, Sapienza University, Viale del Policlinico 155, 00186, Rome, Italy.
| | - Luigi Tonino Marsella
- Department of Biomedicine and Prevention, Tor Vergata University, Viale Oxford 81, 00133, Rome, Italy.
| | - Crispian Scully
- University College London, Gower Street WC1E 6BT, London, UK.
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21
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Ladner JT, Wiley MR, Mate S, Dudas G, Prieto K, Lovett S, Nagle ER, Beitzel B, Gilbert ML, Fakoli L, Diclaro JW, Schoepp RJ, Fair J, Kuhn JH, Hensley LE, Park DJ, Sabeti PC, Rambaut A, Sanchez-Lockhart M, Bolay FK, Kugelman JR, Palacios G. Evolution and Spread of Ebola Virus in Liberia, 2014-2015. Cell Host Microbe 2015; 18:659-69. [PMID: 26651942 PMCID: PMC4711363 DOI: 10.1016/j.chom.2015.11.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/11/2015] [Accepted: 11/19/2015] [Indexed: 10/22/2022]
Abstract
The 2013-present Western African Ebola virus disease (EVD) outbreak is the largest ever recorded with >28,000 reported cases. Ebola virus (EBOV) genome sequencing has played an important role throughout this outbreak; however, relatively few sequences have been determined from patients in Liberia, the second worst-affected country. Here, we report 140 EBOV genome sequences from the second wave of the Liberian outbreak and analyze them in combination with 782 previously published sequences from throughout the Western African outbreak. While multiple early introductions of EBOV to Liberia are evident, the majority of Liberian EVD cases are consistent with a single introduction, followed by spread and diversification within the country. Movement of the virus within Liberia was widespread, and reintroductions from Liberia served as an important source for the continuation of the already ongoing EVD outbreak in Guinea. Overall, little evidence was found for incremental adaptation of EBOV to the human host.
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Affiliation(s)
- Jason T Ladner
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD, 21702, USA.
| | - Michael R Wiley
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD, 21702, USA
| | - Suzanne Mate
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD, 21702, USA
| | - Gytis Dudas
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Karla Prieto
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD, 21702, USA
| | - Sean Lovett
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD, 21702, USA
| | - Elyse R Nagle
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD, 21702, USA
| | - Brett Beitzel
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD, 21702, USA
| | - Merle L Gilbert
- Molecular and Translational Sciences Division, US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD, 21702, USA
| | - Lawrence Fakoli
- Liberian Institute for Biomedical Research, Charlesville, Liberia
| | - Joseph W Diclaro
- Naval Medical Research Unit 3, 3A Imtidad Ramses Street, Cairo, Egypt 11517
| | - Randal J Schoepp
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD, 21702, USA
| | - Joseph Fair
- MRI Global, 1330 Piccard Avenue, Rockville, MD, 20850, USA; The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, NIH, B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Lisa E Hensley
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, NIH, B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Daniel J Park
- Broad Institute, 75 Ames St, Cambridge, MA, 02142, USA
| | - Pardis C Sabeti
- Broad Institute, 75 Ames St, Cambridge, MA, 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA, 02138, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; Centre for Immunology, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; Fogarty International Center, NIH, 31 Center Drive, Bethesda, MD, 20892, USA
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD, 21702, USA
| | - Fatorma K Bolay
- Liberian Institute for Biomedical Research, Charlesville, Liberia
| | - Jeffrey R Kugelman
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD, 21702, USA
| | - Gustavo Palacios
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD, 21702, USA.
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22
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de La Vega MA, Caleo G, Audet J, Qiu X, Kozak RA, Brooks JI, Kern S, Wolz A, Sprecher A, Greig J, Lokuge K, Kargbo DK, Kargbo B, Di Caro A, Grolla A, Kobasa D, Strong JE, Ippolito G, Van Herp M, Kobinger GP. Ebola viral load at diagnosis associates with patient outcome and outbreak evolution. J Clin Invest 2015; 125:4421-8. [PMID: 26551677 DOI: 10.1172/jci83162] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/28/2015] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Ebola virus (EBOV) causes periodic outbreaks of life-threatening EBOV disease in Africa. Historically, these outbreaks have been relatively small and geographically contained; however, the magnitude of the EBOV outbreak that began in 2014 in West Africa has been unprecedented. The aim of this study was to describe the viral kinetics of EBOV during this outbreak and identify factors that contribute to outbreak progression. METHODS From July to December 2014, one laboratory in Sierra Leone processed over 2,700 patient samples for EBOV detection by quantitative PCR (qPCR). Viremia was measured following patient admission. Age, sex, and approximate time of symptom onset were also recorded for each patient. The data was analyzed using various mathematical models to find trends of potential interest. RESULTS The analysis revealed a significant difference (P = 2.7 × 10(-77)) between the initial viremia of survivors (4.02 log10 genome equivalents [GEQ]/ml) and nonsurvivors (6.18 log10 GEQ/ml). At the population level, patient viral loads were higher on average in July than in November, even when accounting for outcome and time since onset of symptoms. This decrease in viral loads temporally correlated with an increase in circulating EBOV-specific IgG antibodies among individuals who were suspected of being infected but shown to be negative for the virus by PCR. CONCLUSIONS Our results indicate that initial viremia is associated with outcome of the individual and outbreak duration; therefore, care must be taken in planning clinical trials and interventions. Additional research in virus adaptation and the impacts of host factors on EBOV transmission and pathogenesis is needed.
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23
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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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24
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Latest Ebola data rule out rapid mutation. Nature 2015. [DOI: 10.1038/nature.2015.17554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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