1
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Rollins RE, Sato K, Nakao M, Tawfeeq MT, Herrera-Mesías F, Pereira RJ, Kovalev S, Margos G, Fingerle V, Kawabata H, Becker NS. Out of Asia? Expansion of Eurasian Lyme borreliosis causing genospecies display unique evolutionary trajectories. Mol Ecol 2023; 32:786-799. [PMID: 36461660 DOI: 10.1111/mec.16805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 10/25/2022] [Accepted: 11/30/2022] [Indexed: 12/04/2022]
Abstract
Vector-borne pathogens exist in obligate transmission cycles between vector and reservoir host species. Host and vector shifts can lead to geographic expansion of infectious agents and the emergence of new diseases in susceptible individuals. Three bacterial genospecies (Borrelia afzelii, Borrelia bavariensis, and Borrelia garinii) predominantly utilize two distinct tick species as vectors in Asia (Ixodes persulcatus) and Europe (Ixodes ricinus). Through these vectors, the bacteria can infect various vertebrate groups (e.g., rodents, birds) including humans where they cause Lyme borreliosis, the most common vector-borne disease in the Northern hemisphere. Yet, how and in which order the three Borrelia genospecies colonized each continent remains unclear including the evolutionary consequences of this geographic expansion. Here, by reconstructing the evolutionary history of 142 Eurasian isolates, we found evidence that the ancestors of each of the three genospecies probably have an Asian origin. Even so, each genospecies studied displayed a unique substructuring and evolutionary response to the colonization of Europe. The pattern of allele sharing between continents is consistent with the dispersal rate of the respective vertebrate hosts, supporting the concept that adaptation of Borrelia genospecies to the host is important for pathogen dispersal. Our results highlight that Eurasian Lyme borreliosis agents are all capable of geographic expansion with host association influencing their dispersal; further displaying the importance of host and vector association to the geographic expansion of vector-borne pathogens and potentially conditioning their capacity as emergent pathogens.
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Affiliation(s)
- Robert E Rollins
- Institute of Avian Research "Vogelwarte Helgoland", Wilhelmshaven, Germany.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians Universität, Munich, Germany
| | - Kozue Sato
- Department of Bacteriology I, National Institute for Infectious Disease, Tokyo, Japan
| | - Minoru Nakao
- Department of Parasitology, Asahikawa Medical University, Asahikawa, Japan
| | - Mohammed T Tawfeeq
- Institute of Avian Research "Vogelwarte Helgoland", Wilhelmshaven, Germany.,VIB - KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research (LIBR), Leuven, Belgium
| | - Fernanda Herrera-Mesías
- Institute of Avian Research "Vogelwarte Helgoland", Wilhelmshaven, Germany.,Department of Animal Ecology, Evolution, and Biodiversity, Ruhr-Universität Bochum, Bochum, Germany.,Musée National d'histoire Naturelle de Luxembourg, Luxembourg, Luxembourg
| | - Ricardo J Pereira
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians Universität, Munich, Germany.,Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Sergey Kovalev
- Laboratory of Molecular Genetics, Department of Biology, Ural Federal University, Yekaterinburg, Russia
| | - Gabriele Margos
- National Reference Center for Borrelia, Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Oberschleißheim, Germany
| | - Volker Fingerle
- National Reference Center for Borrelia, Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Oberschleißheim, Germany
| | - Hiroki Kawabata
- Department of Bacteriology I, National Institute for Infectious Disease, Tokyo, Japan
| | - Noémie S Becker
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians Universität, Munich, Germany
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2
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Hoehn KB, Pybus OG, Kleinstein SH. Phylogenetic analysis of migration, differentiation, and class switching in B cells. PLoS Comput Biol 2022; 18:e1009885. [PMID: 35468128 PMCID: PMC9037912 DOI: 10.1371/journal.pcbi.1009885] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 01/31/2022] [Indexed: 11/20/2022] Open
Abstract
B cells undergo rapid mutation and selection for antibody binding affinity when producing antibodies capable of neutralizing pathogens. This evolutionary process can be intermixed with migration between tissues, differentiation between cellular subsets, and switching between functional isotypes. B cell receptor (BCR) sequence data has the potential to elucidate important information about these processes. However, there is currently no robust, generalizable framework for making such inferences from BCR sequence data. To address this, we develop three parsimony-based summary statistics to characterize migration, differentiation, and isotype switching along B cell phylogenetic trees. We use simulations to demonstrate the effectiveness of this approach. We then use this framework to infer patterns of cellular differentiation and isotype switching from high throughput BCR sequence datasets obtained from patients in a study of HIV infection and a study of food allergy. These methods are implemented in the R package dowser, available at https://dowser.readthedocs.io. B cells produce high affinity antibodies through an evolutionary process of mutation and selection during adaptive immune responses. Migration between tissues, differentiation to cellular subtypes, and switching between different antibody isotypes can be important factors in shaping the role B cells play in response to infection, autoimmune disease, and allergies. B cell receptor (BCR) sequence data has the potential to elucidate important information about these processes. However, there is currently no robust, generalizable framework for making such inferences from BCR sequence data. Here, we develop three parsimony-based summary statistics to characterize migration, differentiation, and isotype switching along B cell phylogenetic trees. We confirm the effectiveness of our approach using simulations and further apply our method to data from patients with HIV and allergy. Our methods are released in the R package dowser: https://dowser.readthedocs.io.
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Affiliation(s)
- Kenneth B. Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, United Kingdom
| | - Steven H. Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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3
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Liu P, Song Y, Colijn C, MacPherson A. The impact of sampling bias on viral phylogeographic reconstruction. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000577. [PMID: 36962555 PMCID: PMC10021582 DOI: 10.1371/journal.pgph.0000577] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022]
Abstract
Genomic epidemiology plays an ever-increasing role in our understanding of and response to the spread of infectious pathogens. Phylogeography, the reconstruction of the historical location and movement of pathogens from the evolutionary relationships among sampled pathogen sequences, can inform policy decisions related to viral movement among jurisdictions. However, phylogeographic reconstruction is impacted by the fact that the sampling and virus sequencing policies differ among jurisdictions, and these differences can cause bias in phylogeographic reconstructions. Here we assess the potential impacts of geographic-based sampling bias on estimated viral locations in the past, and on whether key viral movements can be detected. We quantify the effect of bias using simulated phylogenies with known geographic histories, and determine the impact of the biased sampling and of the underlying migration rate on the accuracy of estimated past viral locations. We find that overall, the accuracy of phylogeographic reconstruction is high, particularly when the migration rate is low. However, results depend on sampling, and sampling bias can have a large impact on the numbers and nature of estimated migration events. We apply these insights to the geographic spread of Ebolavirus in the 2014-2016 West Africa epidemic. This work highlights how sampling policy can both impact geographic inference and be optimized to best ensure the accuracy of specific features of geographic spread.
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Affiliation(s)
- Pengyu Liu
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Yexuan Song
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Ailene MacPherson
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
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4
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Modeling and Analyzing Transmission of Infectious Diseases Using Generalized Stochastic Petri Nets. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11188400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Some infectious diseases such as COVID-19 have the characteristics of long incubation period, high infectivity during the incubation period, and carriers with mild or no symptoms which are more likely to cause negligence. Global researchers are working to find out more about the transmission of infectious diseases. Modeling plays a crucial role in understanding the transmission of the new virus and helps show the evolution of the epidemic in stages. In this paper, we propose a new general transmission model of infectious diseases based on the generalized stochastic Petri net (GSPN). First, we qualitatively analyze the transmission mode of each stage of infectious diseases such as COVID-19 and explain the factors that affect the spread of the epidemic. Second, the GSPN model is built to simulate the evolution of the epidemic. Based on this model’s isomorphic Markov chain, the equilibrium state of the system and its changing laws under different influencing factors are analyzed. Our paper demonstrates that the proposed GSPN model is a compelling tool for representing and analyzing the transmission of infectious diseases from system-level understanding, and thus contributes to providing decision support for effective surveillance and response to epidemic development.
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5
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Reimering S, Muñoz S, McHardy AC. Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic. PLoS Comput Biol 2020; 16:e1007101. [PMID: 32032362 PMCID: PMC7032730 DOI: 10.1371/journal.pcbi.1007101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 02/20/2020] [Accepted: 01/12/2020] [Indexed: 12/02/2022] Open
Abstract
Influenza A viruses cause seasonal epidemics and occasional pandemics in the human population. While the worldwide circulation of seasonal influenza is at least partly understood, the exact migration patterns between countries, states or cities are not well studied. Here, we use the Sankoff algorithm for parsimonious phylogeographic reconstruction together with effective distances based on a worldwide air transportation network. By first simulating geographic spread and then phylogenetic trees and genetic sequences, we confirmed that reconstructions with effective distances inferred phylogeographic spread more accurately than reconstructions with geographic distances and Bayesian reconstructions with BEAST that do not use any distance information, and led to comparable results to the Bayesian reconstruction using distance information via a generalized linear model. Our method extends Bayesian methods that estimate rates from the data by using fine-grained locations like airports and inferring intermediate locations not observed among sampled isolates. When applied to sequence data of the pandemic H1N1 influenza A virus in 2009, our approach correctly inferred the origin and proposed airports mainly involved in the spread of the virus. In case of a novel outbreak, this approach allows to rapidly analyze sequence data and infer origin and spread routes to improve disease surveillance and control. Influenza A viruses infect up to 5 million people in recurring epidemics every year. Further, viruses of zoonotic origin constantly pose a pandemic risk. Understanding the geographical spread of these viruses, including the origin and the main spread routes between cities, states or countries, could help to monitor or contain novel outbreaks. Based on genetic sequences and sampling locations, the geographic spread can be reconstructed along a phylogenetic tree. Our approach uses a parsimonious reconstruction with air transportation data and was verified using a simulation of the 2009 H1N1 influenza A pandemic. Applied to real sequence data of the outbreak, our analysis gave detailed insights into spread patterns of influenza A viruses, highlighting the origin as well as airports mainly involved in the spread.
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Affiliation(s)
- Susanne Reimering
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Sebastian Muñoz
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Alice C. McHardy
- Department for Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
- * E-mail:
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6
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Ishikawa SA, Zhukova A, Iwasaki W, Gascuel O. A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios. Mol Biol Evol 2019; 36:2069-2085. [PMID: 31127303 PMCID: PMC6735705 DOI: 10.1093/molbev/msz131] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The reconstruction of ancestral scenarios is widely used to study the evolution of characters along phylogenetic trees. One commonly uses the marginal posterior probabilities of the character states, or the joint reconstruction of the most likely scenario. However, marginal reconstructions provide users with state probabilities, which are difficult to interpret and visualize, whereas joint reconstructions select a unique state for every tree node and thus do not reflect the uncertainty of inferences. We propose a simple and fast approach, which is in between these two extremes. We use decision-theory concepts (namely, the Brier score) to associate each node in the tree to a set of likely states. A unique state is predicted in tree regions with low uncertainty, whereas several states are predicted in uncertain regions, typically around the tree root. To visualize the results, we cluster the neighboring nodes associated with the same states and use graph visualization tools. The method is implemented in the PastML program and web server. The results on simulated data demonstrate the accuracy and robustness of the approach. PastML was applied to the phylogeography of Dengue serotype 2 (DENV2), and the evolution of drug resistances in a large HIV data set. These analyses took a few minutes and provided convincing results. PastML retrieved the main transmission routes of human DENV2 and showed the uncertainty of the human-sylvatic DENV2 geographic origin. With HIV, the results show that resistance mutations mostly emerge independently under treatment pressure, but resistance clusters are found, corresponding to transmissions among untreated patients.
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Affiliation(s)
- Sohta A Ishikawa
- Unité Bioinformatique Evolutive, Institut Pasteur, C3BI USR 3756 IP & CNRS, Paris, France
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
- Evolutionary Genomics of RNA Viruses, Virology Department, Institut Pasteur, Paris, France
| | - Anna Zhukova
- Unité Bioinformatique Evolutive, Institut Pasteur, C3BI USR 3756 IP & CNRS, Paris, France
| | - Wataru Iwasaki
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Olivier Gascuel
- Unité Bioinformatique Evolutive, Institut Pasteur, C3BI USR 3756 IP & CNRS, Paris, France
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7
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Scotch M, Tahsin T, Weissenbacher D, O'Connor K, Magge A, Vaiente M, Suchard MA, Gonzalez-Hernandez G. Incorporating sampling uncertainty in the geospatial assignment of taxa for virus phylogeography. Virus Evol 2019; 5:vey043. [PMID: 30838129 PMCID: PMC6395475 DOI: 10.1093/ve/vey043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Discrete phylogeography using software such as BEAST considers the sampling location of each taxon as fixed; often to a single location without uncertainty. When studying viruses, this implies that there is no possibility that the location of the infected host for that taxa is somewhere else. Here, we relaxed this strong assumption and allowed for analytic integration of uncertainty for discrete virus phylogeography. We used automatic language processing methods to find and assign uncertainty to alternative potential locations. We considered two influenza case studies: H5N1 in Egypt; H1N1 pdm09 in North America. For each, we implemented scenarios in which 25 per cent of the taxa had different amounts of sampling uncertainty including 10, 30, and 50 per cent uncertainty and varied how it was distributed for each taxon. This includes scenarios that: (i) placed a specific amount of uncertainty on one location while uniformly distributing the remaining amount across all other candidate locations (correspondingly labeled 10, 30, and 50); (ii) assigned the remaining uncertainty to just one other location; thus ‘splitting’ the uncertainty among two locations (i.e. 10/90, 30/70, and 50/50); and (iii) eliminated uncertainty via two predefined heuristic approaches: assignment to a centroid location (CNTR) or the largest population in the country (POP). We compared all scenarios to a reference standard (RS) in which all taxa had known (absolutely certain) locations. From this, we implemented five random selections of 25 per cent of the taxa and used these for specifying uncertainty. We performed posterior analyses for each scenario, including: (a) virus persistence, (b) migration rates, (c) trunk rewards, and (d) the posterior probability of the root state. The scenarios with sampling uncertainty were closer to the RS than CNTR and POP. For H5N1, the absolute error of virus persistence had a median range of 0.005–0.047 for scenarios with sampling uncertainty—(i) and (ii) above—versus a range of 0.063–0.075 for CNTR and POP. Persistence for the pdm09 case study followed a similar trend as did our analyses of migration rates across scenarios (i) and (ii). When considering the posterior probability of the root state, we found all but one of the H5N1 scenarios with sampling uncertainty had agreement with the RS on the origin of the outbreak whereas both CNTR and POP disagreed. Our results suggest that assigning geospatial uncertainty to taxa benefits estimation of virus phylogeography as compared to ad-hoc heuristics. We also found that, in general, there was limited difference in results regardless of how the sampling uncertainty was assigned; uniform distribution or split between two locations did not greatly impact posterior results. This framework is available in BEAST v.1.10. In future work, we will explore viruses beyond influenza. We will also develop a web interface for researchers to use our language processing methods to find and assign uncertainty to alternative potential locations for virus phylogeography.
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Affiliation(s)
- Matthew Scotch
- College of Health Solutions, Arizona State University, 550 N. 3rd St., Phoenix, AZ, USA.,Biodesign Center for Environmental Health Engineering, Arizona State University, 727 E. Tyler St, Tempe, AZ, USA
| | - Tasnia Tahsin
- College of Health Solutions, Arizona State University, 550 N. 3rd St., Phoenix, AZ, USA
| | - Davy Weissenbacher
- Department of Biostatistics, Epidemiology, and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 423 Guardian Drive, Philadelphia, PA, USA
| | - Karen O'Connor
- Department of Biostatistics, Epidemiology, and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 423 Guardian Drive, Philadelphia, PA, USA
| | - Arjun Magge
- College of Health Solutions, Arizona State University, 550 N. 3rd St., Phoenix, AZ, USA.,Biodesign Center for Environmental Health Engineering, Arizona State University, 727 E. Tyler St, Tempe, AZ, USA
| | - Matteo Vaiente
- College of Health Solutions, Arizona State University, 550 N. 3rd St., Phoenix, AZ, USA.,Biodesign Center for Environmental Health Engineering, Arizona State University, 727 E. Tyler St, Tempe, AZ, USA
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, 621 Charles E. Young Dr. South, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Dr. South, Los Angeles, CA, USA.,Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, 650 Charles E Young Dr. South, Los Angeles, CA, USA
| | - Graciela Gonzalez-Hernandez
- Department of Biostatistics, Epidemiology, and Informatics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 423 Guardian Drive, Philadelphia, PA, USA
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8
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Wu T, Perrings C. The live poultry trade and the spread of highly pathogenic avian influenza: Regional differences between Europe, West Africa, and Southeast Asia. PLoS One 2018; 13:e0208197. [PMID: 30566454 PMCID: PMC6300203 DOI: 10.1371/journal.pone.0208197] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/13/2018] [Indexed: 01/21/2023] Open
Abstract
In the past two decades, avian influenzas have posed an increasing international threat to human and livestock health. In particular, highly pathogenic avian influenza H5N1 has spread across Asia, Africa, and Europe, leading to the deaths of millions of poultry and hundreds of people. The two main means of international spread are through migratory birds and the live poultry trade. We focus on the role played by the live poultry trade in the spread of H5N1 across three regions widely infected by the disease, which also correspond to three major trade blocs: the European Union (EU), the Economic Community of West African States (ECOWAS), and the Association of Southeast Asian Nations (ASEAN). Across all three regions, we found per-capita GDP (a proxy for modernization, general biosecurity, and value-at-risk) to be risk reducing. A more specific biosecurity measure-general surveillance-was also found to be mitigating at the all-regions level. However, there were important inter-regional differences. For the EU and ASEAN, intra-bloc live poultry imports were risk reducing while extra-bloc imports were risk increasing; for ECOWAS the reverse was true. This is likely due to the fact that while the EU and ASEAN have long-standing biosecurity standards and stringent enforcement (pursuant to the World Trade Organization's Agreement on the Application of Sanitary and Phytosanitary Measures), ECOWAS suffered from a lack of uniform standards and lax enforcement.
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Affiliation(s)
- Tong Wu
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Charles Perrings
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
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9
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A Fréchet tree distance measure to compare phylogeographic spread paths across trees. Sci Rep 2018; 8:17000. [PMID: 30451977 PMCID: PMC6242967 DOI: 10.1038/s41598-018-35421-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/01/2018] [Indexed: 11/29/2022] Open
Abstract
Phylogeographic methods reconstruct the origin and spread of taxa by inferring locations for internal nodes of the phylogenetic tree from sampling locations of genetic sequences. This is commonly applied to study pathogen outbreaks and spread. To evaluate such reconstructions, the inferred spread paths from root to leaf nodes should be compared to other methods or references. Usually, ancestral state reconstructions are evaluated by node-wise comparisons, therefore requiring the same tree topology, which is usually unknown. Here, we present a method for comparing phylogeographies across different trees inferred from the same taxa. We compare paths of locations by calculating discrete Fréchet distances. By correcting the distances by the number of paths going through a node, we define the Fréchet tree distance as a distance measure between phylogeographies. As an application, we compare phylogeographic spread patterns on trees inferred with different methods from hemagglutinin sequences of H5N1 influenza viruses, finding that both tree inference and ancestral reconstruction cause variation in phylogeographic spread that is not directly reflected by topological differences. The method is suitable for comparing phylogeographies inferred with different tree or phylogeographic inference methods to each other or to a known ground truth, thus enabling a quality assessment of such techniques.
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10
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Shi B, Zhan XM, Zheng JX, Qiu H, Liang D, Ye YM, Yang GJ, Liu Y, Liu J. Identifying key bird species and geographical hotspots of avian influenza A (H7N9) virus in China. Infect Dis Poverty 2018; 7:97. [PMID: 30305184 PMCID: PMC6180610 DOI: 10.1186/s40249-018-0480-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In China since the first human infection of avian influenza A (H7N9) virus was identified in 2013, it has caused serious public health concerns due to its wide spread and high mortality rate. Evidence shows that bird migration plays an essential role in global spread of avian influenza viruses. Accordingly, in this paper, we aim to identify key bird species and geographical hotspots that are relevant to the transmission of avian influenza A (H7N9) virus in China. METHODS We first conducted phylogenetic analysis on 626 viral sequences of avian influenza A (H7N9) virus isolated in chicken, which were collected from the Global Initiative on Sharing All Influenza Data (GISAID), to reveal geographical spread and molecular evolution of the virus in China. Then, we adopted the cross correlation function (CCF) to explore the relationship between the identified influenza A (H7N9) cases and the spatiotemporal distribution of migratory birds. Here, the spatiotemporal distribution of bird species was generated based on bird observation data collected from China Bird Reports, which consists of 157 272 observation records about 1145 bird species. Finally, we employed a kernel density estimator to identify geographical hotspots of bird habitat/stopover that are relevant to the influenza A (H7N9) infections. RESULTS Phylogenetic analysis reveals the evolutionary and geographical patterns of influenza A (H7N9) infections, where cases in the same or nearby municipality/provinces are clustered together with small evolutionary differences. Moreover, three epidemic waves in chicken along the East Asian-Australasian flyway in China are distinguished from the phylogenetic tree. The CCF analysis identifies possible migratory bird species that are relevant to the influenza A(H7N9) infections in Shanghai, Jiangsu, Zhejiang, Fujian, Jiangxi, and Guangdong in China, where the six municipality/provinces account for 91.2% of the total number of isolated H7N9 cases in chicken in GISAID. Based on the spatial distribution of identified bird species, geographical hotspots are further estimated and illustrated within these typical municipality/provinces. CONCLUSIONS In this paper, we have identified key bird species and geographical hotspots that are relevant to the spread of influenza A (H7N9) virus. The results and findings could provide sentinel signal and evidence for active surveillance, as well as strategic control of influenza A (H7N9) transmission in China.
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Affiliation(s)
- Benyun Shi
- School of Cyberspace, Hangzhou Dianzi University, Hangzhou, 310018, People's Republic of China.
| | - Xiao-Ming Zhan
- School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, 310018, People's Republic of China
| | - Jin-Xin Zheng
- Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, People's Republic of China
| | - Hongjun Qiu
- School of Cyberspace, Hangzhou Dianzi University, Hangzhou, 310018, People's Republic of China
| | - Dan Liang
- State Key Laboratory of Biocontrol, Department of Ecology and School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yan-Ming Ye
- School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, 310018, People's Republic of China
| | - Guo-Jing Yang
- Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, People's Republic of China.,Department of Epidemiology and Public Healthy, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Yang Liu
- State Key Laboratory of Biocontrol, Department of Ecology and School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Jiming Liu
- Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong, People's Republic of China.
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11
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Balasubramaniam K, Beisner B, Guan J, Vandeleest J, Fushing H, Atwill E, McCowan B. Social network community structure and the contact-mediated sharing of commensal E. coli among captive rhesus macaques ( Macaca mulatta). PeerJ 2018; 6:e4271. [PMID: 29372120 PMCID: PMC5775753 DOI: 10.7717/peerj.4271] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/27/2017] [Indexed: 01/17/2023] Open
Abstract
In group-living animals, heterogeneity in individuals' social connections may mediate the sharing of microbial infectious agents. In this regard, the genetic relatedness of individuals' commensal gut bacterium Escherichia coli may be ideal to assess the potential for pathogen transmission through animal social networks. Here we use microbial phylogenetics and population genetics approaches, as well as host social network reconstruction, to assess evidence for the contact-mediated sharing of E. coli among three groups of captively housed rhesus macaques (Macaca mulatta), at multiple organizational scales. For each group, behavioral data on grooming, huddling, and aggressive interactions collected for a six-week period were used to reconstruct social network communities via the Data Cloud Geometry (DCG) clustering algorithm. Further, an E. coli isolate was biochemically confirmed and genotypically fingerprinted from fecal swabs collected from each macaque. Population genetics approaches revealed that Group Membership, in comparison to intrinsic attributes like age, sex, and/or matriline membership of individuals, accounted for the highest proportion of variance in E. coli genotypic similarity. Social network approaches revealed that such sharing was evident at the community-level rather than the dyadic level. Specifically, although we found no links between dyadic E. coli similarity and social contact frequencies, similarity was significantly greater among macaques within the same social network communities compared to those across different communities. Moreover, tests for one of our study-groups confirmed that E. coli isolated from macaque rectal swabs were more genotypically similar to each other than they were to isolates from environmentally deposited feces. In summary, our results suggest that among frequently interacting, spatially constrained macaques with complex social relationships, microbial sharing via fecal-oral, social contact-mediated routes may depend on both individuals' direct connections and on secondary network pathways that define community structure. They lend support to the hypothesis that social network communities may act as bottlenecks to contain the spread of infectious agents, thereby encouraging disease control strategies to focus on multiple organizational scales. Future directions includeincreasing microbial sampling effort per individual to better-detect dyadic transmission events, and assessments of the co-evolutionary links between sociality, infectious agent risk, and host immune function.
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Affiliation(s)
- Krishna Balasubramaniam
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Brianne Beisner
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States of America
- Brain, Mind & Behavior, California National Primate Research Center, University of California, Davis, CA, United States of America
| | - Jiahui Guan
- Department of Statistics, University of California, Davis, CA, United States of America
| | - Jessica Vandeleest
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States of America
- Brain, Mind & Behavior, California National Primate Research Center, University of California, Davis, CA, United States of America
| | - Hsieh Fushing
- Department of Statistics, University of California, Davis, CA, United States of America
| | - Edward Atwill
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Brenda McCowan
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States of America
- Brain, Mind & Behavior, California National Primate Research Center, University of California, Davis, CA, United States of America
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12
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Hu M, Jin Y, Zhou J, Huang Z, Li B, Zhou W, Ren H, Yue J, Liang L. Genetic Characteristic and Global Transmission of Influenza A H9N2 Virus. Front Microbiol 2017; 8:2611. [PMID: 29312274 PMCID: PMC5744263 DOI: 10.3389/fmicb.2017.02611] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/14/2017] [Indexed: 11/20/2022] Open
Abstract
The H9N2 virus has been demonstrated to donate its genes to other subtypes of influenza A virus, forming new reassortant virus which may infect human beings. Understanding the genetic characteristic and the global transmission patterns of the virus would guide the prevention and control of potentially emerging avian influenza A virus. In this paper, we hierarchically classified the evolution of the H9N2 virus into three main lineages based on the phylogenetic characteristics of the virus. Due to the distribution of sampling locations, we named the three lineages as Worldwide lineage, Asia-Africa lineage, and China lineage. Codon usage analysis and selective positive site analysis of the lineages further showed the lineage-specific evolution of the virus. We reconstructed the transmission routes of the virus in the three lineages through phylogeography analysis, by which several epicenters for migration of the virus were identified. The hierarchical classification of the lineages implied a possible original seeding process of the virus, starting from the Worldwide lineages to the Asian-Africa lineages and to the China lineages. In the process of H9N2 virus global transmission, the United States was the origin of the virus. China Mainland, Hong Kong SAR, Japan, and Korea were important transfer centers. Based on both the transmission route and the distribution of the hosts in each lineage, we concluded that the wild birds' migration has contributed much to the long-distance global spread of the virus, while poultry trade and people's lifestyle may have contributed to the relatively short-distance transmission in some areas of the Asia and Africa.
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Affiliation(s)
- Mingda Hu
- Laboratory of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Yuan Jin
- Laboratory of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Jing Zhou
- Laboratory of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Zhisong Huang
- Laboratory of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Beiping Li
- Laboratory of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Wei Zhou
- Laboratory of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Hongguang Ren
- Laboratory of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Junjie Yue
- Laboratory of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
| | - Long Liang
- Laboratory of Genetic Engineering, Beijing Institute of Biotechnology, Beijing, China
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13
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Abstract
BACKGROUND Little is known about the phylogeography of norovirus (NoV) in China. In norovirus, a clear understanding for the characteristics of tree topology, migration patterns and its demographic dynamics in viral circulation are needed to identify its prevalence trends, which can help us better prepare for its epidemics as well as develop useful control strategies. The aim of this study was to explore the genetic diversity, temporal distribution, demographic dynamics and migration patterns of NoV that circulated in China. RESULTS Our analysis showed that two major genogroups, GI and GII, were identified in China, in which GII.3, GII.4 and GII.17 accounted for the majority with a total proportion around 70%. Our demography inference suggested that during the long-term migration process, NoV evolved into multiple lineages and then experienced a selective sweep, which reduced its genetic diversity. The phylogeography results suggested that the norovirus may have originated form the South China (Hong Kong and Guangdong), followed by multicenter direction outbreaks across the country. CONCLUSIONS From these analyses, we indicate that domestic poultry trade and frequent communications of people from different regions have all contributed to the spread of the NoV in China. Together with recent advances in phylogeographic inference, our researches also provide powerful illustrations of how coalescent-based methods can extract adequate information in molecular epidemiology.
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Affiliation(s)
- Niu Qiao
- Key Laboratory of Medical Molecular Virology of MoE & MoH and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, 138 Yi Xue Yuan Rd, Shanghai, 200032 People’s Republic of China
| | - He Ren
- Key Laboratory of Medical Molecular Virology of MoE & MoH and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, 138 Yi Xue Yuan Rd, Shanghai, 200032 People’s Republic of China
- Shanghai University of Medicine & Health Sciences, Shanghai, 201318 People’s Republic of China
| | - Lei Liu
- Key Laboratory of Medical Molecular Virology of MoE & MoH and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, 138 Yi Xue Yuan Rd, Shanghai, 200032 People’s Republic of China
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14
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Brown I, Mulatti P, Smietanka K, Staubach C, Willeberg P, Adlhoch C, Candiani D, Fabris C, Zancanaro G, Morgado J, Verdonck F. Avian influenza overview October 2016-August 2017. EFSA J 2017; 15:e05018. [PMID: 32625308 PMCID: PMC7009863 DOI: 10.2903/j.efsa.2017.5018] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The A(H5N8) highly pathogenic avian influenza (HPAI) epidemic occurred in 29 European countries in 2016/2017 and has been the largest ever recorded in the EU in terms of number of poultry outbreaks, geographical extent and number of dead wild birds. Multiple primary incursions temporally related with all major poultry sectors affected but secondary spread was most commonly associated with domestic waterfowl species. A massive effort of all the affected EU Member States (MSs) allowed a descriptive epidemiological overview of the cases in poultry, captive birds and wild birds, providing also information on measures applied at the individual MS level. Data on poultry population structure are required to facilitate data and risk factor analysis, hence to strengthen science-based advice to risk managers. It is suggested to promote common understanding and application of definitions related to control activities and their reporting across MSs. Despite a large number of human exposures to infected poultry occurred during the ongoing outbreaks, no transmission to humans has been identified. Monitoring the avian influenza (AI) situation in other continents indicated a potential risk of long-distance spread of HPAI virus (HPAIV) A(H5N6) from Asia to wintering grounds towards Western Europe, similarly to what happened with HPAIV A(H5N8) and HPAIV A(H5N1) in previous years. Furthermore, the HPAI situation in Africa with A(H5N8) and A(H5N1) is rapidly evolving. Strengthening collaborations at National, EU and Global levels would allow close monitoring of the AI situation, ultimately helping to increase preparedness. No human case was reported in the EU due to AIVs subtypes A(H5N1), A(H5N6), A(H7N9) and A(H9N2). Direct transmission of these viruses to humans has only been reported in areas, mainly in Asia and Egypt, with a substantial involvement of wild bird and/or poultry populations. It is suggested to improve the collection and reporting of exposure events of people to AI.
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15
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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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16
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Fourment M, Darling AE, Holmes EC. The impact of migratory flyways on the spread of avian influenza virus in North America. BMC Evol Biol 2017; 17:118. [PMID: 28545432 PMCID: PMC5445350 DOI: 10.1186/s12862-017-0965-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/11/2017] [Indexed: 11/16/2022] Open
Abstract
Background Wild birds are the major reservoir hosts for influenza A viruses (AIVs) and have been implicated in the emergence of pandemic events in livestock and human populations. Understanding how AIVs spread within and across continents is therefore critical to the development of successful strategies to manage and reduce the impact of influenza outbreaks. In North America many bird species undergo seasonal migratory movements along a North-South axis, thereby providing opportunities for viruses to spread over long distances. However, the role played by such avian flyways in shaping the genetic structure of AIV populations remains uncertain. Results To assess the relative contribution of bird migration along flyways to the genetic structure of AIV we performed a large-scale phylogeographic study of viruses sampled in the USA and Canada, involving the analysis of 3805 to 4505 sequences from 36 to 38 geographic localities depending on the gene segment data set. To assist in this we developed a maximum likelihood-based genetic algorithm to explore a wide range of complex spatial models, depicting a more complete picture of the migration network than determined previously. Conclusions Based on phylogenies estimated from nucleotide sequence data sets, our results show that AIV migration rates are significantly higher within than between flyways, indicating that the migratory patterns of birds play a key role in viral dispersal. These findings provide valuable insights into the evolution, maintenance and transmission of AIVs, in turn allowing the development of improved programs for surveillance and risk assessment.
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Affiliation(s)
- Mathieu Fourment
- ithree institute, University of Technology Sydney, Sydney, Australia. .,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, Australia.
| | - Aaron E Darling
- ithree institute, University of Technology Sydney, Sydney, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
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17
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Byrne AQ, Rothstein AP, Poorten TJ, Erens J, Settles ML, Rosenblum EB. Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus
Batrachochytrium dendrobatidis. Mol Ecol Resour 2017; 17:1283-1292. [DOI: 10.1111/1755-0998.12675] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/26/2016] [Accepted: 03/15/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Allison Q. Byrne
- Department of Environmental Science Policy and Management University of California, Berkeley Berkeley CA USA
| | - Andrew P. Rothstein
- Department of Environmental Science Policy and Management University of California, Berkeley Berkeley CA USA
| | - Thomas J. Poorten
- Department of Environmental Science Policy and Management University of California, Berkeley Berkeley CA USA
| | - Jesse Erens
- Department of Environmental Science Policy and Management University of California, Berkeley Berkeley CA USA
- Wageningen University Wageningen The Netherlands
| | | | - Erica Bree Rosenblum
- Department of Environmental Science Policy and Management University of California, Berkeley Berkeley CA USA
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18
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Abente EJ, Kitikoon P, Lager KM, Gauger PC, Anderson TK, Vincent AL. A highly pathogenic avian-derived influenza virus H5N1 with 2009 pandemic H1N1 internal genes demonstrates increased replication and transmission in pigs. J Gen Virol 2017; 98:18-30. [PMID: 28206909 DOI: 10.1099/jgv.0.000678] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
This study investigated the pathogenicity and transmissibility of a reverse-genetics-derived highly pathogenic avian influenza (HPAI) H5N1 lineage influenza A virus that was isolated from a human, A/Iraq/755/06. We also examined surface gene reassortant viruses composed of the haemagglutinin and neuraminidase from A/Iraq/755/06 and the internal genes of a 2009 pandemic H1N1 virus, A/New York/18/2009 (2Iraq/06 : 6NY/09 H5N1), and haemagglutinin and neuraminidase from A/New York/18/2009 with the internal genes of A/Iraq/755/06 (2NY/09 : 6Iraq/06 H1N1). The parental A/Iraq/755/06 caused little to no lesions in swine, limited virus replication was observed in the upper respiratory and lower respiratory tracts and transmission was detected in 3/5 direct-contact pigs based on seroconversion, detection of viral RNA or virus isolation. In contrast, the 2Iraq/06 : 6NY/09 H5N1 reassortant caused mild lung lesions, demonstrated sustained virus replication in the upper and lower respiratory tracts and transmitted to all contacts (5/5). The 2NY/09 : 6Iraq/06 H1N1 reassortant also caused mild lung lesions, there was evidence of virus replication in the upper respiratory and lower respiratory tracts and transmission was detected in all contacts (5/5). These studies indicate that an HPAI-derived H5N1 reassortant with pandemic internal genes may be more successful in sustaining infection in swine and that HPAI-derived internal genes were marginally compatible with pandemic 2009 H1N1 surface genes. Comprehensive surveillance in swine is critical to identify a possible emerging HPAI reassortant in all regions with HPAI in wild birds and poultry and H1N1pdm09 in pigs or other susceptible hosts.
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Affiliation(s)
- Eugenio J Abente
- Virus and Prion Research Unit, USDA, Agricultural Research Service, National Animal Disease Center, Ames, Iowa, USA
| | - Pravina Kitikoon
- Present address: Merck Animal Health, De Soto, Kansas, USA.,Virus and Prion Research Unit, USDA, Agricultural Research Service, National Animal Disease Center, Ames, Iowa, USA
| | - Kelly M Lager
- Virus and Prion Research Unit, USDA, Agricultural Research Service, National Animal Disease Center, Ames, Iowa, USA
| | - Phillip C Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Tavis K Anderson
- Virus and Prion Research Unit, USDA, Agricultural Research Service, National Animal Disease Center, Ames, Iowa, USA
| | - Amy L Vincent
- Virus and Prion Research Unit, USDA, Agricultural Research Service, National Animal Disease Center, Ames, Iowa, USA
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19
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Peng Y, Li X, Zhou H, Wu A, Dong L, Zhang Y, Gao R, Bo H, Yang L, Wang D, Lin X, Jin M, Shu Y, Jiang T. Continual Antigenic Diversification in China Leads to Global Antigenic Complexity of Avian Influenza H5N1 Viruses. Sci Rep 2017; 7:43566. [PMID: 28262734 PMCID: PMC5337931 DOI: 10.1038/srep43566] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/25/2017] [Indexed: 12/31/2022] Open
Abstract
The highly pathogenic avian influenza (HPAI) H5N1 virus poses a significant potential threat to human society due to its wide spread and rapid evolution. In this study, we present a comprehensive antigenic map for HPAI H5N1 viruses including 218 newly sequenced isolates from diverse regions of mainland China, by computationally separating almost all HPAI H5N1 viruses into 15 major antigenic clusters (ACs) based on their hemagglutinin sequences. Phylogenetic analysis showed that 12 of these 15 ACs originated in China in a divergent pattern. Further analysis of the dissemination of HPAI H5N1 virus in China identified that the virus's geographic expansion was co-incident with a significant divergence in antigenicity. Moreover, this antigenic diversification leads to global antigenic complexity, as typified by the recent HPAI H5N1 spread, showing extensive co-circulation and local persistence. This analysis has highlighted the challenge in H5N1 prevention and control that requires different planning strategies even inside China.
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Affiliation(s)
- Yousong Peng
- College of Biology, Human University, Changsha, 410082, China
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaodan Li
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China
| | - Hongbo Zhou
- College of Animal Science & Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Aiping Wu
- Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China
| | - Libo Dong
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China
| | - Ye Zhang
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China
| | - Rongbao Gao
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China
| | - Hong Bo
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China
| | - Xian Lin
- College of Animal Science & Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meilin Jin
- College of Animal Science & Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuelong Shu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 100052, China
| | - Taijiao Jiang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Center of System Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
- Suzhou Institute of Systems Medicine, Suzhou, Jiangsu, 215123, China
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20
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Magiorkinis G, Angelis K, Mamais I, Katzourakis A, Hatzakis A, Albert J, Lawyer G, Hamouda O, Struck D, Vercauteren J, Wensing A, Alexiev I, Åsjö B, Balotta C, Gomes P, Camacho RJ, Coughlan S, Griskevicius A, Grossman Z, Horban A, Kostrikis LG, Lepej SJ, Liitsola K, Linka M, Nielsen C, Otelea D, Paredes R, Poljak M, Puchhammer-Stöckl E, Schmit JC, Sönnerborg A, Staneková D, Stanojevic M, Stylianou DC, Boucher CAB, Nikolopoulos G, Vasylyeva T, Friedman SR, van de Vijver D, Angarano G, Chaix ML, de Luca A, Korn K, Loveday C, Soriano V, Yerly S, Zazzi M, Vandamme AM, Paraskevis D. The global spread of HIV-1 subtype B epidemic. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2016; 46:169-179. [PMID: 27262355 PMCID: PMC5157885 DOI: 10.1016/j.meegid.2016.05.041] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/25/2016] [Accepted: 05/31/2016] [Indexed: 01/04/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) was discovered in the early 1980s when the virus had already established a pandemic. For at least three decades the epidemic in the Western World has been dominated by subtype B infections, as part of a sub-epidemic that traveled from Africa through Haiti to United States. However, the pattern of the subsequent spread still remains poorly understood. Here we analyze a large dataset of globally representative HIV-1 subtype B strains to map their spread around the world over the last 50years and describe significant spread patterns. We show that subtype B travelled from North America to Western Europe in different occasions, while Central/Eastern Europe remained isolated for the most part of the early epidemic. Looking with more detail in European countries we see that the United Kingdom, France and Switzerland exchanged viral isolates with non-European countries than with European ones. The observed pattern is likely to mirror geopolitical landmarks in the post-World War II era, namely the rise and the fall of the Iron Curtain and the European colonialism. In conclusion, HIV-1 spread through specific migration routes which are consistent with geopolitical factors that affected human activities during the last 50years, such as migration, tourism and trade. Our findings support the argument that epidemic control policies should be global and incorporate political and socioeconomic factors.
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Affiliation(s)
| | - Konstantinos Angelis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Ioannis Mamais
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | | | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Glenn Lawyer
- Department of Computational Biology, Max Planck Institute for Informatics, Saarbrücken, Germany
| | | | - Daniel Struck
- Centre de Recherche Public de la Sante, Luxembourg, Luxembourg
| | - Jurgen Vercauteren
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Annemarie Wensing
- Department of Virology, University Medical Center, Utrecht, The Netherlands
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | | | - Perpétua Gomes
- Molecular Biology Lab, LMCBM, SPC, HEM, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Ricardo J Camacho
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | | | | | | | | | | | - Snjezana J Lepej
- Department of Molecular Diagnostics and Flow Cytometry, University Hospital for Infectious Diseases "Dr. F. Mihaljevic", Zagreb, Croatia
| | - Kirsi Liitsola
- National Institute of Health and Welfare, Helsinki, Finland
| | - Marek Linka
- National Reference Laboratory of AIDS, National Institute of Health, Prague, Czech Republic
| | | | - Dan Otelea
- National Institute for Infectious Diseases "Prof. Dr. Matei Bals", Bucharest, Romania
| | | | - Mario Poljak
- Slovenian HIV/AIDS Reference Centre, University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
| | | | | | - Anders Sönnerborg
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Divisions of Infectious Diseases and Clinical Virology, Karolinska Institute, Stockholm, Sweden
| | | | - Maja Stanojevic
- University of Belgrade Faculty of Medicine, Belgrade, Serbia
| | | | | | - Georgios Nikolopoulos
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | | | - Samuel R Friedman
- Institute of Infectious Diseases Research, National Development and Research Institutes, Inc., New York, USA
| | - David van de Vijver
- Eijkman Winkler Institute, Department of Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Andrea de Luca
- Institute of Clinical Infectious Diseases, Catholic university, Rome, Italy
| | - Klaus Korn
- University of Erlangen, Erlangen, Germany
| | - Clive Loveday
- International Clinical Virology Centre, Buckinghamshire, England, United Kingdom
| | | | | | | | - Anne-Mieke Vandamme
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece.
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21
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Shi J, Hu S, Liu X, Yang J, Liu D, Wu L, Wang H, Hu Z, Deng F, Shen S. Migration, recombination, and reassortment are involved in the evolution of severe fever with thrombocytopenia syndrome bunyavirus. INFECTION GENETICS AND EVOLUTION 2016; 47:109-117. [PMID: 27884653 DOI: 10.1016/j.meegid.2016.11.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/15/2016] [Accepted: 11/16/2016] [Indexed: 01/20/2023]
Abstract
Severe fever with thrombocytopenia syndrome bunyavirus (SFTSV) has been identified as the etiological agent causing severe fever with thrombocytopenia syndrome (SFTS). SFTSV was reported in recent years as a newly emerging tick-borne virus in China, Japan and South Korea and is a novel member of the genus Phlebovirus, family Bunyaviridae, which is suspected to be transmitted by the tick Haemaphysalis longicornis. The genetic diversity and evolutionary relationships between geographically distributed SFTSV strains are currently unclear. In this study we used extensive bioinformatics analyses to provide deep insight into the mechanisms of evolution and relationships among SFTSV strains. The genetic diversity of SFTSV was characterized and found to be generated through recombination and reassortment events. Further, potential correlations between the geographic distribution and migration pathways of SFTSV were subject to in-depth analysis. The potential of birds migration related to SFTSV migration were also discussed. The results of this study will facilitate better understanding of the mechanisms of evolution of SFTSV, which will be important in developing public-health interventions and strategies for SFTS disease control and prevention in endemic areas.
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Affiliation(s)
- Junming Shi
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Sheng Hu
- School of Information Engineering, China University of Geosciences, Wuhan, PR China
| | - Xiaoping Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Juan Yang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Dan Liu
- School of Medicine, Wuhan University of Science and Technology, Wuhan, PR China
| | - Liang Wu
- School of Information Engineering, China University of Geosciences, Wuhan, PR China
| | - Hualin Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhihong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Fei Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Shu Shen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
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Paraskevis D, Nikolopoulos GK, Magiorkinis G, Hodges-Mameletzis I, Hatzakis A. The application of HIV molecular epidemiology to public health. INFECTION GENETICS AND EVOLUTION 2016; 46:159-168. [PMID: 27312102 DOI: 10.1016/j.meegid.2016.06.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 02/02/2023]
Abstract
HIV is responsible for one of the largest viral pandemics in human history. Despite a concerted global response for prevention and treatment, the virus persists. Thus, urgent public health action, utilizing novel interventions, is needed to prevent future transmission events, critical to eliminating HIV. For public health planning to prove effective and successful, we need to understand the dynamics of regional epidemics and to intervene appropriately. HIV molecular epidemiology tools as implemented in phylogenetic, phylodynamic and phylogeographic analyses have proven to be powerful tools in public health planning across many studies. Numerous applications with HIV suggest that molecular methods alone or in combination with mathematical modelling can provide inferences about the transmission dynamics, critical epidemiological parameters (prevalence, incidence, effective number of infections, Re, generation times, time between infection and diagnosis), or the spatiotemporal characteristics of epidemics. Molecular tools have been used to assess the impact of an intervention and outbreak investigation which are of great public health relevance. In some settings, molecular sequence data may be more readily available than HIV surveillance data, and can therefore allow for molecular analyses to be conducted more easily. Nonetheless, classic methods have an integral role in monitoring and evaluation of public health programmes, and should supplement emerging techniques from the field of molecular epidemiology. Importantly, molecular epidemiology remains a promising approach in responding to viral diseases.
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Affiliation(s)
- D Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
| | - G K Nikolopoulos
- Hellenic Center for Diseases Control and Prevention, Maroussi, Greece
| | - G Magiorkinis
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, Oxford, United Kingdom
| | | | - A Hatzakis
- Hellenic Center for Diseases Control and Prevention, Maroussi, Greece
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23
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Cheng J, Qi X, Chen D, Xu X, Wang G, Dai Y, Cui D, Chen Q, Fan P, Ni L, Liu M, Zhu F, Yang M, Wang C, Li Y, Sun C, Wang Z. Epidemiology and transmission characteristics of human adenovirus type 7 caused acute respiratory disease outbreak in military trainees in East China. Am J Transl Res 2016; 8:2331-2342. [PMID: 27347341 PMCID: PMC4891446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/04/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Human adenovirus type 7 (HAdV7) is globally attracting great concern as its high morbidity and severity in respiratory diseases, especially in Asia. OBJECTIVE To investigate the clinical and epidemiologic characteristics of HAdV7 infection outbreak in East China. METHODS The clinical samples were collected from the patients of an ARD outbreak in East Chinafor the detection of causative pathogens by multiplex PCR. The molecular type of human adenovirus isolates were identified by sequencing and homologous comparison based on their hexon genes. The spatiotemporal dynamics of global HAdV7 was investigated using the phylogenetic and phylogeographic analyses. Total 67 referenced HAdV7 hexon sequences (>800 bp) from GenBank were selected for constructing the maximum likelihood tree by MEGA 5.1.0, grouped according to the tree topology for the further migration analysis by PAUP* 4.0 and MigraPhyla 1.0 b to understand the transmission patterns of HAdV7 in global epidemics. RESULTS The results showed HAdV7 as the causative pathogen in this outbreak, and the outbreak strains had the hexon sequences highly identical with the isolates in Shaanxi (2012). The origin of HAdV7 was inferred as California, meanwhile a total of 21 migration routes were acquired. HAdV7 in this outbreak was statistically proven dispersed from Shaanxi province (2012). CONCLUSIONS The analyses of epidemiology and transmission pattern of HAdV7 would not only enrich the molecular biological basic database but also provide theoretical basis for HAdV7 prevention and control strategy.
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Affiliation(s)
- Jun Cheng
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou, China
- Department of Clinical Laboratory Science, The 117th Hospital of PLAHangzhou,China
| | - Xiaoping Qi
- Department of Respiratory Medicine, The 117th Hospital of PLAHangzhou, China
| | - Dawei Chen
- Department of Respiratory Medicine, The 117th Hospital of PLAHangzhou, China
| | - Xujian Xu
- Department of Biotechnology, The University of TokyoTokyo, Japan
| | - Guozheng Wang
- Department of Clinical Laboratory Science, The 117th Hospital of PLAHangzhou,China
| | - Yuzhu Dai
- Department of Clinical Laboratory Science, The 117th Hospital of PLAHangzhou,China
| | - Dawei Cui
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang UniversityHangzhou, China
| | - Qingyong Chen
- Department of Respiratory Medicine, The 117th Hospital of PLAHangzhou, China
| | - Ping Fan
- Department of Infectious Diseases, The 113rd Hospital of PLANingbo, China
| | - Liuda Ni
- Department of Infectious Diseases, The 85th Hospital of PLAShanghai, China
| | - Miao Liu
- Department of Radio Diagnosis and Imaging, The 117th Hospital of PLAHangzhou, China
| | - Feiyan Zhu
- Department of Infectious Diseases, The 117th Hospital of PLAHangzhou, China
| | - Mei Yang
- Department of Epidemiology and Infection Control, The 117th Hospital of PLAHangzhou, China
| | - Changjun Wang
- Institute of Military Medical Sciences of Nanjing Military CommandNanjing, China
| | - Yuexi Li
- Center for Disease Control and Prevention of Nanjing Military CommandNanjing, China
| | - Changgui Sun
- Department of Clinical Laboratory Science, The 117th Hospital of PLAHangzhou,China
| | - Zhongyong Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou, China
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24
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Shen S, Shi J, Wang J, Tang S, Wang H, Hu Z, Deng F. Phylogenetic analysis revealed the central roles of two African countries in the evolution and worldwide spread of Zika virus. Virol Sin 2016; 31:118-30. [PMID: 27129451 DOI: 10.1007/s12250-016-3774-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 04/21/2016] [Indexed: 12/21/2022] Open
Abstract
Recent outbreaks of Zika virus (ZIKV) infections in Oceania's islands and the Americas were characterized by high numbers of cases and the spread of the virus to new areas. To better understand the origin of ZIKV, its epidemic history was reviewed. Although the available records and information are limited, two major genetic lineages of ZIKV were identified in previous studies. However, in this study, three lineages were identified based on a phylogenetic analysis of all virus sequences from GenBank, including those of the envelope protein (E) and non-structural protein 5 (NS5) coding regions. The spatial and temporal distributions of the three identified ZIKV lineages and the recombination events and mechanisms underlying their divergence and evolution were further elaborated. The potential migration pathway of ZIKV was also characterized. Our findings revealed the central roles of two African countries, Senegal and Cote d'Ivoire, in ZIKV evolution and genotypic divergence. Furthermore, our results suggested that the outbreaks in Asia and the Pacific islands originated from Africa. The results provide insights into the geographic origins of ZIKV outbreaks and the spread of the virus, and also contribute to a better understanding of ZIKV evolution, which is important for the prevention and control of ZIKV infections.
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Affiliation(s)
- Shu Shen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Junming Shi
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jun Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Shuang Tang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hualin Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhihong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Fei Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
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25
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Li X, Zhang Z, Yu A, Ho SYW, Carr MJ, Zheng W, Zhang Y, Zhu C, Lei F, Shi W. Global and local persistence of influenza A(H5N1) virus. Emerg Infect Dis 2016; 20:1287-95. [PMID: 25061965 PMCID: PMC4111173 DOI: 10.3201/eid2008.130910] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
An understanding of the global migration dynamics of highly pathogenic avian influenza A(H5N1) virus is helpful for surveillance and disease prevention. To characterize the migration network of this virus, we used genetic analysis, which supported a global persistence model in which each of 9 regions acts to some extent as a source. Siberia is the major hub for the dispersal of the virus. Southeast Asia and Africa are major sources of genetically and antigenically novel strains. We found evidence of local persistence of the virus in Southeast Asia and Africa, which is rare for human influenza A viruses. The differences in migration dynamics between avian and human influenza viruses might help with the design of region-specific surveillance efforts and the selection of vaccine candidates.
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Affiliation(s)
| | | | | | | | | | | | | | - Chaodong Zhu
- These authors contributed equally to this article
| | - Fumin Lei
- These authors contributed equally to this article
| | - Weifeng Shi
- These authors contributed equally to this article
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26
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Arafa A, El-Masry I, Kholosy S, Hassan MK, Dauphin G, Lubroth J, Makonnen YJ. Phylodynamics of avian influenza clade 2.2.1 H5N1 viruses in Egypt. Virol J 2016; 13:49. [PMID: 27000533 PMCID: PMC4802640 DOI: 10.1186/s12985-016-0477-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 01/26/2016] [Indexed: 12/03/2022] Open
Abstract
Background Highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype are widely distributed within poultry populations in Egypt and have caused multiple human infections. Linking the epidemiological and sequence data is important to understand the transmission, persistence and evolution of the virus. This work describes the phylogenetic dynamics of H5N1 based on molecular characterization of the hemagglutinin (HA) gene of isolates collected from February 2006 to May 2014. Methods Full-length HA sequences of 368 H5N1 viruses were generated and were genetically analysed to study their genetic evolution. They were collected from different poultry species, production sectors, and geographic locations in Egypt. The Bayesian Markov Chain Monte Carlo (BMCMC) method was applied to estimate the evolutionary rates among different virus clusters; additionally, an analysis of selection pressures in the HA gene was performed using the Single Likelihood Ancestor Counting (SLAC) method. Results The phylogenetic analysis of the H5 gene from 2006–14 indicated the presence of one virus introduction of the classic clade (2.2.1) from which two main subgroups were originated, the variant subgroup which was further subdivided into 2 sub-divisions (2.2.1.1 and 2.2.1.1a) and the endemic subgroup (2.2.1.2). The clade 2.2.1.2 showed a high evolution rate over a period of 6 years (6.9 × 10−3 sub/site/year) in comparison to the 2.2.1.1a variant cluster (7.2 × 10−3 over a period of 4 years). Those two clusters are under positive selection as they possess 5 distinct positively selected sites in the HA gene. The mutations at 120, 154, and 162 HA antigenic sites and the other two mutations (129∆, I151T) that occurred from 2009–14 were found to be stable in the 2.2.1.2 clade. Additionally, 13 groups of H5N1 HPAI viruses were identified based on their amino acid sequences at the cleavage site and “EKRRKKR” became the dominant pattern beginning in 2013. Conclusions Continuous evolution of H5N1 HPAI viruses in Egypt has been observed in all poultry farming and production systems in almost all regions of the country. The wide circulation of the 2.2.1.2 clade carrying triple mutations (120, 129∆, I151T) associated with increased binding affinity to human receptors is an alarming finding of public health importance. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0477-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Abdelsatar Arafa
- Food and Agriculture Organization of the United Nations (FAO) - Emergency Center of Transboundary Animal Diseases (ECTAD), 11 Al Eslah El Zerai St, P.O. Box, 2223, Giza, Egypt. .,National Laboratory for Veterinary Quality Control on Poultry Production (NLQP), Animal Health Research Institute, P.O. Box, 264, Giza, Egypt.
| | - Ihab El-Masry
- Food and Agriculture Organization of the United Nations (FAO) - Emergency Center of Transboundary Animal Diseases (ECTAD), 11 Al Eslah El Zerai St, P.O. Box, 2223, Giza, Egypt
| | - Shereen Kholosy
- National Laboratory for Veterinary Quality Control on Poultry Production (NLQP), Animal Health Research Institute, P.O. Box, 264, Giza, Egypt
| | - Mohammed K Hassan
- National Laboratory for Veterinary Quality Control on Poultry Production (NLQP), Animal Health Research Institute, P.O. Box, 264, Giza, Egypt
| | - Gwenaelle Dauphin
- Food and Agriculture Organization of the United Nations (FAO), Viale delle Terme di Caracalla, 00153, Rome, Italy
| | - Juan Lubroth
- Food and Agriculture Organization of the United Nations (FAO), Viale delle Terme di Caracalla, 00153, Rome, Italy
| | - Yilma J Makonnen
- Food and Agriculture Organization of the United Nations (FAO) - Emergency Center of Transboundary Animal Diseases (ECTAD), 11 Al Eslah El Zerai St, P.O. Box, 2223, Giza, Egypt.
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27
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Millman AJ, Havers F, Iuliano AD, Davis CT, Sar B, Sovann L, Chin S, Corwin AL, Vongphrachanh P, Douangngeun B, Lindblade KA, Chittaganpitch M, Kaewthong V, Kile JC, Nguyen HT, Pham DV, Donis RO, Widdowson MA. Detecting Spread of Avian Influenza A(H7N9) Virus Beyond China. Emerg Infect Dis 2016; 21:741-9. [PMID: 25897654 PMCID: PMC4412232 DOI: 10.3201/eid2105.141756] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This virus is unlikely to have spread substantially among humans in Vietnam, Thailand, Cambodia, and Laos. During February 2013–March 2015, a total of 602 human cases of low pathogenic avian influenza A(H7N9) were reported; no autochthonous cases were reported outside mainland China. In contrast, since highly pathogenic avian influenza A(H5N1) reemerged during 2003 in China, 784 human cases in 16 countries and poultry outbreaks in 53 countries have been reported. Whether the absence of reported A(H7N9) outside mainland China represents lack of spread or lack of detection remains unclear. We compared epidemiologic and virologic features of A(H5N1) and A(H7N9) and used human and animal influenza surveillance data collected during April 2013–May 2014 from 4 Southeast Asia countries to assess the likelihood that A(H7N9) would have gone undetected during 2014. Surveillance in Vietnam and Cambodia detected human A(H5N1) cases; no A(H7N9) cases were detected in humans or poultry in Southeast Asia. Although we cannot rule out the possible spread of A(H7N9), substantial spread causing severe disease in humans is unlikely.
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28
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Crevar CJ, Carter DM, Lee KYJ, Ross TM. Cocktail of H5N1 COBRA HA vaccines elicit protective antibodies against H5N1 viruses from multiple clades. Hum Vaccin Immunother 2015; 11:572-83. [PMID: 25671661 DOI: 10.1080/21645515.2015.1012013] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Pandemic outbreaks of influenza are caused by the emergence of a pathogenic and transmissible virus to which the human population is immunologically naïve. Recent outbreaks of highly pathogenic avian influenza (HPAI) of the H5N1 subtype are of particular concern because of the high mortality rate (60% case fatality rate) and novel subtype. In this study, we have engineered an influenza virus-like particle (VLP) that contains a synthetic, consensus-based HA molecule using a new methodology, computationally optimized broadly reactive antigen (COBRA). Three COBRA H5N1 HA proteins have been engineered based upon (1) human clade 2 H5N1 sequences, (2) human and avian clade 2 sequences, and (3) all H5N1 influenza sequences recorded between 2005-2008. Each hemagglutinin protein retained the ability to bind the appropriate receptors, as well as the ability to mediate particle fusion, following purification from a mammalian expression system. COBRA VLP vaccines were administered to mice and the humoral immune responses were compared to those induced by VLPs containing an HA derived from a primary viral isolate. Using a single vaccination (0.6 ug HA dose with an adjuvant) all animals vaccinated with COBRA clade 2 HA H5N1 VLPs had protective levels of HAI antibodies to a representative isolate from each subclade of clade 2, but lower titers against other clades. The addition of avian sequences from other clades expanded breadth of HAI antibodies to the divergent clades, but still not all of the 25 H5N1 viruses in the panel were recognized by antibodies elicited any one H5N1 COBRA VLP vaccine. Vaccination of mice with a cocktail of all 3 COBRA HA VLP vaccines, in a prime-boost regimen, elicited an average HAI titer greater than 1:40 against all 25 viruses. Collectively, our findings indicate that the elicited antibody response following VLP vaccination with all 3 COBRA HA vaccine simultaneously elicited a broadly-reactive set of antibodies that recognized H5N1 viruses from 11 H5N1 clades/subclades isolated over a 12-year span.
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Affiliation(s)
- Corey J Crevar
- a Vaccine and Gene Therapy Institute of Florida ; Port St. Lucie , FL USA
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29
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Trovão NS, Suchard MA, Baele G, Gilbert M, Lemey P. Bayesian Inference Reveals Host-Specific Contributions to the Epidemic Expansion of Influenza A H5N1. Mol Biol Evol 2015; 32:3264-75. [PMID: 26341298 DOI: 10.1093/molbev/msv185] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Since its first isolation in 1996 in Guangdong, China, the highly pathogenic avian influenza virus (HPAIV) H5N1 has circulated in avian hosts for almost two decades and spread to more than 60 countries worldwide. The role of different avian hosts and the domestic-wild bird interface has been critical in shaping the complex HPAIV H5N1 disease ecology, but remains difficult to ascertain. To shed light on the large-scale H5N1 transmission patterns and disentangle the contributions of different avian hosts on the tempo and mode of HPAIV H5N1 dispersal, we apply Bayesian evolutionary inference techniques to comprehensive sets of hemagglutinin and neuraminidase gene sequences sampled between 1996 and 2011 throughout Asia and Russia. Our analyses demonstrate that the large-scale H5N1 transmission dynamics are structured according to different avian flyways, and that the incursion of the Central Asian flyway specifically was driven by Anatidae hosts coinciding with rapid rate of spread and an epidemic wavefront acceleration. This also resulted in long-distance dispersal that is likely to be explained by wild bird migration. We identify a significant degree of asymmetry in the large-scale transmission dynamics between Anatidae and Phasianidae, with the latter largely representing poultry as an evolutionary sink. A joint analysis of host dynamics and continuous spatial diffusion demonstrates that the rate of viral dispersal and host diffusivity is significantly higher for Anatidae compared with Phasianidae. These findings complement risk modeling studies and satellite tracking of wild birds in demonstrating a continental-scale structuring into areas of H5N1 persistence that are connected through migratory waterfowl.
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Affiliation(s)
- Nídia Sequeira Trovão
- Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
| | - Marc A Suchard
- Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
| | - Marius Gilbert
- Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium Fonds National de la Recherche Scientifique, Brussels, Belgium
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
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30
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Dearlove BL, Frost SDW. Measuring Asymmetry in Time-Stamped Phylogenies. PLoS Comput Biol 2015; 11:e1004312. [PMID: 26147205 PMCID: PMC4492995 DOI: 10.1371/journal.pcbi.1004312] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 05/04/2015] [Indexed: 01/26/2023] Open
Abstract
Previous work has shown that asymmetry in viral phylogenies may be indicative of heterogeneity in transmission, for example due to acute HIV infection or the presence of ‘core groups’ with higher contact rates. Hence, evidence of asymmetry may provide clues to underlying population structure, even when direct information on, for example, stage of infection or contact rates, are missing. However, current tests of phylogenetic asymmetry (a) suffer from false positives when the tips of the phylogeny are sampled at different times and (b) only test for global asymmetry, and hence suffer from false negatives when asymmetry is localised to part of a phylogeny. We present a simple permutation-based approach for testing for asymmetry in a phylogeny, where we compare the observed phylogeny with random phylogenies with the same sampling and coalescence times, to reduce the false positive rate. We also demonstrate how profiles of measures of asymmetry calculated over a range of evolutionary times in the phylogeny can be used to identify local asymmetry. In combination with different metrics of asymmetry, this combined approach offers detailed insights of how phylogenies reconstructed from real viral datasets may deviate from the simplistic assumptions of commonly used coalescent and birth-death process models. Phylogenetic trees of viruses sampled from different individuals provide clues to the dynamics of transmission. The extent to which the tree is asymmetric may be influenced by biological factors such as differences in infectiousness or contact rates between individuals, but also by nuisance factors such as the pattern of sampling. We have devised a simple statistical test for asymmetry, which controls for sampling patterns and potentially complex temporal dynamics by conditioning on the sampling and coalescence times in a phylogeny, and can also detect whether specific clades in the phylogeny drive patterns of asymmetry. We apply our approach to data on HIV, influenza A virus H5N1, and ebola virus.
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Affiliation(s)
- Bethany L. Dearlove
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | - Simon D. W. Frost
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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31
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Alkhamis MA, Moore BR, Perez AM. Phylodynamics of H5N1 Highly Pathogenic Avian Influenza in Europe, 2005-2010: Potential for Molecular Surveillance of New Outbreaks. Viruses 2015; 7:3310-28. [PMID: 26110587 PMCID: PMC4488740 DOI: 10.3390/v7062773] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/02/2015] [Accepted: 06/16/2015] [Indexed: 11/16/2022] Open
Abstract
Previous Bayesian phylogeographic studies of H5N1 highly pathogenic avian influenza viruses (HPAIVs) explored the origin and spread of the epidemic from China into Russia, indicating that HPAIV circulated in Russia prior to its detection there in 2005. In this study, we extend this research to explore the evolution and spread of HPAIV within Europe during the 2005-2010 epidemic, using all available sequences of the hemagglutinin (HA) and neuraminidase (NA) gene regions that were collected in Europe and Russia during the outbreak. We use discrete-trait phylodynamic models within a Bayesian statistical framework to explore the evolution of HPAIV. Our results indicate that the genetic diversity and effective population size of HPAIV peaked between mid-2005 and early 2006, followed by drastic decline in 2007, which coincides with the end of the epidemic in Europe. Our results also suggest that domestic birds were the most likely source of the spread of the virus from Russia into Europe. Additionally, estimates of viral dispersal routes indicate that Russia, Romania, and Germany were key epicenters of these outbreaks. Our study quantifies the dynamics of a major European HPAIV pandemic and substantiates the ability of phylodynamic models to improve molecular surveillance of novel AIVs.
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Affiliation(s)
- Mohammad A Alkhamis
- Environmental and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait City, Safat 13109, Kuwait.
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MA 55108, USA.
| | - Brian R Moore
- Department of Evolution and Ecology, Center for Population Biology, University of California Davis, Davis, CA 95616, USA.
| | - Andres M Perez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MA 55108, USA.
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32
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Díez-Fuertes F, Cabello M, Thomson MM. Bayesian phylogeographic analyses clarify the origin of the HIV-1 subtype A variant circulating in former Soviet Union's countries. INFECTION GENETICS AND EVOLUTION 2015; 33:197-205. [PMID: 25952568 DOI: 10.1016/j.meegid.2015.05.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/24/2015] [Accepted: 05/04/2015] [Indexed: 10/23/2022]
Abstract
The HIV-1 subtype A variant dominating the HIV-1 epidemics in former Soviet Union (FSU) countries (A(FSU)) represents one of the major clades of the HIV-1 pandemic. This variant was reported to have begun spreading among injecting drug users (IDUs) in the Ukrainian city of Odessa in late 1994. Two competing hypotheses have been proposed on the ancestral origin of the A(FSU) variant, locating it either in the Democratic Republic of Congo (DRC) or in the Republic of Guinea (RG). The studies supporting these hypotheses employed phylogenetic analyses to identify HIV-1 sequences collected outside FSU countries ancestrally related to A(FSU). A different approach, based on Bayesian phylogenetic inference and coalescent-based population genetics, has been employed here to elucidate the ancestry of this HIV-1 variant and to improve our knowledge on its spread in FSU countries. The analyses were carried out using env (C2-V3-C3) and p24(gag) fragments of the HIV-1 genome. The inferred migration for the HIV-1 A(FSU) variant revealed only one significantly supported migration pathway from Africa to Eastern Europe, supporting the hypothesis of its origin in the DRC and estimating the upper limit of the migration of the ancestral virus from Africa around 1970. The support for an origin in the RG was negligible. The results supported the main role of Odessa as the epicenter of the A(FSU) epidemic, dating the tMRCA of the A(FSU) variant around 1984, ten years before its explosive expansion among IDUs. The estimated origin of the AFSU subcluster responsible for the IDU outbreak was also located in Odessa, with the estimated tMRCA around 1993. Statistically supported migration routes from Odessa to other cities of Ukraine, Russia, Kazakhstan, Uzbekistan and Belarus were also inferred by the Bayesian phylogeographic analysis. These results shed new light on the origin and spread of the HIV-1 A(FSU) variant.
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Affiliation(s)
- Francisco Díez-Fuertes
- AIDS Immunopathology Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain
| | - Marina Cabello
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain; Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Michael M Thomson
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain.
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Jin Y, Yu D, Ren H, Yin Z, Huang Z, Hu M, Li B, Zhou W, Yue J, Liang L. Phylogeography of Avian influenza A H9N2 in China. BMC Genomics 2014; 15:1110. [PMID: 25511561 PMCID: PMC4523017 DOI: 10.1186/1471-2164-15-1110] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 12/08/2014] [Indexed: 11/10/2022] Open
Abstract
Background During the past two decades, avian influenza A H9N2 viruses have spread geographically and ecologically in China. Other than its current role in causing outbreaks in poultry and sporadic human infections by direct transmission, H9N2 virus could also serve as an progenitor for novel human avian influenza viruses including H5N1, H7N9 and H10N8. Hence, H9N2 virus is becoming a notable threat to public health. However, despite multiple lineages and genotypes that were detected by previous studies, the migration dynamics of the H9N2 virus in China is unclear. Increasing such knowledge would help us better prevent and control H9N2 as well as other future potentially threatening viruses from spreading across China. The objectives of this study were to determine the source, migration patterns, and the demography history of avian influenza A H9N2 virus that circulated in China. Results Using Bayesian phylogeography framework, we showed that the H9N2 virus in mainland China may have originated from the Hong Kong Special Administrative Region (SAR). Southern China, most likely the Guangdong province acts as the primary epicentre for multiple H9N2 strains spreading across the whole country, and eastern China, most likely the Jiangsu province, acts as an important secondary source to seed outbreaks. Our demography inference suggests that during the long-term migration process, H9N2 evolved into multiple diverse lineages and then experienced a selective sweep, which reduced its genetic diversity. Importantly, such a selective sweep may pose a greater threat to public health because novel strains confer higher fitness advantages than strains being replaced and could generate new viruses through reassortment. Conclusion Our analyses indicate that migratory birds, poultry trade and transportation have all contributed to the spreading of the H9N2 virus in China. The ongoing migration and evolution of H9N2, which poses a constant threat to the human population, highlights the need for a more comprehensive surveillance of wild birds and for the enhancement of biosafety for China’s poultry industry. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1110) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuan Jin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China.
| | - Dong Yu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China.
| | - Hongguang Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China.
| | - Zhiqiu Yin
- School of Life Sciences, Anhui University, Anhui, 230601, China.
| | - Zhisong Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China.
| | - Mingda Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China.
| | - Beiping Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China.
| | - Wei Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China.
| | - Junjie Yue
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China.
| | - Long Liang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China.
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Dalby AR, Iqbal M. A global phylogenetic analysis in order to determine the host species and geography dependent features present in the evolution of avian H9N2 influenza hemagglutinin. PeerJ 2014; 2:e655. [PMID: 25374791 PMCID: PMC4217197 DOI: 10.7717/peerj.655] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 10/15/2014] [Indexed: 01/18/2023] Open
Abstract
A complete phylogenetic analysis of all of the H9N2 hemagglutinin sequences that were collected between 1966 and 2012 was carried out in order to build a picture of the geographical and host specific evolution of the hemagglutinin protein. To improve the quality and applicability of the output data the sequences were divided into subsets based upon location and host species. The phylogenetic analysis of hemagglutinin reveals that the protein has distinct lineages between China and the Middle East, and that wild birds in both regions retain a distinct form of the H9 molecule, from the same lineage as the ancestral hemagglutinin. The results add further evidence to the hypothesis that the current predominant H9N2 hemagglutinin lineage might have originated in Southern China. The study also shows that there are sampling problems that affect the reliability of this and any similar analysis. This raises questions about the surveillance of H9N2 and the need for wider sampling of the virus in the environment. The results of this analysis are also consistent with a model where hemagglutinin has predominantly evolved by neutral drift punctuated by occasional selection events. These selective events have produced the current pattern of distinct lineages in the Middle East, Korea and China. This interpretation is in agreement with existing studies that have shown that there is widespread intra-country sequence evolution.
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Affiliation(s)
- Andrew R Dalby
- Faculty of Science and Technology, University of Westminster , Westminster , UK
| | - Munir Iqbal
- Avian Viral Diseases Programme, The Pirbright Institute, Compton Laboratory , Newbury, Berkshire , UK
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Global distribution patterns of highly pathogenic H5N1 avian influenza: environmental vs. socioeconomic factors. C R Biol 2014; 337:459-65. [PMID: 25103831 DOI: 10.1016/j.crvi.2014.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 05/28/2014] [Accepted: 06/01/2014] [Indexed: 11/20/2022]
Abstract
In this report, we quantitatively analyzed the essential ecological factors that were strongly correlated with the global outbreak of highly pathogenic H5N1 avian influenza. The ecological niche modeling (ENM) was used to reveal the potential outbreak hotspots of H5N1. A two-step modeling procedure has been proposed: we first used BioClim model to obtain the coarse suitable areas of H5N1, and then those suitable areas with very high probabilities were retained as the inputs of multiple-variable autologistic regression analysis (MAR) for model refinement. MAR was implemented taking spatial autocorrelation into account. The final performance of ENM was evaluated using the areas under the curve (AUC) of receiver-operating characteristic. In addition, principal component analysis (PCA) was employed to reveal the most important variables and relevant ecological gradients of H5N1 outbreak. Niche visualization was used to identify potential spreading trend of H5N1 along important ecological gradients. For the first time, we combined socioeconomic and environmental variables as joint predictors in developing ecological niche modeling. Environmental variables represented the natural element related to H5N1 outbreak, whereas socioeconomic ones represented the anthropogenic element. Our results indicated that: (1) the high-risk hotspots are mainly located in temperate zones (indicated by ENM)-correspondingly, we argued that the "ecoregions hypothesis" was reasonable to some extent; (2) evaporation, humidity, human population density, livestock population density were the first four important factors (in descending order) that were associated with the H5N1 global outbreak (indicated by PCA); (3) influenza had a tendency to expand into areas with low evaporation (indicated by niche visualization). In conclusion, our study substantiates that both the environmental and socioeconomic variables jointly determined the global spreading trend of H5N1, but environmental variables played a more important role. Consequently, our study is consistent with the assumption that the natural element is more important than the anthropogenic element as the underlying ecological mechanisms explaining global H5N1 transmission.
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Saha K, Firdaus R, Biswas A, Mukherjee A, Sarkar K, Chakrabarti S, Sadhukhan PC. Transmission dynamics of hepatitis C virus among intra venous drug users in the border state of Manipur, India. INFECTION GENETICS AND EVOLUTION 2014; 24:57-67. [PMID: 24650917 DOI: 10.1016/j.meegid.2014.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/04/2014] [Accepted: 03/07/2014] [Indexed: 02/06/2023]
Abstract
Intra venous drug users (IVDUs) are at high risk for hepatitis C virus (HCV) infection owing to their high rate of drug abuses. The north-eastern part of India has a high prevalence of IVDUs with Manipur being the worst hit state. The aim of the study was to document the molecular epidemiology, the patterns of HCV transmission, genomic variation and recombination events within HCV genome among IVDUs of Manipur, India. 91 anti-HCV sero-reactive blood samples were collected from IVDUs in Manipur. The samples were processed for RNA extraction, nested RT-PCR, sequencing and quantitative viral RNA estimation. Phylogeographic analysis of the sequenced core and NS5B regions of HCV genome was performed to determine the probable transmission route and recombinant HCV strains. 83 out of 91 anti-HCV seropositive samples were RNA positive (91.20%) based on 5'UTR of HCV genome by nested RT-PCR. Of the RNA positive samples, 73 paired partial core and NS5B gene were sequenced. Three major genotype and eight subtypes were detected while no recombinant strains were found. Individuals with genotype 1 had the mean viral load (5.94 ± 0.705 log10IU/ml) followed by genotype 3 (4.91 ± 0.49 log10IU/ml) and 6 (3.96 ± 0.32 log10IU/ml). The viral load was statistically significant among the male individuals at 4.822 ± 1.36 log10IU/ml compared to 4.767 ± 0.49 log10IU/ml for females (t=3.249, p<0.005). The phylogeographic results indicated 3b, 6h originated from Vietnam, 1a had Indian origin, 3a, 6k originated from southern China while 1b originated from Myanmar, respectively. The incidence of eight different subtypes in Manipur reflects the transmission of these strains from the "Golden Triangle" drug trafficking regions. Sequence analysis confirmed the transmission routes of HCV, which is linked to China and Vietnam for the newly emergent genotype 6 in north-eastern India.
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Affiliation(s)
| | | | | | | | - Kamalesh Sarkar
- National Institute of Cholera and Enteric Diseases, Kolkata, India
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Claes F, Kuznetsov D, Liechti R, Von Dobschuetz S, Truong BD, Gleizes A, Conversa D, Colonna A, Demaio E, Ramazzotto S, Larfaoui F, Pinto J, Le Mercier P, Xenarios I, Dauphin G. The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau008. [PMID: 24608033 PMCID: PMC3945526 DOI: 10.1093/database/bau008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Combining epidemiological information, genetic characterization and geomapping in the analysis of influenza can contribute to a better understanding and description of influenza epidemiology and ecology, including possible virus reassortment events. Furthermore, integration of information such as agroecological farming system characteristics can provide new knowledge on risk factors of influenza emergence and spread. Integrating viral characteristics into an animal disease information system is therefore expected to provide a unique tool to trace-and-track particular virus strains; generate clade distributions and spatiotemporal clusters; screen for distribution of viruses with specific molecular markers; identify potential risk factors; and analyze or map viral characteristics related to vaccines used for control and/or prevention. For this purpose, a genetic module was developed within EMPRES-i (FAO’s global animal disease information system) linking epidemiological information from influenza events with virus characteristics and enabling combined analysis. An algorithm was developed to act as the interface between EMPRES-i disease event data and publicly available influenza virus sequences in OpenfluDB. This algorithm automatically computes potential links between outbreak event and sequences, which are subsequently manually validated by experts. Subsequently, other virus characteristics such as antiviral resistance can then be associated to outbreak data. To visualize such characteristics on a geographic map, shape files with virus characteristics to overlay on other EMPRES-i map layers (e.g. animal densities) can be generated. The genetic module allows export of associated epidemiological and sequence data for further analysis. FAO has made this tool available for scientists and policy makers. Contributions are expected from users to improve and validate the number of linked influenza events and isolate information as well as the quality of information. Possibilities to interconnect with other influenza sequence databases or to expand the genetic module to other viral diseases (e.g. foot and mouth disease) are being explored. Database OpenfluDB URL:http://openflu.vital-it.ch Database EMPRES-i URL:http://EMPRES-i.fao.org/
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Affiliation(s)
- Filip Claes
- Animal Health Service, Food and Agriculture Organization of the United Nations (FAO), Viale delle Terme di Caracalla, 10532 Rome, Italy and Vital-IT/Swiss-Prot Groups, SIB, Swiss Institute for Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
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Gascuel O, Steel M. Predicting the ancestral character changes in a tree is typically easier than predicting the root state. Syst Biol 2014; 63:421-35. [PMID: 24562915 DOI: 10.1093/sysbio/syu010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed for this purpose. Theoretical results are available that show that when the substitution rates become too large, reconstructing the ancestral state at the tree root is no longer feasible. Here, we also study the reconstruction of the ancestral changes that occurred along the tree edges. We show that, that, depending on the tree and branch length distribution, reconstructing these changes (i.e., reconstructing the ancestral state of all internal nodes in the tree) may be easier or harder than reconstructing the ancestral root state. However, results from information theory indicate that for the standard Yule tree, the task of reconstructing internal node states remains feasible, even for very high substitution rates. Moreover, computer simulations demonstrate that for more complex trees and scenarios, this result still holds. For a large variety of counting, parsimony- and likelihood-based methods, the predictive accuracy of a randomly selected internal node in the tree is indeed much higher than the accuracy of the same method when applied to the tree root. Moreover, parsimony- and likelihood-based methods appear to be remarkably robust to sampling bias and model mis-specification.
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Affiliation(s)
- Olivier Gascuel
- Institut de Biologie Computationnelle, LIRMM, UMR 5506 CNRS - Univ. Montpellier 2, Case courrier 06011, 95 rue de la Galéra, 34095 Montpellier, France; Allan Wilson Centre, University of Canterbury, Ilam Road 8041, Christchurch, New Zealand
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39
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Aris-Brosou S. Inferring influenza global transmission networks without complete phylogenetic information. Evol Appl 2014; 7:403-12. [PMID: 24665342 PMCID: PMC3962300 DOI: 10.1111/eva.12138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 11/06/2013] [Indexed: 11/30/2022] Open
Abstract
Influenza is one of the most severe respiratory infections affecting humans throughout the world, yet the dynamics of its global transmission network are still contentious. Here, I describe a novel combination of phylogenetics, time series, and graph theory to analyze 14.25 years of data stratified in space and in time, focusing on the main target of the human immune response, the hemagglutinin gene. While bypassing the complete phylogenetic inference of huge data sets, the method still extracts information suggesting that waves of genetic or of nucleotide diversity circulate continuously around the globe for subtypes that undergo sustained transmission over several seasons, such as H3N2 and pandemic H1N1/09, while diversity of prepandemic H1N1 viruses had until 2009 a noncontinuous transmission pattern consistent with a source/sink model. Irrespective of the shift in the structure of H1N1 diversity circulation with the emergence of the pandemic H1N1/09 strain, US prevalence peaks during the winter months when genetic diversity is at its lowest. This suggests that a dominant strain is generally responsible for epidemics and that monitoring genetic and/or nucleotide diversity in real time could provide public health agencies with an indirect estimate of prevalence.
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Affiliation(s)
- Stéphane Aris-Brosou
- Department of Biology, Center for Advanced Research in Environmental Genomics, University of Ottawa Ottawa, ON, Canada ; Department of Mathematics and Statistics, University of Ottawa Ottawa, ON, Canada
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40
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Sandie R, Aris-Brosou S. Predicting the emergence of H3N2 influenza viruses reveals contrasted modes of evolution of HA and NA antigens. J Mol Evol 2013; 78:1-12. [PMID: 24343641 DOI: 10.1007/s00239-013-9608-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 12/06/2013] [Indexed: 02/01/2023]
Abstract
Vaccine design for rapidly changing viruses is based on empirical surveillance of strains circulating in a given season to assess those that will most likely spread during the next season. The choice of which strains to include in the vaccine is critical, as an erroneous decision can lead to a nonimmunized human population that will then be at risk in the face of an epidemic or, worse, a pandemic. Here, we present the first steps toward a very general phylogenetic approach to predict the emergence of novel viruses. Our genomic model builds upon natural features of viral evolution such as selection and recombination / reassortment, and incorporates episodic bursts of evolution and or of recombination. As a proof-of-concept, we assess the performance of this model in a retrospective study, focusing: (i) on the emergence of an unexpected H3N2 influenza strain in 2007, and (ii) on a longitudinal design. Based on the analysis of hemagglutinin (HA) and neuraminidase (NA) genes, our results show a lack of predictive power in both experimental designs, but shed light on the mode of evolution of these two antigens: (i) supporting the lack of significance of recombination in the evolution of this influenza virus, and (ii) showing that HA evolves episodically while NA changes gradually.
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Affiliation(s)
- Reatha Sandie
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
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41
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Lu QB, Wo Y, Wang HY, Wei MT, Zhang L, Yang H, Liu EM, Li TY, Zhao ZT, Liu W, Cao WC. Detection of enterovirus 68 as one of the commonest types of enterovirus found in patients with acute respiratory tract infection in China. J Med Microbiol 2013; 63:408-414. [PMID: 24324030 DOI: 10.1099/jmm.0.068247-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Human enterovirus 68 (HEV-68) is an enterovirus associated with respiratory illness. In China, no information about HEV-68 is available for children yet. This study aimed to investigate the presence of HEV-68 in mainland China between 2009 and 2012 and to explore the migration events of HEV-68 across the world. Among 1565 samples tested from children, 41 (2.6%) were positive for HEV and 223 (14.3%) for human rhinovirus (HRV). Seven (17.1%) of 41 HEVs were HEV-68. Two HEV-68- and five HRV-positive samples were detected in 585 adult samples. HEV-68 is the predominant type of enterovirus in children with acute respiratory tract infection (ARTI), followed by HEV-71 and coxsackievirus A6. Three HEV-68-infected children presented with severe pneumonia and one presented with a severe asthma attack. The viruses were attributed to two novel distinct sublineages of HEV-68 based on phylogenetic analysis of partial VP1 gene sequences. Migration events analysis showed that the USA and the Netherlands were possible geographical sources of HEV-68, from where three strains migrated to China. In conclusion, HEV-68 may play a predominant role among the enteroviruses associated with ARTI in children. Additional surveillance is needed to clarify the reason why HEV-68 causes such a wide spectrum of disease, from asymptomatic to severe respiratory disease and even death.
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Affiliation(s)
- Qing-Bin Lu
- School of Public Health, Peking University, Beijing, 100191, PR China
| | - Ying Wo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Hong-Yu Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Mao-Ti Wei
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Lei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Hong Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - En-Mei Liu
- Children's Hospital, Chongqing Medical University, Chongqing, 400014, PR China
| | - Ting-Yu Li
- Children's Hospital, Chongqing Medical University, Chongqing, 400014, PR China
| | - Zhong-Tang Zhao
- Department of Epidemiology and Health Statistics, Shandong University, Jinan, 250012, PR China
| | - Wei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Wu-Chun Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
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42
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Wei K, Lin Y, Xie D. Evolutionary and Ecological Dynamics of Transboundary Disease Caused by H5N1 Virus in Southeast Asia. Transbound Emerg Dis 2013; 62:315-27. [PMID: 23952973 DOI: 10.1111/tbed.12147] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Indexed: 01/03/2023]
Abstract
Southeast Asia has been the breeding ground for many emerging diseases in the past decade, and it is in this region that new genetic variants of HPAI H5N1 viruses have been emerging. Cross-border movement of animals accelerates the spread of H5N1, and the changing environmental conditions also exert strong selective pressure on the viruses. The transboundary zoonotic diseases caused by H5N1 pose a serious and continual threat to global economy and public health. Here, we divided the H5N1 viruses isolated in Southeast Asia during 2003-2009 into four groups according to their phylogenetic relationships among HA gene sequences. Molecular evolution analysis suggests populations in expansion rather than a positive selection for group 2 and group 3, yet group 4 is under strong positive selection. Site 193 was found to be a potential glycosylation site and located in receptor-binding domain. Note that site 193 tends to appear in avian isolates instead of human strains. Population dynamics analysis reveals that the effective population size of infections in Southeast Asia has undergone three obvious increases, and the results are consistent with the epidemiological analysis. Ecological and phylogeographical analyses show that agro-ecological environments, migratory birds, domestic waterfowl, especially free-ranging ducks, are crucial in the occurrence, maintenance and spread of H5N1 virus. The epidemiological links between Indonesia and Suphanburi observed suggest that viruses in Indonesia were originated from multiple introductions.
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Affiliation(s)
- K Wei
- Department of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
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Zhou Z, Deng F, Han N, Wang H, Sun S, Zhang Y, Hu Z, Rayner S. Reassortment and migration analysis of Crimean-Congo haemorrhagic fever virus. J Gen Virol 2013; 94:2536-2548. [PMID: 23939975 DOI: 10.1099/vir.0.056374-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Crimean-Congo haemorrhagic fever virus (CCHFV) is a tick-borne virus with high pathogenicity to humans. CCHFV contains a three-segment [small (S), medium (M) and large (L)] genome and is prone to reassortment. Investigation of identified reassortment events can yield insight into the evolutionary history of the virus, while migration events reflect its geographical dissemination. While many studies have already considered these issues, they have investigated small numbers of isolates and lack statistical support for their findings. Here, we consider a larger set of 30 full genomes to investigate reassortment using recombination methods, as well as two sets of partial S segments comprising 393 isolates, reflecting a broader geographical range, to investigate migration events. Phylogenetic analysis revealed that the S segment showed strong geographical subdivision, but this was less apparent in the M and L segments. A total of 16 reassortment events with 22 isolates were identified with strong statistical support. Migration analysis on the partial S segments identified both long- and short-range migration events that spanned the entire geographical region in which the CCHFV has been isolated, reflecting the complex processes associated with the dissemination of the virus.
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Affiliation(s)
- Zhaorui Zhou
- State Key Laboratory of Virology and China Center for Virus Culture Collection, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Fei Deng
- State Key Laboratory of Virology and China Center for Virus Culture Collection, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Na Han
- State Key Laboratory of Virology and China Center for Virus Culture Collection, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Hualin Wang
- State Key Laboratory of Virology and China Center for Virus Culture Collection, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Surong Sun
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumuqi, Xinjiang 830046, PR China
| | - Yujiang Zhang
- Center for Disease Control and Prevention of Xinjiang Uygur Autonomous Region, 4 Jianquan First Street, Urumuqi, Xinjiang 830046, PR China
| | - Zhihong Hu
- State Key Laboratory of Virology and China Center for Virus Culture Collection, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Simon Rayner
- State Key Laboratory of Virology and China Center for Virus Culture Collection, Chinese Academy of Sciences, Wuhan 430071, PR China
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The antigenic architecture of the hemagglutinin of influenza H5N1 viruses. Mol Immunol 2013; 56:705-19. [PMID: 23933511 DOI: 10.1016/j.molimm.2013.07.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 07/06/2013] [Accepted: 07/14/2013] [Indexed: 11/22/2022]
Abstract
Human infection with the highly pathogenic avian influenza A virus H5N1 is associated with a high mortality and morbidity. H5N1 continues to transmit from poultry to the human population, raising serious concerns about its pandemic potential. Current influenza H5N1 vaccines are based upon the elicitation of a neutralizing antibody (Ab) response against the major epitope regions of the viral surface glycoprotein, hemagglutinin (HA). However, antigenic drift mutations in immune-dominant regions on the HA structure allow the virus to escape Ab neutralization. Epitope mapping using neutralizing monoclonal antibodies (mAb) helps define mechanisms of antigenic drift, neutralizing escape and can facilitate pre-pandemic vaccine design. This review explores the current knowledge base of the antigenic sites of the H5N1 HA molecule. The relationship between the epitope architecture of the H5N1 HA, antigenic evolution of the different H5N1 lineages and the antigenic complexity of the H5N1 virus lineages that constitute potential pandemic strains are discussed in detail.
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45
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The effect of the PB2 mutation 627K on highly pathogenic H5N1 avian influenza virus is dependent on the virus lineage. J Virol 2013; 87:9983-96. [PMID: 23843645 DOI: 10.1128/jvi.01399-13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clade 2.2 Eurasian-lineage H5N1 highly pathogenic avian influenza viruses (HPAIVs) were first detected in Qinghai Lake, China, in 2005 and subsequently spread through Asia, Europe, and Africa. Importantly, these viruses carried a lysine at amino acid position 627 of the PB2 protein (PB2 627K), a known mammalian adaptation motif. Previous avian influenza virus isolates have carried glutamic acid in this position (PB2 627E), commonly described to restrict virus polymerase function in the mammalian host. We sought to examine the effect of PB2 627K on viral maintenance in the avian reservoir. Viruses constructed by reverse genetics were engineered to contain converse PB2 627K/E mutations in a Eurasian H5N1 virus (A/turkey/Turkey/5/2005 [Ty/05]) and, for comparison, a historical pre-Asian H5N1 HPAIV that naturally bears PB2 627E (A/turkey/England/50-92/1991 [50-92]). The 50-92 PB2 627K was genetically unstable during virus propagation, resulting in reversion to PB2 627E or the accumulation of the additional mutation PB2 628R and/or a synonymous mutation from an A to a G nucleotide at nucleotide position 1869 (PB2 A1869G). Intriguingly, PB2 628R and/or A1869G appeared to improve the genetic stability of 50-92 PB2 627K. However, the replication of 50-92 PB2 627K in conjunction with these stabilizing mutations was significantly restricted in experimentally infected chickens, where reversion to PB2 627E occurred. In contrast, no significant effects on viral fitness were observed for Ty/05 PB2 627E or 627K in in vitro or in vivo experiments. Our observations suggest that PB2 627K is supported in Eurasian-lineage viruses; in contrast, PB2 627K carries a significant fitness cost in the historical pre-Asian 50-92 virus.
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46
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Kramvis A, Paraskevis D. Subgenotype A1 of HBV--tracing human migrations in and out of Africa. Antivir Ther 2013; 18:513-21. [PMID: 23792935 DOI: 10.3851/imp2657] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2012] [Indexed: 12/14/2022]
Abstract
BACKGROUND HBV subgenotype A1 is the dominant genotype A strain in Africa, with molecular characteristics differentiating it from A2, which prevails elsewhere. Outside Africa, A1 is confined to areas with migration history from Africa, including India and Latin America. The aim of this study was to reconstruct A1 phylogeny on a spatial scale in order to determine whether A1 can be used to track human migrations. METHODS A phylogenetic comparison of A1 was established using neighbour-joining analysis of complete genomes, and the Bayesian method, implemented in BEAST, was performed on the S region of isolates from 22 countries. Migration events were estimated by ancestral state reconstruction using the criterion of parsimony. RESULTS From the tree reconstruction, nucleotide divergence calculations and migration analysis, it was evident that Africa was the source of dispersal of A1 globally, and its dispersal to Asia and Latin America occurred at a similar time period. Strains from South Africa were the most divergent, clustering in both the African and Asian/American clades and a South African subclade was the origin of A1. The effect of the 9th to 19th century trade and slave routes on the dispersal of A1 was evident and certain unexpected findings, such as the co-clustering of Somalian and Latin American strains, and the dispersal of A1 from India to Haiti, correlated with historical evidence. CONCLUSIONS Phylogeographic analyses of subgenotype A1 can be used to trace human migrations in and out of Africa and the plausible sites of origin and migration routes are presented.
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Affiliation(s)
- Anna Kramvis
- Hepatitis Virus Diversity Research Programme, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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Cybis GB, Sinsheimer JS, Lemey P, Suchard MA. Graph hierarchies for phylogeography. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120206. [PMID: 23382428 DOI: 10.1098/rstb.2012.0206] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Bayesian phylogeographic methods simultaneously integrate geographical and evolutionary modelling, and have demonstrated value in assessing spatial spread patterns of measurably evolving organisms. We improve on existing phylogeographic methods by combining information from multiple phylogeographic datasets in a hierarchical setting. Consider N exchangeable datasets or strata consisting of viral sequences and locations, each evolving along its own phylogenetic tree and according to a conditionally independent geographical process. At the hierarchical level, a random graph summarizes the overall dispersion process by informing which migration rates between sampling locations are likely to be relevant in the strata. This approach provides an efficient and improved framework for analysing inherently hierarchical datasets. We first examine the evolutionary history of multiple serotypes of dengue virus in the Americas to showcase our method. Additionally, we explore an application to intrahost HIV evolution across multiple patients.
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Affiliation(s)
- Gabriela B Cybis
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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Guo Z, Tao X, Yin C, Han N, Yu J, Li H, Liu H, Fang W, Adams J, Wang J, Liang G, Tang Q, Rayner S. National borders effectively halt the spread of rabies: the current rabies epidemic in China is dislocated from cases in neighboring countries. PLoS Negl Trop Dis 2013; 7:e2039. [PMID: 23383359 PMCID: PMC3561166 DOI: 10.1371/journal.pntd.0002039] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 12/14/2012] [Indexed: 12/25/2022] Open
Abstract
China has seen a massive resurgence of rabies cases in the last 15 years with more than 25,000 human fatalities. Initial cases were reported in the southwest but are now reported in almost every province. There have been several phylogenetic investigations into the origin and spread of the virus within China but few reports investigating the impact of the epidemic on neighboring countries. We therefore collected nucleoprotein sequences from China and South East Asia and investigated their phylogenetic and phylogeographic relationship. Our results indicate that within South East Asia, isolates mainly cluster according to their geographic origin. We found evidence of sporadic exchange of strains between neighboring countries, but it appears that the major strain responsible for the current Chinese epidemic has not been exported. This suggests that national geographical boundaries and border controls are effective at halting the spread of rabies from China into adjacent regions. We further investigated the geographic structure of Chinese sequences and found that the current epidemic is dominated by variant strains that were likely present at low levels in previous domestic epidemics. We also identified epidemiological linkages between high incidence provinces consistent with observations based on surveillance data from human rabies cases.
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Affiliation(s)
- Zhenyang Guo
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xiaoyan Tao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Cuiping Yin
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Na Han
- State Key Laboratory for Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Jinning Yu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hao Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Haizhou Liu
- State Key Laboratory for Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Wei Fang
- State Key Laboratory for Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - James Adams
- State Key Laboratory for Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Jun Wang
- State Key Laboratory for Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Guodong Liang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qing Tang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- * E-mail: (QT); (SR)
| | - Simon Rayner
- State Key Laboratory for Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- * E-mail: (QT); (SR)
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49
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Abstract
Motivation: Large phylogenies are being built today to study virus evolution, trace the origin of epidemics, establish the mode of transmission and survey the appearance of drug resistance. However, no tool is available to quickly inspect these phylogenies and combine them with extrinsic traits (e.g. geographic location, risk group, presence of a given resistance mutation), seeking to extract strain groups of specific interest or requiring surveillance. Results: We propose a new method for obtaining such groups, which we call phylotypes, from a phylogeny having taxa (strains) annotated with extrinsic traits. Phylotypes are subsets of taxa with close phylogenetic relationships and common trait values. The method combines ancestral trait reconstruction using parsimony, with combinatorial and numerical criteria measuring tree shape characteristics and the diversity and separation of the potential phylotypes. A shuffling procedure is used to assess the statistical significance of phylotypes. All algorithms have linear time complexity. This results in low computing times, typically a few minutes for the larger data sets with a number of shuffling steps. Two HIV-1 data sets are analyzed, one of which is large, containing >3000 strains of HIV-1 subtype C collected worldwide, where the method shows its ability to recover known clusters and transmission routes, and to detect new ones. Availability: This method and companion tools are implemented in an interactive Web interface (www.phylotype.org), which provides a wide choice of graphical views and output formats, and allows for exploratory analyses of large data sets. Contact:francois.chevenet@ird.fr, gascuel@lirmm.fr Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- François Chevenet
- Institut de Biologie Computationnelle, LIRMM, UMR 5506 CNRS - Université Montpellier 2, Montpellier, France.
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Fajardo D, Gardner LM. Inferring Contagion Patterns in Social Contact Networks with Limited Infection Data. NETWORKS AND SPATIAL ECONOMICS 2013; 13:399-426. [PMID: 32288688 PMCID: PMC7111645 DOI: 10.1007/s11067-013-9186-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The spread of infectious disease is an inherently stochastic process. As such, real time control and prediction methods present a significant challenge. For diseases which spread through direct human interaction, (e.g., transferred from infected to susceptible individuals) the contagion process can be modeled on a social-contact network where individuals are represented as nodes, and contacts between individuals are represented as links. The model presented in this paper seeks to identify the infection pattern which depicts the current state of an ongoing outbreak. This is accomplished by inferring the most likely paths of infection through a contact network under the assumption of partially available infection data. The problem is formulated as a bi-linear integer program, and heuristic solution methods are developed based on sub-problems which can be solved much more efficiently. The heuristic performance is presented for a range of randomly generated networks and different levels of information. The model results, which include the most likely set of infection spreading contacts, can be used to provide insight into future epidemic outbreak patterns, and aid in the development of intervention strategies.
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Affiliation(s)
- David Fajardo
- CE 113 School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW 2052 Australia
| | - Lauren M. Gardner
- CE 112 School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW 2052 Australia
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