51
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Dellicour S, Baele G, Dudas G, Faria NR, Pybus OG, Suchard MA, Rambaut A, Lemey P. Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak. Nat Commun 2018; 9:2222. [PMID: 29884821 PMCID: PMC5993714 DOI: 10.1038/s41467-018-03763-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/12/2018] [Indexed: 01/25/2023] Open
Abstract
Genetic analyses have provided important insights into Ebola virus spread during the recent West African outbreak, but their implications for specific intervention scenarios remain unclear. Here, we address this issue using a collection of phylodynamic approaches. We show that long-distance dispersal events were not crucial for epidemic expansion and that preventing viral lineage movement to any given administrative area would, in most cases, have had little impact. However, major urban areas were critical in attracting and disseminating the virus: preventing viral lineage movement to all three capitals simultaneously would have contained epidemic size to one-third. We also show that announcements of border closures were followed by a significant but transient effect on international virus dispersal. By quantifying the hypothetical impact of different intervention strategies, as well as the impact of barriers on dispersal frequency, our study illustrates how phylodynamic analyses can help to address specific epidemiological and outbreak control questions. During the last Ebola virus outbreak in West Africa, a large amount of viral genomic data was obtained. Here, Dellicour et al. use phylodynamic approaches to assess effect of intervention strategies such as border closures.
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Affiliation(s)
- Simon Dellicour
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Gytis Dudas
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, 98109, Seattle, WA, USA
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom
| | - Marc A Suchard
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA.,Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, 90095, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, 90095, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3FL, UK.,Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium
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52
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Pollett S, Melendrez MC, Maljkovic Berry I, Duchêne S, Salje H, Cummings DAT, Jarman RG. Understanding dengue virus evolution to support epidemic surveillance and counter-measure development. INFECTION GENETICS AND EVOLUTION 2018; 62:279-295. [PMID: 29704626 DOI: 10.1016/j.meegid.2018.04.032] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 11/30/2022]
Abstract
Dengue virus (DENV) causes a profound burden of morbidity and mortality, and its global burden is rising due to the co-circulation of four divergent DENV serotypes in the ecological context of globalization, travel, climate change, urbanization, and expansion of the geographic range of the Ae.aegypti and Ae.albopictus vectors. Understanding DENV evolution offers valuable opportunities to enhance surveillance and response to DENV epidemics via advances in RNA virus sequencing, bioinformatics, phylogenetic and other computational biology methods. Here we provide a scoping overview of the evolution and molecular epidemiology of DENV and the range of ways that evolutionary analyses can be applied as a public health tool against this arboviral pathogen.
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Affiliation(s)
- S Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Marie Bashir Institute, University of Sydney, NSW, Australia; Institute for Global Health Sciences, University of California at San Francisco, CA, USA.
| | - M C Melendrez
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - I Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - S Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Australia
| | - H Salje
- Institut Pasteur, Paris, France; Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - D A T Cummings
- Johns Hopkins School of Public Health, Baltimore, MD, USA; University of Florida, FL, USA
| | - R G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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53
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Andras JP, Fields PD, Ebert D. Spatial population genetic structure of a bacterial parasite in close coevolution with its host. Mol Ecol 2018; 27:1371-1384. [DOI: 10.1111/mec.14545] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Jason P. Andras
- Department of Biological Sciences; Clapp Laboratory; Mount Holyoke College; South Hadley MA USA
| | - Peter D. Fields
- Department of Environmental Sciences - Zoology; University of Basel; Basel Switzerland
| | - Dieter Ebert
- Department of Environmental Sciences - Zoology; University of Basel; Basel Switzerland
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54
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Brunker K, Lemey P, Marston DA, Fooks AR, Lugelo A, Ngeleja C, Hampson K, Biek R. Landscape attributes governing local transmission of an endemic zoonosis: Rabies virus in domestic dogs. Mol Ecol 2018; 27:773-788. [PMID: 29274171 PMCID: PMC5900915 DOI: 10.1111/mec.14470] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 12/24/2022]
Abstract
Landscape heterogeneity plays an important role in disease spread and persistence, but quantifying landscape influences and their scale dependence is challenging. Studies have focused on how environmental features or global transport networks influence pathogen invasion and spread, but their influence on local transmission dynamics that underpin the persistence of endemic diseases remains unexplored. Bayesian phylogeographic frameworks that incorporate spatial heterogeneities are promising tools for analysing linked epidemiological, environmental and genetic data. Here, we extend these methodological approaches to decipher the relative contribution and scale-dependent effects of landscape influences on the transmission of endemic rabies virus in Serengeti district, Tanzania (area ~4,900 km2 ). Utilizing detailed epidemiological data and 152 complete viral genomes collected between 2004 and 2013, we show that the localized presence of dogs but not their density is the most important determinant of diffusion, implying that culling will be ineffective for rabies control. Rivers and roads acted as barriers and facilitators to viral spread, respectively, and vaccination impeded diffusion despite variable annual coverage. Notably, we found that landscape effects were scale-dependent: rivers were barriers and roads facilitators on larger scales, whereas the distribution of dogs was important for rabies dispersal across multiple scales. This nuanced understanding of the spatial processes that underpin rabies transmission can be exploited for targeted control at the scale where it will have the greatest impact. Moreover, this research demonstrates how current phylogeographic frameworks can be adapted to improve our understanding of endemic disease dynamics at different spatial scales.
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Affiliation(s)
- Kirstyn Brunker
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- The Boyd Orr Centre for Population and Ecosystem HealthUniversity of GlasgowGlasgowUK
- Animal and Plant Health AgencyAddlestoneUK
| | - Philippe Lemey
- Department of Microbiology and ImmunologyKU Leuven – University of LeuvenLeuvenBelgium
| | | | | | - Ahmed Lugelo
- Department of Veterinary Medicine and Public HealthSokoine University of AgricultureMorogoroUnited Republic of Tanzania
| | - Chanasa Ngeleja
- Tanzania Veterinary Laboratory AgencyDar es SalaamUnited Republic of Tanzania
| | - Katie Hampson
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- The Boyd Orr Centre for Population and Ecosystem HealthUniversity of GlasgowGlasgowUK
| | - Roman Biek
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- The Boyd Orr Centre for Population and Ecosystem HealthUniversity of GlasgowGlasgowUK
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55
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Gill MS, Tung Ho LS, Baele G, Lemey P, Suchard MA. A Relaxed Directional Random Walk Model for Phylogenetic Trait Evolution. Syst Biol 2018; 66:299-319. [PMID: 27798403 DOI: 10.1093/sysbio/syw093] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 10/10/2016] [Indexed: 12/26/2022] Open
Abstract
Understanding the processes that give rise to quantitative measurements associated with molecular sequence data remains an important issue in statistical phylogenetics. Examples of such measurements include geographic coordinates in the context of phylogeography and phenotypic traits in the context of comparative studies. A popular approach is to model the evolution of continuously varying traits as a Brownian diffusion process acting on a phylogenetic tree. However, standard Brownian diffusion is quite restrictive and may not accurately characterize certain trait evolutionary processes. Here, we relax one of the major restrictions of standard Brownian diffusion by incorporating a nontrivial estimable mean into the process. We introduce a relaxed directional random walk (RDRW) model for the evolution of multivariate continuously varying traits along a phylogenetic tree. Notably, the RDRW model accommodates branch-specific variation of directional trends while preserving model identifiability. Furthermore, our development of a computationally efficient dynamic programming approach to compute the data likelihood enables scaling of our method to large data sets frequently encountered in phylogenetic comparative studies and viral evolution. We implement the RDRW model in a Bayesian inference framework to simultaneously reconstruct the evolutionary histories of molecular sequence data and associated multivariate continuous trait data, and provide tools to visualize evolutionary reconstructions. We demonstrate the performance of our model on synthetic data, and we illustrate its utility in two viral examples. First, we examine the spatiotemporal spread of HIV-1 in central Africa and show that the RDRW model uncovers a clearer, more detailed picture of the dynamics of viral dispersal than standard Brownian diffusion. Second, we study antigenic evolution in the context of HIV-1 resistance to three broadly neutralizing antibodies. Our analysis reveals evidence of a continuous drift at the HIV-1 population level towards enhanced resistance to neutralization by the VRC01 monoclonal antibody over the course of the epidemic. [Brownian Motion; Diffusion Processes; Phylodynamics; Phylogenetics; Phylogeography; Trait Evolution.].
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Affiliation(s)
- Mandev S Gill
- Department of Statistics, Columbia University, New York, NY 10027, USA
| | - Lam Si Tung Ho
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Minderbroedersstaat 10, 3000, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Minderbroedersstaat 10, 3000, Leuven, Belgium
| | - Marc A Suchard
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA.,Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Universtiy of California, Los Angeles, CA, USA
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56
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Saxenhofer M, Weber de Melo V, Ulrich RG, Heckel G. Revised time scales of RNA virus evolution based on spatial information. Proc Biol Sci 2018; 284:rspb.2017.0857. [PMID: 28794221 DOI: 10.1098/rspb.2017.0857] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 07/06/2017] [Indexed: 12/18/2022] Open
Abstract
The time scales of pathogen evolution are of major concern in the context of public and veterinary health, epidemiology and evolutionary biology. Dating the emergence of a pathogen often relies on estimates of evolutionary rates derived from nucleotide sequence data. For many viruses, this has yielded estimates of evolutionary origins only a few hundred years in the past. Here we demonstrate through the incorporation of geographical information from virus sampling that evolutionary age estimates of two European hantaviruses are severely underestimated because of pervasive mutational saturation of nucleotide sequences. We detected very strong relationships between spatial distance and genetic divergence for both Puumala and Tula hantavirus-irrespective of whether nucleotide or derived amino acid sequences were analysed. Extrapolations from these relationships dated the emergence of these viruses most conservatively to at least 3700 and 2500 years ago, respectively. Our minimum estimates for the age of these hantaviruses are ten to a hundred times older than results from current non-spatial methods, and in much better accordance with the biogeography of these viruses and their respective hosts. Spatial information can thus provide valuable insights on the deeper time scales of pathogen evolution and improve our understanding of disease emergence.
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Affiliation(s)
- Moritz Saxenhofer
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge-Bâtiment Génopode, Lausanne, Switzerland
| | - Vanessa Weber de Melo
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Rainer G Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany.,German Center for Infection Research (DZIF), partner site Hamburg-Luebeck-Borstel-Insel Riems, Germany
| | - Gerald Heckel
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland .,Swiss Institute of Bioinformatics, Quartier Sorge-Bâtiment Génopode, Lausanne, Switzerland
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57
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Schultz MJ, Connor JH, Frydman HM. Group B Wolbachia Strain-Dependent Inhibition of Arboviruses. DNA Cell Biol 2018; 37:2-6. [PMID: 29297702 DOI: 10.1089/dna.2017.4025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mosquito-borne viruses, including Zika virus (ZIKV) and dengue virus (DENV), are global threats that continue to infect millions annually. Historically, efforts to combat the spread of these diseases have sought to eradicate the mosquito population. This has had limited success. Recent efforts to combat the spread of these diseases have targeted the mosquito population and the mosquito's ability to transmit viruses by altering the mosquito's microbiome. The introduction of particular strains of Wolbachia bacteria into mosquitos suppresses viral growth and blocks disease transmission. This novel strategy is being tested worldwide to reduce DENV and has early indications of success. The Wolbachia genus comprised divergent strains that are divided in major phylogenetic clades termed supergroups. All Wolbachia field trials currently utilize supergroup A Wolbachia in Aedes aegypti mosquitos to limit virus transmission. Here we discuss our studies of Wolbachia strains not yet used in virus control strategies but that show strong potential to reduce ZIKV replication. These strains are important opportunities in the search for novel tools to reduce the levels of mosquito-borne viruses and provide additional models for mechanistic studies.
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Affiliation(s)
- Michaela J Schultz
- 1 Department of Biology, Boston University , Boston Massachusetts.,2 National Emerging Infectious Diseases Laboratories, Boston University , Boston, Massachusetts
| | - John H Connor
- 2 National Emerging Infectious Diseases Laboratories, Boston University , Boston, Massachusetts.,3 Department of Microbiology, Boston University School of Medicine , Boston, Massachusetts
| | - Horacio M Frydman
- 1 Department of Biology, Boston University , Boston Massachusetts.,2 National Emerging Infectious Diseases Laboratories, Boston University , Boston, Massachusetts
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58
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Development of small-molecule viral inhibitors targeting various stages of the life cycle of emerging and re-emerging viruses. Front Med 2017; 11:449-461. [PMID: 29170916 PMCID: PMC7089273 DOI: 10.1007/s11684-017-0589-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/22/2017] [Indexed: 01/22/2023]
Abstract
In recent years, unexpected outbreaks of infectious diseases caused by emerging and re-emerging viruses have become more frequent, which is possibly due to environmental changes. These outbreaks result in the loss of life and economic hardship. Vaccines and therapeutics should be developed for the prevention and treatment of infectious diseases. In this review, we summarize and discuss the latest progress in the development of small-molecule viral inhibitors against highly pathogenic coronaviruses, including severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus, Ebola virus, and Zika virus. These viruses can interfere with the specific steps of viral life cycle by blocking the binding between virus and host cells, disrupting viral endocytosis, disturbing membrane fusion, and interrupting viral RNA replication and translation, thereby demonstrating potent therapeutic effect against various emerging and re-emerging viruses. We also discuss some general strategies for developing small-molecule viral inhibitors.
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59
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Emerging new HCV strains among intravenous drug users and their route of transmission in the north eastern state of Mizoram, India. Mol Phylogenet Evol 2017; 116:239-247. [PMID: 28916154 DOI: 10.1016/j.ympev.2017.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 07/28/2017] [Accepted: 09/11/2017] [Indexed: 11/20/2022]
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60
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Mavian C, Rife BD, Dollar JJ, Cella E, Ciccozzi M, Prosperi MCF, Lednicky J, Morris JG, Capua I, Salemi M. Emergence of recombinant Mayaro virus strains from the Amazon basin. Sci Rep 2017; 7:8718. [PMID: 28821712 PMCID: PMC5562835 DOI: 10.1038/s41598-017-07152-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/26/2017] [Indexed: 01/31/2023] Open
Abstract
Mayaro virus (MAYV), causative agent of Mayaro Fever, is an arbovirus transmitted by Haemagogus mosquitoes. Despite recent attention due to the identification of several cases in South and Central America and the Caribbean, limited information on MAYV evolution and epidemiology exists and represents a barrier to prevention of further spread. We present a thorough spatiotemporal evolutionary study of MAYV full-genome sequences collected over the last sixty years within South America and Haiti, revealing recent recombination events and adaptation to a broad host and vector range, including Aedes mosquito species. We employed a Bayesian phylogeography approach to characterize the emergence of recombinants in Brazil and Haiti and report evidence in favor of the putative role of human mobility in facilitating recombination among MAYV strains from geographically distinct regions. Spatiotemporal characteristics of recombination events and the emergence of this previously neglected virus in Haiti, a known hub for pathogen spread to the Americas, warrants close monitoring of MAYV infection in the immediate future.
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Affiliation(s)
- Carla Mavian
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Brittany D Rife
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - James Jarad Dollar
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Eleonora Cella
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Massimo Ciccozzi
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy.,Unit of Clinical Pathology and Microbiology, University Campus Bio-Medico of Rome, Rome, Italy
| | | | - John Lednicky
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - J Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Ilaria Capua
- One Health Center of Excellence, University of Florida, Gainesville, FL, USA.
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA. .,Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA.
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61
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Thelaus J, Lindberg A, Thisted Lambertz S, Byström M, Forsman M, Lindmark H, Knutsson R, Båverud V, Bråve A, Jureen P, Lundin Zumpe A, Melefors Ö. Network Experiences from a Cross-Sector Biosafety Level-3 Laboratory Collaboration: A Swedish Forum for Biopreparedness Diagnostics. Health Secur 2017; 15:384-391. [PMID: 28805472 PMCID: PMC5576262 DOI: 10.1089/hs.2016.0082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Swedish Forum for Biopreparedness Diagnostics (FBD) is a network that fosters collaboration among the 4 agencies with responsibility for the laboratory diagnostics of high-consequence pathogens, covering animal health and feed safety, food safety, public health and biodefense, and security. The aim of the network is to strengthen capabilities and capacities for diagnostics at the national biosafety level-3 (BSL-3) laboratories to improve Sweden's biopreparedness, in line with recommendations from the EU and WHO. Since forming in 2007, the FBD network has contributed to the harmonization of diagnostic methods, equipment, quality assurance protocols, and biosafety practices among the national BSL-3 laboratories. Lessons learned from the network include: (1) conducting joint projects with activities such as method development and validation, ring trials, exercises, and audits has helped to build trust and improve communication among participating agencies; (2) rotating the presidency of the network steering committee has fostered trust and commitment from all agencies involved; and (3) planning for the implementation of project outcomes is important to maintain gained competencies in the agencies over time. Contacts have now been established with national agencies of the other Nordic countries, with an aim to expanding the collaboration, broadening the network, finding synergies in new areas, strengthening the ability to share resources, and consolidating long-term financing in the context of harmonized European biopreparedness. The Swedish Forum for Biopreparedness Diagnostics (FBD) is a network that fosters collaboration among the 4 agencies with responsibility for the laboratory diagnostics of high-consequence pathogens, covering animal health and feed safety, food safety, public health and biodefense, and security.
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62
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Picard C, Dallot S, Brunker K, Berthier K, Roumagnac P, Soubeyrand S, Jacquot E, Thébaud G. Exploiting Genetic Information to Trace Plant Virus Dispersal in Landscapes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:139-160. [PMID: 28525307 DOI: 10.1146/annurev-phyto-080516-035616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology. We present existing approaches and their limitations and contributions to the understanding of plant virus epidemiology.
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Affiliation(s)
- Coralie Picard
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Sylvie Dallot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | | | - Philippe Roumagnac
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | | | - Emmanuel Jacquot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Gaël Thébaud
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
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63
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Tian H, Sun Z, Faria NR, Yang J, Cazelles B, Huang S, Xu B, Yang Q, Pybus OG, Xu B. Increasing airline travel may facilitate co-circulation of multiple dengue virus serotypes in Asia. PLoS Negl Trop Dis 2017; 11:e0005694. [PMID: 28771468 PMCID: PMC5542384 DOI: 10.1371/journal.pntd.0005694] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/08/2017] [Indexed: 12/26/2022] Open
Abstract
The incidence of dengue has grown dramatically in recent decades worldwide, especially in Southeast Asia and the Americas with substantial transmission in 2014-2015. Yet the mechanisms underlying the spatio-temporal circulation of dengue virus (DENV) serotypes at large geographical scales remain elusive. Here we investigate the co-circulation in Asia of DENV serotypes 1-3 from 1956 to 2015, using a statistical framework that jointly estimates migration history and quantifies potential predictors of viral spatial diffusion, including socio-economic, air transportation and maritime mobility data. We find that the spread of DENV-1, -2 and -3 lineages in Asia is significantly associated with air traffic. Our analyses suggest the network centrality of air traffic hubs such as Thailand and India contribute to seeding dengue epidemics, whilst China, Cambodia, Indonesia, and Singapore may establish viral diffusion links with multiple countries in Asia. Phylogeographic reconstructions help to explain how growing air transportation networks could influence the dynamics of DENV circulation.
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Affiliation(s)
- Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Zhe Sun
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, School of Environment, Tsinghua University, Beijing, China
| | | | - Jing Yang
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Bernard Cazelles
- Ecologie & Evolution, UMR 7625, UPMC-ENS, Paris, France
- UMMISCO UMI 209 IRD - UPMC, Bondy, France
| | - Shanqian Huang
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Bo Xu
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, School of Environment, Tsinghua University, Beijing, China
| | - Qiqi Yang
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail: (OP); (BiX)
| | - Bing Xu
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, School of Environment, Tsinghua University, Beijing, China
- * E-mail: (OP); (BiX)
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64
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Affiliation(s)
- James O Lloyd-Smith
- Department of Ecology &Evolutionary Biology, University of California, Los Angeles, Los Angeles, California 90095-7239, USA, and at the Fogarty International Centre, National Institutes of Health, Bethesda, Maryland
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Baranzelli MC, Cosacov A, Ferreiro G, Johnson LA, Sérsic AN. Travelling to the south: Phylogeographic spatial diffusion model in Monttea aphylla (Plantaginaceae), an endemic plant of the Monte Desert. PLoS One 2017; 12:e0178827. [PMID: 28582433 PMCID: PMC5459442 DOI: 10.1371/journal.pone.0178827] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/20/2017] [Indexed: 11/20/2022] Open
Abstract
Effects of Pleistocene climatic oscillations on plant phylogeographic patterns are relatively well studied in forest, savanna and grassland biomes, but such impacts remain less explored on desert regions of the world, especially in South America. Here, we performed a phylogeographical study of Monttea aphylla, an endemic species of the Monte Desert, to understand the evolutionary history of vegetation communities inhabiting the South American Arid Diagonal. We obtained sequences of three chloroplast (trnS–trnfM, trnH–psbA and trnQ–rps16) and one nuclear (ITS) intergenic spacers from 272 individuals of 34 localities throughout the range of the species. Population genetic and Bayesian coalescent analyses were performed to infer genealogical relationships among haplotypes, population genetic structure, and demographic history of the study species. Timing of demographic events was inferred using Bayesian Skyline Plot and the spatio-temporal patterns of lineage diversification was reconstructed using Bayesian relaxed diffusion models. Palaeo-distribution models (PDM) were performed through three different timescales to validate phylogeographical patterns. Twenty-five and 22 haplotypes were identified in the cpDNA and nDNA data, respectively. that clustered into two main genealogical lineages following a latitudinal pattern, the northern and the southern Monte (south of 35° S). The northern Monte showed two lineages of high genetic structure, and more relative stable demography than the southern Monte that retrieved three groups with little phylogenetic structure and a strong signal of demographic expansion that would have started during the Last Interglacial period (ca. 120 Ka). The PDM and diffusion models analyses agreed in the southeast direction of the range expansion. Differential effect of climatic oscillations across the Monte phytogeographic province was observed in Monttea aphylla lineages. In northern Monte, greater genetic structure and more relative stable demography resulted from a more stable climate than in the southern Monte. Pleistocene glaciations drastically decreased the species area in the southern Monte, which expanded in a southeastern direction to the new available areas during the interglacial periods.
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Affiliation(s)
- Matias C Baranzelli
- Laboratorio de Ecología Evolutiva-Biología Floral, Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Andrea Cosacov
- Laboratorio de Ecología Evolutiva-Biología Floral, Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Gabriela Ferreiro
- Laboratorio de Ecología Evolutiva-Biología Floral, Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Leigh A Johnson
- Department of Biology and M. L. Bean Life Science Museum, Brigham Young University, Provo, Utah, United States of America
| | - Alicia N Sérsic
- Laboratorio de Ecología Evolutiva-Biología Floral, Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
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66
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Panigutti C, Tizzoni M, Bajardi P, Smoreda Z, Colizza V. Assessing the use of mobile phone data to describe recurrent mobility patterns in spatial epidemic models. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160950. [PMID: 28572990 PMCID: PMC5451791 DOI: 10.1098/rsos.160950] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/19/2017] [Indexed: 05/21/2023]
Abstract
The recent availability of large-scale call detail record data has substantially improved our ability of quantifying human travel patterns with broad applications in epidemiology. Notwithstanding a number of successful case studies, previous works have shown that using different mobility data sources, such as mobile phone data or census surveys, to parametrize infectious disease models can generate divergent outcomes. Thus, it remains unclear to what extent epidemic modelling results may vary when using different proxies for human movements. Here, we systematically compare 658 000 simulated outbreaks generated with a spatially structured epidemic model based on two different human mobility networks: a commuting network of France extracted from mobile phone data and another extracted from a census survey. We compare epidemic patterns originating from all the 329 possible outbreak seed locations and identify the structural network properties of the seeding nodes that best predict spatial and temporal epidemic patterns to be alike. We find that similarity of simulated epidemics is significantly correlated to connectivity, traffic and population size of the seeding nodes, suggesting that the adequacy of mobile phone data for infectious disease models becomes higher when epidemics spread between highly connected and heavily populated locations, such as large urban areas.
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Affiliation(s)
- Cecilia Panigutti
- Dipartimento di Fisica, Università degli Studi di Torino, via Giuria 1, Torino 10125, Italy
- ISI Foundation, via Alassio 11/C, Torino 10126, Italy
| | - Michele Tizzoni
- ISI Foundation, via Alassio 11/C, Torino 10126, Italy
- Author for correspondence: Michele Tizzoni e-mail:
| | - Paolo Bajardi
- Aizoon Technology Consulting, Str. del Lionetto 6, Torino, Italy
| | - Zbigniew Smoreda
- Sociology and Economics of Networks and Services Department, Orange Laboratories, Issy-les-Moulineaux, France
| | - Vittoria Colizza
- ISI Foundation, via Alassio 11/C, Torino 10126, Italy
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (IPLESP, UMR–S 1136), Paris, France
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van de Laar TJ, Bezemer D, van Laethem K, Vandewalle G, de Smet A, van Wijngaerden E, Claas EC, van Sighem AI, Vandamme AM, Compernolle V, Zaaijer HL. Phylogenetic evidence for underreporting of male-to-male sex among human immunodeficiency virus-infected donors in the Netherlands and Flanders. Transfusion 2017; 57:1235-1247. [PMID: 28375576 DOI: 10.1111/trf.14097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/14/2016] [Accepted: 01/08/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND Separate transmission networks for human immunodeficiency virus (HIV) coexist. Molecular typing of viral genomes can provide insight in HIV transmission routes in donors for whom risk behavior-based donor selection failed. STUDY DESIGN AND METHODS This study includes all HIV-infected Dutch and Flemish donors in the period 2005 to 2014 (n = 55). Part of the HIV polymerase (pol) gene was amplified, sequenced, and compared with more than 10,000 HIV strains obtained from HIV-infected Dutch and Flemish patients. The most likely transmission route was determined based on HIV phylogeny and the donor's self-reported risk behavior during the exit interview. RESULTS HIV-infected donors were predominantly male (69%), were repeat donors (73%), were born in the Netherlands or Belgium (95%), and harbored HIV Subtype B (68%). Seventy-five percent of HIV-infected male donors were part of robust phylogenetic clusters linked to male-to-male sex, while only 24% of HIV-infected male donors reported male-to-male sex during posttest counseling. Sex between men and women accounted for 13% of HIV infections in male donors and 93% of HIV infections in female donors based on phylogenetic analysis. Only 40% of HIV-infected female donors had HIV Subtype B; 65% of female donors reported a foreign partner and indeed HIV sequences interspersed with sequences from HIV-endemic areas abroad, in particular sub-Saharan Africa. CONCLUSION HIV typing helps to understand HIV transmission routes in donor populations. We found substantial underreporting of male-to-male sex among HIV-infected male donors. Donor education on HIV risk factors and the danger of window-period donations and a donor environment that encourages frank disclosure of sexual behavior will contribute to a decrease of HIV-infected donors.
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Affiliation(s)
- Thijs J van de Laar
- Department of Blood-borne Infections, Sanquin Research, Amsterdam, the Netherlands
| | | | - Kristel van Laethem
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven-Leuven University, Leuven, Belgium.,AIDS Reference Laboratory, University Hospitals Leuven, Leuven, Belgium
| | | | - Annie de Smet
- Blood Service, Belgian Red Cross-Flanders, Mechelen, Belgium
| | - Eric van Wijngaerden
- AIDS Reference Center, University Hospitals Leuven, Leuven, Belgium.,Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology and Immunology, KU Leuven-Leuven University, Leuven, Belgium
| | - Eric C Claas
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, the Netherlands.,Department of Molecular Biology, MC Slotervaart, Amsterdam, the Netherlands
| | | | - Anne-Mieke Vandamme
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven-Leuven University, Leuven, Belgium.,Center for Global Health and Tropical Medicine, Microbiology Unit, Institute for Hygiene and Tropical Medicine, University Nova de Lisboa, Lisbon, Portugal
| | - Veerle Compernolle
- Blood Service, Belgian Red Cross-Flanders, Mechelen, Belgium.,Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Hans L Zaaijer
- Department of Blood-borne Infections, Sanquin Research, Amsterdam, the Netherlands.,Department of Medical Microbiology (CINIMA), Academic Medical Center/University of Amsterdam, Amsterdam, the Netherlands
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68
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Al-Qahtani AA, Baele G, Khalaf N, Suchard MA, Al-Anazi MR, Abdo AA, Sanai FM, Al-Ashgar HI, Khan MQ, Al-Ahdal MN, Lemey P, Vrancken B. The epidemic dynamics of hepatitis C virus subtypes 4a and 4d in Saudi Arabia. Sci Rep 2017; 7:44947. [PMID: 28322313 PMCID: PMC5359580 DOI: 10.1038/srep44947] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/15/2017] [Indexed: 02/06/2023] Open
Abstract
The relatedness between viral variants sampled at different locations through time can provide information pertinent to public health that cannot readily be obtained through standard surveillance methods. Here, we use virus genetic data to identify the transmission dynamics that drive the hepatitis C virus subtypes 4a (HCV4a) and 4d (HCV4d) epidemics in Saudi Arabia. We use a comprehensive dataset of newly generated and publicly available sequence data to infer the HCV4a and HCV4d evolutionary histories in a Bayesian statistical framework. We also introduce a novel analytical method for an objective assessment of the migration intensity between locations. We find that international host mobility patterns dominate over within country spread in shaping the Saudi Arabia HCV4a epidemic, while this may be different for the HCV4d epidemic. This indicates that the subtypes 4a and 4d burden can be most effectively reduced by combining the prioritized screening and treatment of Egyptian immigrants with domestic prevention campaigns. Our results highlight that the joint investigation of evolutionary and epidemiological processes can provide valuable public health information, even in the absence of extensive metadata information.
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Affiliation(s)
- Ahmed A Al-Qahtani
- Department of Infection and Immunity, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia.,Department of Microbiology and Immunology, Alfaisal University School of Medicine, Riyadh, Saudi Arabia
| | - Guy Baele
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Nisreen Khalaf
- Department of Infection and Immunity, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, USA
| | - Mashael R Al-Anazi
- Department of Infection and Immunity, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia
| | - Ayman A Abdo
- Section of Gastroenterology, Department of Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Faisal M Sanai
- Gastroenterology Unit, Department of Medicine, King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Hamad I Al-Ashgar
- Gastroenterology Unit, Department of Medicine, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia
| | - Mohammed Q Khan
- Gastroenterology Unit, Department of Medicine, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia
| | - Mohammed N Al-Ahdal
- Department of Infection and Immunity, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia.,Department of Microbiology and Immunology, Alfaisal University School of Medicine, Riyadh, Saudi Arabia
| | - Philippe Lemey
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Bram Vrancken
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, B-3000 Leuven, Belgium
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69
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Implications of hepatitis C virus subtype 1a migration patterns for virus genetic sequencing policies in Italy. BMC Evol Biol 2017; 17:70. [PMID: 28270091 PMCID: PMC5341469 DOI: 10.1186/s12862-017-0913-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 02/14/2017] [Indexed: 02/06/2023] Open
Abstract
Background In-depth phylogeographic analysis can reveal migration patterns relevant for public health planning. Here, as a model, we focused on the provenance, in the current Italian HCV subtype 1a epidemic, of the NS3 resistance-associated variant (RAV) Q80K, known to interfere with the action of NS3/4A protease inhibitor simeprevir. HCV1a migration patterns were analysed using Bayesian phylodynamic tools, capitalising on newly generated and publicly available time and geo-referenced NS3 encoding virus genetic sequence data. Results Our results showed that both immigration and local circulation fuel the current Italian HCV1a epidemic. The United States and European continental lineages dominate import into Italy, with the latter taking the lead from the 1970s onwards. Since similar migration patterns were found for Q80K and other lineages, no clear differentiation of the risk for failing simeprevir can be made between patients based on their migration and travel history. Importantly, since HCV only occasionally recombines, these results are readily transferable to the genetic sequencing policy concerning NS5A RAVs. Conclusions The patient migration and travel history cannot be used to target only part of the HCV1a infected population for drug resistance testing before start of antiviral therapy. Consequently, it may be cost-effective to expand genotyping efforts to all HCV1a infected patients eligible for simeprevir-based therapies. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0913-3) contains supplementary material, which is available to authorized users.
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70
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Isoe J, Petchampai N, Isoe YE, Co K, Mazzalupo S, Scaraffia PY. Xanthine dehydrogenase-1 silencing in Aedes aegypti mosquitoes promotes a blood feeding-induced adulticidal activity. FASEB J 2017; 31:2276-2286. [PMID: 28179423 DOI: 10.1096/fj.201601185r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/23/2017] [Indexed: 01/03/2023]
Abstract
Aedesaegypti has 2 genes encoding xanthine dehydrogenase (XDH). We analyzed XDH1 and XDH2 gene expression by real-time quantitative PCR in tissues from sugar- and blood-fed females. Differential XDH1 and XDH2 gene expression was observed in tissues dissected throughout a time course. We next exposed females to blood meals supplemented with allopurinol, a well-characterized XDH inhibitor. We also tested the effects of injecting double-stranded RNA (dsRNA) against XDH1, XDH2, or both. Disruption of XDH by allopurinol or XDH1 by RNA interference significantly affected mosquito survival, causing a disruption in blood digestion, excretion, oviposition, and reproduction. XDH1-deficient mosquitoes showed a persistence of serine proteases in the midgut at 48 h after blood feeding and a reduction in the uptake of vitellogenin by the ovaries. Surprisingly, analysis of the fat body from dsRNA-XDH1-injected mosquitoes fell into 2 groups: one group was characterized by a reduction of the XDH1 transcript, whereas the other group was characterized by an up-regulation of several transcripts, including XDH1, glutamine synthetase, alanine aminotransferase, catalase, superoxide dismutase, ornithine decarboxylase, glutamate receptor, and ammonia transporter. Our data demonstrate that XDH1 plays an essential role and that XDH1 has the potential to be used as a metabolic target for Ae.aegypti vector control.-Isoe, J., Petchampai, N., Isoe, Y. E., Co, K., Mazzalupo, S., Scaraffia, P. Y. Xanthine dehydrogenase-1 silencing in Aedes aegypti mosquitoes promotes a blood feeding-induced adulticidal activity.
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Affiliation(s)
- Jun Isoe
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Natthida Petchampai
- Department of Tropical Medicine, Vector-Borne Infectious Disease Research Center, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, USA
| | - Yurika E Isoe
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Katrina Co
- Department of Tropical Medicine, Vector-Borne Infectious Disease Research Center, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, USA
| | - Stacy Mazzalupo
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, USA
| | - Patricia Y Scaraffia
- Department of Tropical Medicine, Vector-Borne Infectious Disease Research Center, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, USA;
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71
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Martina BE, Barzon L, Pijlman GP, de la Fuente J, Rizzoli A, Wammes LJ, Takken W, van Rij RP, Papa A. Human to human transmission of arthropod-borne pathogens. Curr Opin Virol 2016; 22:13-21. [PMID: 27915056 DOI: 10.1016/j.coviro.2016.11.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/07/2016] [Accepted: 11/11/2016] [Indexed: 12/17/2022]
Abstract
Human-to-human (H2H) transmitted arthropod-borne pathogens are a growing burden worldwide, with malaria and dengue being the most common mosquito-borne H2H transmitted diseases. The ability of vectors to get infected by humans during a blood meal to further propel an epidemic depends on complex interactions between pathogens, vectors and humans, in which human interventions and demographic and environmental conditions play a significant role. Herein, we discuss the distal and proximal drivers affecting H2H vector-borne pathogen transmission and identify knowledge gaps and future perspectives.
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Affiliation(s)
- Byron E Martina
- Viroscience Laboratory, Erasmus Medical Centre, Rotterdam, The Netherlands; Artemis One Health Research Institute, Utrecht, The Netherlands
| | - Luisa Barzon
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain; Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Annapaola Rizzoli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige (Trento), Italy
| | - Linda J Wammes
- Department of Microbiology & Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands
| | - Willem Takken
- Laboratory of Entomology, Wageningen University, Wageningen, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece.
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72
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Mackay IM, Arden KE. Mayaro virus: a forest virus primed for a trip to the city? Microbes Infect 2016; 18:724-734. [PMID: 27989728 DOI: 10.1016/j.micinf.2016.10.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 10/21/2016] [Indexed: 11/16/2022]
Abstract
Mayaro virus (MAYV) is an emerging arthropod-borne virus (arbovirus). Infection by MAYV can produce Mayaro virus disease (MAYVD) which is usually a clinically diagnosed, acute, febrile illness associated with prolonged and painful joint inflammation and swelling. MAYVD may be clinically indistinguishable from dengue, chikungunya fever, malaria, rabies, measles or other arboviral diseases. The full spectrum of disease, sequelae, routes of infection, virus shedding and any rarer means of transmission remain undefined. MAYVD cases in humans have so far been localised to Central and South America, particularly regions in and around the Amazon basin. MAYV usually circulates in a sylvan cycle of forest mosquitoes and vertebrates, however it has also been found in more urban locations alongside anthropophilic (preferring humans) insect vectors. If transmission via anthropophilic mosquitoes becomes more efficient following viral change, or existing vectors change their habitat and biting habits, the risk of urban establishment and further spread into non-forested areas will grow. Surveillance, testing and vector control remain key to monitoring and preventing global spread and establishment. The possibility of MAYV becoming further urbanized is worthy of note, consideration and action to ensure MAYV does not spread beyond the forests and establish in the world's cities.
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Affiliation(s)
- Ian M Mackay
- Department of Health, Public and Environmental Health Virology Laboratory, Forensic and Scientific Services, Archerfield, QLD, Australia; The University of Queensland, St Lucia, QLD, Australia.
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73
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van de Laar TJ, Richel O. Emerging viral STIs among HIV-positive men who have sex with men: the era of hepatitis C virus and human papillomavirus. Sex Transm Infect 2016; 93:368-373. [PMID: 27789574 DOI: 10.1136/sextrans-2016-052677] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/14/2016] [Accepted: 10/10/2016] [Indexed: 12/26/2022] Open
Abstract
The number of infectious disease outbreaks and the number of unique pathogens responsible have significantly increased since the 1980s. HIV-positive men who have sex with men (MSM) are a vulnerable population with regards to the introduction, spread and clinical consequences of (newly introduced) STIs. After the introduction of combination antiretroviral treatment (cART), the incidence of sexually acquired hepatitis C virus (HCV) infection and human papillomavirus (HPV)-induced anal cancers have significantly increased among HIV-positive MSM. The introduction and expansion of HCV is the result of increased sexual risk behaviour and sexually acquired mucosal trauma within large interconnected networks of HIV-positive MSM in particular. With the availability of cART, postexposure and pre-exposure prophylaxis (PEP and PrEP) and direct-acting antivirals (DAAs) for HCV, less concern for HIV and HCV might require a new approach to develop effective behavioural intervention strategies among MSM. The marked rise in HPV-induced anal cancers can be ascribed to the long-term immunologic defects in an ageing population affected by HIV. More evidence with regards to effective treatment options for anal dysplastic lesions and the usefulness of anal malignancy screening programmes is urgently needed. Most anal cancers in the future generation of HIV-positive MSM could be prevented with the inclusion of boys in addition to girls in current HPV vaccination programmes.
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Affiliation(s)
- Thijs Jw van de Laar
- Department of Blood-Borne Infections, Sanquin Research, Amsterdam, The Netherlands
| | - Olivier Richel
- Department of Infectious Diseases, University of Amsterdam/Academic Medical Centre, Amsterdam, The Netherlands
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74
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Li HJ, Cheng Q, Wang L. Understanding spatial spread of emerging infectious diseases in contemporary populations: Comment on "Pattern transitions in spatial epidemics: Mechanisms and emergent properties" by Gui-Quan Sun et al. Phys Life Rev 2016; 19:95-97. [PMID: 27818036 DOI: 10.1016/j.plrev.2016.10.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 10/21/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Hui-Jia Li
- School of Management Science and Engineering, Central University of Finance and Economics, Beijing 100080, China
| | - Qing Cheng
- Science and Technology on Information Systems Engineering Laboratory, National University of Defense Technology, Changsha 410073, China
| | - Lin Wang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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Sorichetta A, Bird TJ, Ruktanonchai NW, zu Erbach-Schoenberg E, Pezzulo C, Tejedor N, Waldock IC, Sadler JD, Garcia AJ, Sedda L, Tatem AJ. Mapping internal connectivity through human migration in malaria endemic countries. Sci Data 2016; 3:160066. [PMID: 27529469 PMCID: PMC5127488 DOI: 10.1038/sdata.2016.66] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/01/2016] [Indexed: 12/22/2022] Open
Abstract
Human mobility continues to increase in terms of volumes and reach, producing growing global connectivity. This connectivity hampers efforts to eliminate infectious diseases such as malaria through reintroductions of pathogens, and thus accounting for it becomes important in designing global, continental, regional, and national strategies. Recent works have shown that census-derived migration data provides a good proxy for internal connectivity, in terms of relative strengths of movement between administrative units, across temporal scales. To support global malaria eradication strategy efforts, here we describe the construction of an open access archive of estimated internal migration flows in endemic countries built through pooling of census microdata. These connectivity datasets, described here along with the approaches and methods used to create and validate them, are available both through the WorldPop website and the WorldPop Dataverse Repository.
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Affiliation(s)
- Alessandro Sorichetta
- WorldPop, Geography and Environment, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
- Flowminder Foundation, Roslagsgatan 17, Stockholm SE-11355, Sweden
- Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Tom J. Bird
- WorldPop, Geography and Environment, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
- Flowminder Foundation, Roslagsgatan 17, Stockholm SE-11355, Sweden
| | - Nick W. Ruktanonchai
- WorldPop, Geography and Environment, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
- Flowminder Foundation, Roslagsgatan 17, Stockholm SE-11355, Sweden
| | - Elisabeth zu Erbach-Schoenberg
- WorldPop, Geography and Environment, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
- Flowminder Foundation, Roslagsgatan 17, Stockholm SE-11355, Sweden
| | - Carla Pezzulo
- WorldPop, Geography and Environment, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
- Flowminder Foundation, Roslagsgatan 17, Stockholm SE-11355, Sweden
| | - Natalia Tejedor
- WorldPop, Geography and Environment, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
- Flowminder Foundation, Roslagsgatan 17, Stockholm SE-11355, Sweden
- GeoData, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Ian C. Waldock
- GeoData, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Jason D. Sadler
- GeoData, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Andres J. Garcia
- Bill and Melinda Gates Foundation, 440 5th Ave N., Seattle, Washington 98109, USA
| | - Luigi Sedda
- CHICAS, Lancaster Medical School, Lancaster University, Lancaster LA1 4YG, UK
| | - Andrew J. Tatem
- WorldPop, Geography and Environment, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
- Flowminder Foundation, Roslagsgatan 17, Stockholm SE-11355, Sweden
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Gaulton TG, Gaulton GN. The Multifactorial Background of Emerging Viral Infections with Neurological Manifestation. EUROPEAN MEDICAL JOURNAL 2016. [DOI: 10.33590/emj/10313458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
The events of the past year have highlighted the continuing importance of emerging virus infections on the diagnosis and treatment of neurological disease. This review focusses on clarifying the effects of the multiple overlapping factors that impact emergence, including viral richness, transmission opportunity, and establishment. Case studies of the West Nile, chikungunya, and Zika viruses are utilised to illustrate the dramatic effects of expansion in the range and geographical distribution of emerging infectious disease, the acquisition of new virus vectors, and of increasing human anthropogenic factors such as global transport, climate change, and mosquito abatement programmes on the regional spread and clinical consequences of emerging infectious disease.
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Affiliation(s)
- Timothy G. Gaulton
- Department of Anesthesiology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Glen N. Gaulton
- Department of Pathology and Laboratory Medicine, and Center for Global Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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77
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Faria NR, Azevedo RDSDS, Kraemer MUG, Souza R, Cunha MS, Hill SC, Thézé J, Bonsall MB, Bowden TA, Rissanen I, Rocco IM, Nogueira JS, Maeda AY, Vasami FGDS, Macedo FLDL, Suzuki A, Rodrigues SG, Cruz ACR, Nunes BT, Medeiros DBDA, Rodrigues DSG, Queiroz ALN, da Silva EVP, Henriques DF, da Rosa EST, de Oliveira CS, Martins LC, Vasconcelos HB, Casseb LMN, Simith DDB, Messina JP, Abade L, Lourenço J, Alcantara LCJ, de Lima MM, Giovanetti M, Hay SI, de Oliveira RS, Lemos PDS, de Oliveira LF, de Lima CPS, da Silva SP, de Vasconcelos JM, Franco L, Cardoso JF, Vianez-Júnior JLDSG, Mir D, Bello G, Delatorre E, Khan K, Creatore M, Coelho GE, de Oliveira WK, Tesh R, Pybus OG, Nunes MRT, Vasconcelos PFC. Zika virus in the Americas: Early epidemiological and genetic findings. Science 2016; 352:345-349. [PMID: 27013429 DOI: 10.1126/science.aaf5036] [Citation(s) in RCA: 742] [Impact Index Per Article: 92.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 03/16/2016] [Indexed: 12/16/2022]
Abstract
Brazil has experienced an unprecedented epidemic of Zika virus (ZIKV), with ~30,000 cases reported to date. ZIKV was first detected in Brazil in May 2015, and cases of microcephaly potentially associated with ZIKV infection were identified in November 2015. We performed next-generation sequencing to generate seven Brazilian ZIKV genomes sampled from four self-limited cases, one blood donor, one fatal adult case, and one newborn with microcephaly and congenital malformations. Results of phylogenetic and molecular clock analyses show a single introduction of ZIKV into the Americas, which we estimated to have occurred between May and December 2013, more than 12 months before the detection of ZIKV in Brazil. The estimated date of origin coincides with an increase in air passengers to Brazil from ZIKV-endemic areas, as well as with reported outbreaks in the Pacific Islands. ZIKV genomes from Brazil are phylogenetically interspersed with those from other South American and Caribbean countries. Mapping mutations onto existing structural models revealed the context of viral amino acid changes present in the outbreak lineage; however, no shared amino acid changes were found among the three currently available virus genomes from microcephaly cases. Municipality-level incidence data indicate that reports of suspected microcephaly in Brazil best correlate with ZIKV incidence around week 17 of pregnancy, although this correlation does not demonstrate causation. Our genetic description and analysis of ZIKV isolates in Brazil provide a baseline for future studies of the evolution and molecular epidemiology of this emerging virus in the Americas.
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Affiliation(s)
- Nuno Rodrigues Faria
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil.,Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
| | | | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
| | - Renato Souza
- Instituto Adolfo Lutz, University of São Paulo, Brazil
| | | | - Sarah C Hill
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
| | - Julien Thézé
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
| | - Michael B Bonsall
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
| | - Thomas A Bowden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ilona Rissanen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | | | | | | | - Akemi Suzuki
- Instituto Adolfo Lutz, University of São Paulo, Brazil
| | - Sueli Guerreiro Rodrigues
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil
| | - Ana Cecilia Ribeiro Cruz
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil
| | - Bruno Tardeli Nunes
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil
| | | | | | - Alice Louize Nunes Queiroz
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil
| | - Eliana Vieira Pinto da Silva
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil
| | - Daniele Freitas Henriques
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil
| | | | - Consuelo Silva de Oliveira
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil
| | - Livia Caricio Martins
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil
| | - Helena Baldez Vasconcelos
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil
| | - Livia Medeiros Neves Casseb
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil
| | - Darlene de Brito Simith
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil
| | - Jane P Messina
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK.,Metabiota, San Francisco, California 94104, USA
| | - Leandro Abade
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
| | - José Lourenço
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK
| | | | - Maricélia Maia de Lima
- Centre of Post Graduation in Collective Health, Department of Health, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | | | - Simon I Hay
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, USA.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rodrigo Santos de Oliveira
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil
| | - Poliana da Silva Lemos
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil
| | - Layanna Freitas de Oliveira
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil
| | - Clayton Pereira Silva de Lima
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil
| | - Sandro Patroca da Silva
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil
| | - Janaina Mota de Vasconcelos
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil
| | - Luciano Franco
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil
| | - Jedson Ferreira Cardoso
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil
| | | | - Daiana Mir
- Laboratório de AIDS and Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS and Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Edson Delatorre
- Laboratório de AIDS and Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada.,Department of Medicine, Division of Infectious Diseases, University of Toronto, Canada
| | - Marisa Creatore
- Dalla Lana School of Public Health, University of Toronto, Canada
| | | | | | - Robert Tesh
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS UK.,Metabiota, San Francisco, California 94104, USA
| | - Marcio R T Nunes
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, PA, 67030-000, Brazil.,Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pedro F C Vasconcelos
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará State, Brazil
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78
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Dellicour S, Rose R, Pybus OG. Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data. BMC Bioinformatics 2016; 17:82. [PMID: 26864798 PMCID: PMC4750353 DOI: 10.1186/s12859-016-0924-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/28/2016] [Indexed: 11/22/2022] Open
Abstract
Background Phylogenetic analysis is now an important tool in the study of viral outbreaks. It can reconstruct epidemic history when surveillance epidemiology data are sparse, and can indicate transmission linkages among infections that may not otherwise be evident. However, a remaining challenge is to develop an analytical framework that can test hypotheses about the effect of environmental variables on pathogen spatial spread. Recent phylogeographic approaches can reconstruct the history of virus dispersal from sampled viral genomes and infer the locations of ancestral infections. Such methods provide a unique source of spatio-temporal information, and are exploited here. Results We present and apply a new statistical framework that combines genomic and geographic data to test the impact of environmental variables on the mode and tempo of pathogen dispersal during emerging epidemics. First, the spatial history of an emerging pathogen is estimated using standard phylogeographic methods. The inferred dispersal path for each phylogenetic lineage is then assigned a “weight” using environmental data (e.g. altitude, land cover). Next, tests measure the association between each environmental variable and lineage movement. A randomisation procedure is used to assess statistical confidence and we validate this approach using simulated data. We apply our new framework to a set of gene sequences from an epidemic of rabies virus in North American raccoons. We test the impact of six different environmental variables on this epidemic and demonstrate that elevation is associated with a slower rabies spread in a natural population. Conclusion This study shows that it is possible to integrate genomic and environmental data in order to test hypotheses concerning the mode and tempo of virus dispersal during emerging epidemics. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0924-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simon Dellicour
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK. .,Rega Institute for Medical Research, Clinical and Epidemiological Virology, Department of Microbiology and Immunology, KU Leuven, University of Leuven, Minderbroedersstaat 10, 3000, Leuven, Belgium.
| | - Rebecca Rose
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
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79
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Rodrigues Faria N, Lourenço J, Marques de Cerqueira E, Maia de Lima M, Pybus O, Carlos Junior Alcantara L. Epidemiology of Chikungunya Virus in Bahia, Brazil, 2014-2015. PLOS CURRENTS 2016; 8. [PMID: 27330849 PMCID: PMC4747681 DOI: 10.1371/currents.outbreaks.c97507e3e48efb946401755d468c28b2] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Chikungunya is an emerging arbovirus that is characterized into four lineages. One of these, the Asian genotype, has spread rapidly in the Americas after its introduction in the Saint Martin island in October 2013. Unexpectedly, a new lineage, the East-Central-South African genotype, was introduced from Angola in the end of May 2014 in Feira de Santana (FSA), the second largest city in Bahia state, Brazil, where over 5,500 cases have now been reported. Number weekly cases of clinically confirmed CHIKV in FSA were analysed alongside with urban district of residence of CHIKV cases reported between June 2014 and October collected from the municipality's surveillance network. The number of cases per week from June 2014 until September 2015 reveals two distinct transmission waves. The first wave ignited in June and transmission ceased by December 2014. However, a second transmission wave started in January and peaked in May 2015, 8 months after the first wave peak, and this time in phase with Dengue virus and Zika virus transmission, which ceased when minimum temperature dropped to approximately 15°C. We find that shorter travelling times from the district where the outbreak first emerged to other urban districts of FSA were strongly associated with incidence in each district in 2014 (R(2)).
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Affiliation(s)
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Erenilde Marques de Cerqueira
- Centre of Post-Graduation in Collective Health, Department of Health, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Maricélia Maia de Lima
- Centre of Post-Graduation in Collective Health, Department of Health, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Oliver Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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80
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Rodrigues Faria N, Lourenço J, Marques de Cerqueira E, Maia de Lima M, Pybus O, Carlos Junior Alcantara L. Epidemiology of Chikungunya Virus in Bahia, Brazil, 2014-2015. PLOS CURRENTS 2016; 8:ecurrents.outbreaks.c97507e3e48efb946401755d468c28b2. [PMID: 27330849 PMCID: PMC4747681 DOI: 10.2165/00019053-199304050-00006 10.1371/currents.outbreaks.c97507e3e48efb946401755d468c28b2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Chikungunya is an emerging arbovirus that is characterized into four lineages. One of these, the Asian genotype, has spread rapidly in the Americas after its introduction in the Saint Martin island in October 2013. Unexpectedly, a new lineage, the East-Central-South African genotype, was introduced from Angola in the end of May 2014 in Feira de Santana (FSA), the second largest city in Bahia state, Brazil, where over 5,500 cases have now been reported. Number weekly cases of clinically confirmed CHIKV in FSA were analysed alongside with urban district of residence of CHIKV cases reported between June 2014 and October collected from the municipality's surveillance network. The number of cases per week from June 2014 until September 2015 reveals two distinct transmission waves. The first wave ignited in June and transmission ceased by December 2014. However, a second transmission wave started in January and peaked in May 2015, 8 months after the first wave peak, and this time in phase with Dengue virus and Zika virus transmission, which ceased when minimum temperature dropped to approximately 15°C. We find that shorter travelling times from the district where the outbreak first emerged to other urban districts of FSA were strongly associated with incidence in each district in 2014 (R(2)).
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Affiliation(s)
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Erenilde Marques de Cerqueira
- Centre of Post-Graduation in Collective Health, Department of Health, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Maricélia Maia de Lima
- Centre of Post-Graduation in Collective Health, Department of Health, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Oliver Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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81
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Spratt BG, Anderson RM. Special feature on evolution and genetics in medicine. Proc Biol Sci 2015; 282:20152811. [PMID: 26702049 PMCID: PMC4707767 DOI: 10.1098/rspb.2015.2811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Brian G Spratt
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Roy M Anderson
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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