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Vorburger C, Perlman SJ. The role of defensive symbionts in host-parasite coevolution. Biol Rev Camb Philos Soc 2018; 93:1747-1764. [PMID: 29663622 DOI: 10.1111/brv.12417] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/20/2018] [Accepted: 03/23/2018] [Indexed: 02/06/2023]
Abstract
Understanding the coevolution of hosts and parasites is a long-standing goal of evolutionary biology. There is a well-developed theoretical framework to describe the evolution of host-parasite interactions under the assumption of direct, two-species interactions, which can result in arms race dynamics or sustained genotype fluctuations driven by negative frequency dependence (Red Queen dynamics). However, many hosts rely on symbionts for defence against parasites. Whilst the ubiquity of defensive symbionts and their potential importance for disease control are increasingly recognized, there is still a gap in our understanding of how symbionts mediate or possibly take part in host-parasite coevolution. Herein we address this question by synthesizing information already available from theoretical and empirical studies. First, we briefly introduce current hypotheses on how defensive mutualisms evolved from more parasitic relationships and highlight exciting new experimental evidence showing that this can occur very rapidly. We go on to show that defensive symbionts influence virtually all important determinants of coevolutionary dynamics, namely the variation in host resistance available to selection by parasites, the specificity of host resistance, and the trade-off structure between host resistance and other components of fitness. In light of these findings, we turn to the limited theory and experiments available for such three-species interactions to assess the role of defensive symbionts in host-parasite coevolution. Specifically, we discuss under which conditions the defensive symbiont may take over from the host the reciprocal adaptation with parasites and undergo its own selection dynamics, thereby altering or relaxing selection on the hosts' own immune defences. Finally, we address potential effects of defensive symbionts on the evolution of parasite virulence. This is an important problem for which there is no single, clear-cut prediction. The selection on parasite virulence resulting from the presence of defensive symbionts in their hosts will depend on the underlying mechanism of defence. We identify the evolutionary predictions for different functional categories of symbiont-conferred resistance and we evaluate the empirical literature for supporting evidence. We end this review with outstanding questions and promising avenues for future research to improve our understanding of symbiont-mediated coevolution between hosts and parasites.
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Affiliation(s)
- Christoph Vorburger
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Universitätsstrasse 16, 8092, Zürich, Switzerland
| | - Steve J Perlman
- Department of Biology, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8P 5C2, Canada
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52
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Saxenhofer M, Weber de Melo V, Ulrich RG, Heckel G. Revised time scales of RNA virus evolution based on spatial information. Proc Biol Sci 2018; 284:rspb.2017.0857. [PMID: 28794221 DOI: 10.1098/rspb.2017.0857] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 07/06/2017] [Indexed: 12/18/2022] Open
Abstract
The time scales of pathogen evolution are of major concern in the context of public and veterinary health, epidemiology and evolutionary biology. Dating the emergence of a pathogen often relies on estimates of evolutionary rates derived from nucleotide sequence data. For many viruses, this has yielded estimates of evolutionary origins only a few hundred years in the past. Here we demonstrate through the incorporation of geographical information from virus sampling that evolutionary age estimates of two European hantaviruses are severely underestimated because of pervasive mutational saturation of nucleotide sequences. We detected very strong relationships between spatial distance and genetic divergence for both Puumala and Tula hantavirus-irrespective of whether nucleotide or derived amino acid sequences were analysed. Extrapolations from these relationships dated the emergence of these viruses most conservatively to at least 3700 and 2500 years ago, respectively. Our minimum estimates for the age of these hantaviruses are ten to a hundred times older than results from current non-spatial methods, and in much better accordance with the biogeography of these viruses and their respective hosts. Spatial information can thus provide valuable insights on the deeper time scales of pathogen evolution and improve our understanding of disease emergence.
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Affiliation(s)
- Moritz Saxenhofer
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge-Bâtiment Génopode, Lausanne, Switzerland
| | - Vanessa Weber de Melo
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Rainer G Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany.,German Center for Infection Research (DZIF), partner site Hamburg-Luebeck-Borstel-Insel Riems, Germany
| | - Gerald Heckel
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland .,Swiss Institute of Bioinformatics, Quartier Sorge-Bâtiment Génopode, Lausanne, Switzerland
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53
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Patterson Ross Z, Klunk J, Fornaciari G, Giuffra V, Duchêne S, Duggan AT, Poinar D, Douglas MW, Eden JS, Holmes EC, Poinar HN. The paradox of HBV evolution as revealed from a 16th century mummy. PLoS Pathog 2018; 14:e1006750. [PMID: 29300782 PMCID: PMC5754119 DOI: 10.1371/journal.ppat.1006750] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/13/2017] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) is a ubiquitous viral pathogen associated with large-scale morbidity and mortality in humans. However, there is considerable uncertainty over the time-scale of its origin and evolution. Initial shotgun data from a mid-16th century Italian child mummy, that was previously paleopathologically identified as having been infected with Variola virus (VARV, the agent of smallpox), showed no DNA reads for VARV yet did for hepatitis B virus (HBV). Previously, electron microscopy provided evidence for the presence of VARV in this sample, although similar analyses conducted here did not reveal any VARV particles. We attempted to enrich and sequence for both VARV and HBV DNA. Although we did not recover any reads identified as VARV, we were successful in reconstructing an HBV genome at 163.8X coverage. Strikingly, both the HBV sequence and that of the associated host mitochondrial DNA displayed a nearly identical cytosine deamination pattern near the termini of DNA fragments, characteristic of an ancient origin. In contrast, phylogenetic analyses revealed a close relationship between the putative ancient virus and contemporary HBV strains (of genotype D), at first suggesting contamination. In addressing this paradox we demonstrate that HBV evolution is characterized by a marked lack of temporal structure. This confounds attempts to use molecular clock-based methods to date the origin of this virus over the time-frame sampled so far, and means that phylogenetic measures alone cannot yet be used to determine HBV sequence authenticity. If genuine, this phylogenetic pattern indicates that the genotypes of HBV diversified long before the 16th century, and enables comparison of potential pathogenic similarities between modern and ancient HBV. These results have important implications for our understanding of the emergence and evolution of this common viral pathogen.
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Affiliation(s)
- Zoe Patterson Ross
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Gino Fornaciari
- Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Valentina Giuffra
- Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Sebastian Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Ana T. Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Debi Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Mark W. Douglas
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Hendrik N. Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry, McMaster University, Hamilton, ON, Canada
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
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54
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Carrasco-Hernandez R, Jácome R, López Vidal Y, Ponce de León S. Are RNA Viruses Candidate Agents for the Next Global Pandemic? A Review. ILAR J 2017; 58:343-358. [PMID: 28985316 PMCID: PMC7108571 DOI: 10.1093/ilar/ilx026] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 07/14/2017] [Accepted: 07/15/2017] [Indexed: 12/16/2022] Open
Abstract
Pathogenic RNA viruses are potentially the most important group involved in zoonotic disease transmission, and they represent a challenge for global disease control. Their biological diversity and rapid adaptive rates have proved to be difficult to overcome and to anticipate by modern medical technology. Also, the anthropogenic change of natural ecosystems and the continuous population growth are driving increased rates of interspecies contacts and the interchange of pathogens that can develop into global pandemics. The combination of molecular, epidemiological, and ecological knowledge of RNA viruses is therefore essential towards the proper control of these emergent pathogens. This review outlines, throughout different levels of complexity, the problems posed by RNA viral diseases, covering some of the molecular mechanisms allowing them to adapt to new host species-and to novel pharmaceutical developments-up to the known ecological processes involved in zoonotic transmission.
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Affiliation(s)
- R Carrasco-Hernandez
- R. Carrasco-Hernandez, PhD, is a postdoctoral research fellow at the Microbiome Laboratory in the Postgraduate Division of the Faculty of Medicine at the Universidad Nacional Autónoma de México, CDMX
| | - Rodrigo Jácome
- Rodrigo Jácome, MD, PhD, is a postdoctoral research fellow at the Microbiome Laboratory in the Postgraduate Division of the Faculty of Medicine at the Universidad Nacional Autónoma de México, CDMX
| | - Yolanda López Vidal
- Yolanda López-Vidal, MD, PhD, is an associate professor “C” and is responsible for the Program of Microbial Molecular Immunology in the Department of Microbiology and Parasitology of the Faculty of Medicine at the Universidad Nacional Autónoma de México, CDMX
| | - Samuel Ponce de León
- Samuel Ponce-de-León, MD, MSc, is an associate professor “C”, is responsible for the Microbiome Laboratory and Coordinator of the University Program for Health Research of the Faculty of Medicine at the Universidad Nacional Autónoma de México, CDMX
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55
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Cervera H, Lalić J, Elena SF. Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations. Proc Biol Sci 2017; 283:rspb.2016.0984. [PMID: 27534955 DOI: 10.1098/rspb.2016.0984] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/26/2016] [Indexed: 12/25/2022] Open
Abstract
Predicting viral evolution has proven to be a particularly difficult task, mainly owing to our incomplete knowledge of some of the fundamental principles that drive it. Recently, valuable information has been provided about mutation and recombination rates, the role of genetic drift and the distribution of mutational, epistatic and pleiotropic fitness effects. However, information about the topography of virus' adaptive landscapes is still scarce, and to our knowledge no data has been reported so far on how its ruggedness may condition virus' evolvability. Here, we show that populations of an RNA virus move efficiently on a rugged landscape and scape from the basin of attraction of a local optimum. We have evolved a set of Tobacco etch virus genotypes located at increasing distances from a local adaptive optimum in a highly rugged fitness landscape, and we observed that few evolved lineages remained trapped in the local optimum, while many others explored distant regions of the landscape. Most of the diversification in fitness among the evolved lineages was explained by adaptation, while historical contingency and chance events contribution was less important. Our results demonstrate that the ruggedness of adaptive landscapes is not an impediment for RNA viruses to efficiently explore remote parts of it.
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Affiliation(s)
- Héctor Cervera
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 València, Spain
| | - Jasna Lalić
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 València, Spain The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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56
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Rodríguez-Nevado C, Montes N, Pagán I. Ecological Factors Affecting Infection Risk and Population Genetic Diversity of a Novel Potyvirus in Its Native Wild Ecosystem. FRONTIERS IN PLANT SCIENCE 2017; 8:1958. [PMID: 29184567 PMCID: PMC5694492 DOI: 10.3389/fpls.2017.01958] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 10/30/2017] [Indexed: 06/07/2023]
Abstract
Increasing evidence indicates that there is ample diversity of plant virus species in wild ecosystems. The vast majority of this diversity, however, remains uncharacterized. Moreover, in these ecosystems the factors affecting plant virus infection risk and population genetic diversity, two traits intrinsically linked to virus emergence, are largely unknown. Along 3 years, we have analyzed the prevalence and diversity of plant virus species from the genus Potyvirus in evergreen oak forests of the Iberian Peninsula, the main wild ecosystem in this geographic region and in the entire Mediterranean basin. During this period, we have also measured plant species diversity, host density, plant biomass, temperature, relative humidity, and rainfall. Results indicated that potyviruses were always present in evergreen oak forests, with a novel virus species explaining the largest fraction of potyvirus-infected plants. We determined the genomic sequence of this novel virus and we explored its host range in natural and greenhouse conditions. Natural host range was limited to the perennial plant mountain rue (Ruta montana), commonly found in evergreen oak forests of the Iberian Peninsula. In this host, the virus was highly prevalent and was therefore provisionally named mediterranean ruda virus (MeRV). Focusing in this natural host-virus interaction, we analyzed the ecological factors affecting MeRV infection risk and population genetic diversity in its native wild ecosystem. The main predictor of virus infection risk was the host density. MeRV prevalence was the major factor determining genetic diversity and selection pressures in the virus populations. This observation supports theoretical predictions assigning these two traits a key role in parasite epidemiology and evolution. Thus, our analyses contribute both to characterize viral diversity and to understand the ecological determinants of virus population dynamics in wild ecosystems.
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Affiliation(s)
- Cristina Rodríguez-Nevado
- Centro de Biotecnología y Genómica de Plantas – Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Nuria Montes
- Plant Physiology, Pharmaceutical and Health Sciences Department, Faculty of Pharmacy, CEU-San Pablo University, Madrid, Spain
- Rheumatology Service, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas – Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
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57
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Franzo G, Massi P, Tucciarone CM, Barbieri I, Tosi G, Fiorentini L, Ciccozzi M, Lavazza A, Cecchinato M, Moreno A. Think globally, act locally: Phylodynamic reconstruction of infectious bronchitis virus (IBV) QX genotype (GI-19 lineage) reveals different population dynamics and spreading patterns when evaluated on different epidemiological scales. PLoS One 2017; 12:e0184401. [PMID: 28880958 PMCID: PMC5589226 DOI: 10.1371/journal.pone.0184401] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/23/2017] [Indexed: 11/19/2022] Open
Abstract
Infectious bronchitis virus (IBV) represents one of the poultry industry major threats, particularly in high density producing countries. The emergence and spread of new IBV genotypes have frustrated the various disease control efforts implemented over time. Despite that, few comprehensive and large scale studies have been performed to understand the international and local spreading dynamics of this virus. In the present work, these phenomena were evaluated by implementing a Bayesian phylodynamic approach to reconstruct the epidemiological patterns and population history of the QX genotype (currently renamed GI-19 lineage), the most relevant IBV lineage of the Old-World. Our analysis, based on 807 partial S1 sequences of strains collected from 18 countries between 1993 and 2015, demonstrates that this genotype originated in China well before its first identification. After a prolonged local circulation, it started spreading to other European, Asian and Middle East countries in successive waves, which were mirrored by concomitant fluctuations in viral population size. Interestingly, the within-Europe spread was characterized by a higher estimated migration rate compared with the inter-continental one, potentially reflecting the closer geographic and economic relationships among these countries. Nevertheless, the colonization of new states by the GI-19 lineage appeared to occur mostly by single introduction events in both intra and inter-continental spread, likely because of epidemiological factor and health policy combination which seems to prevent the frequent introduction and mixing of different strains. On the other hand, the within Italy QX circulation reconstruction showed a much more intricate connection network among different locations, evidencing the difficulty in controlling IBV spread especially in highly densely poultry populated areas. The presence of several well supported epidemiological links among distantly related Italian regions testifies that animal transportation and indirect transmission routes rather than local airborne diffusion contribute to the QX success and persistence at local scale. Globally, the spreading dynamics and evolution of the QX genotype were reconstructed from its very origin to nowadays, demonstrating the need of more effective direct control measures, particularly within each country. Unfortunately, the incompleteness of available molecular epidemiology data represents an insurmountable limit which leaves many questions currently unsolved, thus highlighting the compulsoriness of a structured monitoring and data sharing system implementation.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Legnaro, Padua, Italy
| | - Paola Massi
- Sezione di Forlì, Istituto sperimentale della Lombardia e Emilia Romagna, Forlì, Forlì Cesena, Italy
| | - Claudia Maria Tucciarone
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Legnaro, Padua, Italy
| | - Ilaria Barbieri
- Department of Virology, Istituto sperimentale della Lombardia e Emilia Romagna, Brescia, Italy
| | - Giovanni Tosi
- Sezione di Forlì, Istituto sperimentale della Lombardia e Emilia Romagna, Forlì, Forlì Cesena, Italy
| | - Laura Fiorentini
- Sezione di Forlì, Istituto sperimentale della Lombardia e Emilia Romagna, Forlì, Forlì Cesena, Italy
| | - Massimo Ciccozzi
- Department of infectious, parasitic and immune-mediated diseases, Istituto Superiore di Sanità, Roma, Italy
| | - Antonio Lavazza
- Department of Virology, Istituto sperimentale della Lombardia e Emilia Romagna, Brescia, Italy
| | - Mattia Cecchinato
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Legnaro, Padua, Italy
| | - Ana Moreno
- Department of Virology, Istituto sperimentale della Lombardia e Emilia Romagna, Brescia, Italy
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58
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Picard C, Dallot S, Brunker K, Berthier K, Roumagnac P, Soubeyrand S, Jacquot E, Thébaud G. Exploiting Genetic Information to Trace Plant Virus Dispersal in Landscapes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:139-160. [PMID: 28525307 DOI: 10.1146/annurev-phyto-080516-035616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology. We present existing approaches and their limitations and contributions to the understanding of plant virus epidemiology.
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Affiliation(s)
- Coralie Picard
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Sylvie Dallot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | | | - Philippe Roumagnac
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | | | - Emmanuel Jacquot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Gaël Thébaud
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
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59
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Different evolutionary trajectories of vaccine-controlled and non-controlled avian infectious bronchitis viruses in commercial poultry. PLoS One 2017; 12:e0176709. [PMID: 28472110 PMCID: PMC5417570 DOI: 10.1371/journal.pone.0176709] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/16/2017] [Indexed: 02/03/2023] Open
Abstract
To determine the genetic and epidemiological relationship of infectious bronchitis virus (IBV) isolates from commercial poultry to attenuated live IBV vaccines we conducted a phylogenetic network analysis on the full-length S1 sequence for Arkansas (Ark), Massachusetts (Mass) and Delmarva/1639 (DMV/1639) type viruses isolated in 2015 from clinical cases by 3 different diagnostic laboratories. Phylogenetic network analysis of Ark isolates showed two predominant groups linked by 2 mutations, consistent with subpopulations found in commercial vaccines for this IBV type. In addition, a number of satellite groups surrounding the two predominant populations were observed for the Ark type virus, which is likely due to mutations associated with the nature of this vaccine to persist in flocks. The phylogenetic network analysis of Mass-type viruses shows two groupings corresponding to different manufacturers vaccine sequences. No satellite groups were observed for Mass-type viruses, which is consistent with no persistence of this vaccine type in the field. At the time of collection, no vaccine was being used for the DMV/1639 type viruses and phylogenetic network analysis showed a dispersed network suggesting no clear change in genetic distribution. Selection pressure analysis showed that the DMV/1639 and Mass-type strains were evolving under negative selection, whereas the Ark type viruses had evolved under positive selection. This data supports the hypothesis that live attenuated vaccine usage does play a role in the genetic profile of similar IB viruses in the field and phylogenetic network analysis can be used to identify vaccine and vaccine origin isolates, which is important for our understanding of the role live vaccines play in the evolutionary trajectory of those viruses.
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60
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Dennehy JJ. Evolutionary ecology of virus emergence. Ann N Y Acad Sci 2016; 1389:124-146. [PMID: 28036113 PMCID: PMC7167663 DOI: 10.1111/nyas.13304] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/24/2016] [Accepted: 11/09/2016] [Indexed: 12/22/2022]
Abstract
The cross-species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between-host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between-host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead-end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment.
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Affiliation(s)
- John J Dennehy
- Biology Department, Queens College of the City University of New York, Queens, New York and The Graduate Center of the City University of New York, New York, New York
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61
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Xiao Y, Rouzine IM, Bianco S, Acevedo A, Goldstein EF, Farkov M, Brodsky L, Andino R. RNA Recombination Enhances Adaptability and Is Required for Virus Spread and Virulence. Cell Host Microbe 2016; 19:493-503. [PMID: 27078068 DOI: 10.1016/j.chom.2016.03.009] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/13/2016] [Accepted: 03/25/2016] [Indexed: 10/21/2022]
Abstract
Mutation and recombination are central processes driving microbial evolution. A high mutation rate fuels adaptation but also generates deleterious mutations. Recombination between two different genomes may resolve this paradox, alleviating effects of clonal interference and purging deleterious mutations. Here we demonstrate that recombination significantly accelerates adaptation and evolution during acute virus infection. We identified a poliovirus recombination determinant within the virus polymerase, mutation of which reduces recombination rates without altering replication fidelity. By generating a panel of variants with distinct mutation rates and recombination ability, we demonstrate that recombination is essential to enrich the population in beneficial mutations and purge it from deleterious mutations. The concerted activities of mutation and recombination are key to virus spread and virulence in infected animals. These findings inform a mathematical model to demonstrate that poliovirus adapts most rapidly at an optimal mutation rate determined by the trade-off between selection and accumulation of detrimental mutations.
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Affiliation(s)
- Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Igor M Rouzine
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Simone Bianco
- Department of Industrial and Applied Genomics, Accelerated Discovery Lab, IBM Almaden Research Center, 650 Harry Road, San Jose, CA 95120-6099, USA
| | - Ashley Acevedo
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Elizabeth Faul Goldstein
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mikhail Farkov
- Tauber Bioinformatics Research Center and Department of Evolutionary and Environmental Biology, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | - Leonid Brodsky
- Tauber Bioinformatics Research Center and Department of Evolutionary and Environmental Biology, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
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62
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McColl KA, Sunarto A, Holmes EC. Cyprinid herpesvirus 3 and its evolutionary future as a biological control agent for carp in Australia. Virol J 2016; 13:206. [PMID: 27931224 PMCID: PMC5146810 DOI: 10.1186/s12985-016-0666-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 12/02/2016] [Indexed: 11/10/2022] Open
Abstract
Biological invasions are a major threat to global biodiversity. Australia has experienced many invasive species, with the common carp (Cyprinus carpio L.) a prominent example. Cyprinid herpesvirus 3 (CyHV-3) has been proposed as a biological control (biocontrol) agent for invasive carp in Australia. Safety and efficacy are critical factors in assessing the suitability of biocontrol agents, and extensive host-specificity testing suggests that CyHV-3 is safe. Efficacy depends on the relationship between virus transmissibility and virulence. Based on observations from natural outbreaks, as well as the biology of virus-host interactions, we hypothesize that (i) close contact between carp provides the most efficient transmission of virus, (ii) transmission occurs at regular aggregations of carp that favour recrudescence of latent virus, and (iii) the initially high virulence of CyHV-3 will decline following its release in Australia. We also suggest that the evolution of carp resistance to CyHV-3 will likely necessitate the future release of progressively more virulent strains of CyHV-3, and/or an additional broad-scale measure(s) to complement the effect of the virus. If the release of CyHV-3 does go ahead, longitudinal studies are required to track the evolution of a virus-host relationship from its inception, and particularly the complex interplay between transmission, virulence and host resistance.
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Affiliation(s)
- Kenneth A McColl
- CSIRO-Australian Animal Health Laboratory, Geelong, VIC, 3220, Australia.,CSIRO Health and Biosecurity, Geelong, VIC, 3220, Australia
| | - Agus Sunarto
- CSIRO-Australian Animal Health Laboratory, Geelong, VIC, 3220, Australia.,CSIRO Health and Biosecurity, Geelong, VIC, 3220, 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, NSW, 2006, Australia.
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63
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A comparison of biological characteristics of three strains of Chinese sacbrood virus in Apis cerana. Sci Rep 2016; 6:37424. [PMID: 27853294 PMCID: PMC5112594 DOI: 10.1038/srep37424] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 10/31/2016] [Indexed: 01/17/2023] Open
Abstract
We selected and sequenced the entire genomes of three strains of Chinese sacbrood virus (CSBV): LNQY-2008 (isolated in Qingyuan, Liaoning Province), SXYL-2015 (isolated in Yulin, Shanxi Province), and JLCBS-2014 (isolated in Changbaishan, Jilin Province), by VP1 amino acid (aa) analysis. These strains are endemic in China and infect Apis cerana. Nucleotide sequences, deduced amino acid sequences, genetic backgrounds, and other molecular biological characteristics were analysed. We also examined sensitivity of these virus strains to temperature, pH, and organic solvents, as well as to other physicochemical properties. On the basis of these observations, we compared pathogenicity and tested cross-immunogenicity and protective immunity, using antisera raised against each of the three strains. Our results showed that compared with SXYL-2015, LNQY-2008 has a 10-aa deletion and 3-aa deletion (positions 282–291 and 299–301, respectively), whereas JLCBS-2014 has a 17-aa deletion (positions 284–300). However, the three strains showed no obvious differences in physicochemical properties or pathogenicity. Moreover, there was immune cross-reactivity among the antisera raised against the different strains, implying good protective effects of such antisera. The present study should significantly advance the understanding of the pathogenesis of Chinese sacbrood disease, and offers insights into comprehensive prevention and treatment of, as well as possible protection from, the disease by means of an antiserum.
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64
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Grubaugh ND, Rückert C, Armstrong PM, Bransfield A, Anderson JF, Ebel GD, Brackney DE. Transmission bottlenecks and RNAi collectively influence tick-borne flavivirus evolution. Virus Evol 2016; 2:vew033. [PMID: 28058113 PMCID: PMC5210029 DOI: 10.1093/ve/vew033] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Arthropod-borne RNA viruses exist within hosts as heterogeneous populations of viral variants and, as a result, possess great genetic plasticity. Understanding the micro-evolutionary forces shaping these viruses can provide insights into how they emerge, adapt, and persist in new and changing ecological niches. While considerable attention has been directed toward studying the population dynamics of mosquito-borne viruses, little is known about tick-borne virus populations. Therefore, using a mouse and Ixodes scapularis tick transmission model, we examined Powassan virus (POWV; Flaviviridae, Flavivirus) populations in and between both the vertebrate host and arthropod vector. We found that genetic bottlenecks, RNAi-mediated diversification, and selective constraints collectively influence POWV evolution. Together, our data provide a mechanistic explanation for the slow, long-term evolutionary trends of POWV, and suggest that all arthropod-borne viruses encounter similar selective pressures at the molecular level (i.e. RNAi), yet evolve much differently due to their unique rates and modes of transmission.
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Affiliation(s)
- Nathan D Grubaugh
- Department of Microbiology Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, USA
| | - Claudia Rückert
- Department of Microbiology Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, USA
| | - Philip M Armstrong
- The Connecticut Agricultural Experiment Station, Center for Vector Biology and Zoonotic Diseases, New Haven, CT, USA
| | - Angela Bransfield
- The Connecticut Agricultural Experiment Station, Center for Vector Biology and Zoonotic Diseases, New Haven, CT, USA
| | - John F Anderson
- The Connecticut Agricultural Experiment Station, Center for Vector Biology and Zoonotic Diseases, New Haven, CT, USA
| | - Gregory D Ebel
- Department of Microbiology Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Fort Collins, CO, USA
| | - Doug E Brackney
- The Connecticut Agricultural Experiment Station, Center for Vector Biology and Zoonotic Diseases, New Haven, CT, USA
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65
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Tibayrenc M, Ayala FJ. Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses? ADVANCES IN PARASITOLOGY 2016; 97:243-325. [PMID: 28325372 DOI: 10.1016/bs.apar.2016.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.
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Affiliation(s)
- M Tibayrenc
- Institut de Recherche pour le Développement, Montpellier, France
| | - F J Ayala
- University of California at Irvine, United States
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Hoyos-López R, Suaza-Vasco J, Rúa-Uribe G, Uribe S, Gallego-Gómez JC. Molecular detection of flaviviruses and alphaviruses in mosquitoes (Diptera: Culicidae) from coastal ecosystems in the Colombian Caribbean. Mem Inst Oswaldo Cruz 2016; 111:625-634. [PMID: 27706377 PMCID: PMC5066328 DOI: 10.1590/0074-02760160096] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/19/2016] [Indexed: 11/21/2022] Open
Abstract
Arboviruses belonging to the genera Flavivirus and Alphavirus were detected in mosquitoes in a rural area of San Bernardo del Viento (Córdoba, Colombia). A total of 22,180 mosquitoes were collected, sorted into 2,102 pools, and tested by generic/nested reverse transcription-polymerase chain reaction. Venezuelan equine encephalitis virus, dengue virus, West Nile virus, St. Louis encephalitis virus, yellow fever virus, and Culex flavivirus were detected and identified by sequencing. The detection of arboviral pathogens in this zone represents possible circulation and indicates a human health risk, demonstrating the importance of virological surveillance activities.
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Affiliation(s)
- Richard Hoyos-López
- Universidad de Antioquia, Translational and Molecular Medicine Group,
Medellín, Antioquia, Colombia
| | - Juan Suaza-Vasco
- Universidad Nacional de Colombia, Grupo de Investigación en Sistemática
Molecular, Medellín, Antioquia, Colombia
| | - Guillermo Rúa-Uribe
- Universidad de Antioquia, Facultad de Medicina, Grupo de Entomología
Médica, Medellín, Antioquia, Colombia
| | - Sandra Uribe
- Universidad Nacional de Colombia, Grupo de Investigación en Sistemática
Molecular, Medellín, Antioquia, Colombia
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Tabachnick WJ. Climate Change and the Arboviruses: Lessons from the Evolution of the Dengue and Yellow Fever Viruses. Annu Rev Virol 2016; 3:125-145. [DOI: 10.1146/annurev-virology-110615-035630] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Walter J. Tabachnick
- Florida Medical Entomology Laboratory, Department of Entomology and Nematology, University of Florida, Vero Beach, Florida 32962;
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68
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Stenger DC, Krugner R, Nouri S, Ferriol I, Falk BW, Sisterson MS. Sequence polymorphism in an insect RNA virus field population: A snapshot from a single point in space and time reveals stochastic differences among and within individual hosts. Virology 2016; 498:209-217. [PMID: 27598532 DOI: 10.1016/j.virol.2016.08.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 08/26/2016] [Accepted: 08/27/2016] [Indexed: 02/02/2023]
Abstract
Population structure of Homalodisca coagulata Virus-1 (HoCV-1) among and within field-collected insects sampled from a single point in space and time was examined. Polymorphism in complete consensus sequences among single-insect isolates was dominated by synonymous substitutions. The mutant spectrum of the C2 helicase region within each single-insect isolate was unique and dominated by nonsynonymous singletons. Bootstrapping was used to correct the within-isolate nonsynonymous:synonymous arithmetic ratio (N:S) for RT-PCR error, yielding an N:S value ~one log-unit greater than that of consensus sequences. Probability of all possible single-base substitutions for the C2 region predicted N:S values within 95% confidence limits of the corrected within-isolate N:S when the only constraint imposed was viral polymerase error bias for transitions over transversions. These results indicate that bottlenecks coupled with strong negative/purifying selection drive consensus sequences toward neutral sequence space, and that most polymorphism within single-insect isolates is composed of newly-minted mutations sampled prior to selection.
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Affiliation(s)
- Drake C Stenger
- USDA, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Ave., Parlier, CA 93648-9757, USA.
| | - Rodrigo Krugner
- USDA, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Ave., Parlier, CA 93648-9757, USA
| | - Shahideh Nouri
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Inmaculada Ferriol
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Bryce W Falk
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Mark S Sisterson
- USDA, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Ave., Parlier, CA 93648-9757, USA
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69
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Levasseur A, Andreani J, Delerce J, Bou Khalil J, Robert C, La Scola B, Raoult D. Comparison of a Modern and Fossil Pithovirus Reveals Its Genetic Conservation and Evolution. Genome Biol Evol 2016; 8:2333-9. [PMID: 27389688 PMCID: PMC5010891 DOI: 10.1093/gbe/evw153] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Most theories on viral evolution are speculative and lack fossil comparison. Here, we isolated a modern Pithovirus-like virus from sewage samples. This giant virus, named Pithovirus massiliensis, was compared with its prehistoric counterpart, Pithovirus sibericum, found in Siberian permafrost. Our analysis revealed near-complete gene repertoire conservation, including horizontal gene transfer and ORFans. Furthermore, all orthologous genes evolved under strong purifying selection with a non-synonymous and synonymous ratio in the same range as the ratio found in the prokaryotic world. The comparison between fossil and modern Pithovirus species provided an estimation of the cadence of the molecular clock, reaching up to 3 × 10−6 mutations/site/year. In addition, the strict conservation of HGTs and ORFans in P. massiliensis revealed the stable genetic mosaicism in giant viruses and excludes the concept of a bag of genes. The genetic stability for 30,000 years of P. massiliensis demonstrates that giant viruses evolve similarly to prokaryotes by classical mechanisms of evolution, including selection and fixation of genes, followed by selective constraints.
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Affiliation(s)
- Anthony Levasseur
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM U1095, IHU Méditerranée Infection, Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille, Faculté de Médecine, Marseille 13005, France
| | - Julien Andreani
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM U1095, IHU Méditerranée Infection, Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille, Faculté de Médecine, Marseille 13005, France
| | - Jeremy Delerce
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM U1095, IHU Méditerranée Infection, Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille, Faculté de Médecine, Marseille 13005, France
| | - Jacques Bou Khalil
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM U1095, IHU Méditerranée Infection, Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille, Faculté de Médecine, Marseille 13005, France
| | - Catherine Robert
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM U1095, IHU Méditerranée Infection, Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille, Faculté de Médecine, Marseille 13005, France
| | - Bernard La Scola
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM U1095, IHU Méditerranée Infection, Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille, Faculté de Médecine, Marseille 13005, France
| | - Didier Raoult
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM U1095, IHU Méditerranée Infection, Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille, Faculté de Médecine, Marseille 13005, France
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70
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Hill NJ, Runstadler JA. A Bird's Eye View of Influenza A Virus Transmission: Challenges with Characterizing Both Sides of a Co-Evolutionary Dynamic. Integr Comp Biol 2016; 56:304-16. [PMID: 27252222 PMCID: PMC5964799 DOI: 10.1093/icb/icw055] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In nature, wild birds and influenza A viruses (IAV) are continually co-evolving, locked into a back-and-forth of resistance and conquest that has approached a stable equilibrium over time. This co-evolutionary relationship between bird host and IAV may appear stable at the organismal level, but is highly dynamic at the molecular level manifesting in a constant trade-off between transmissibility and virulence of the virus. Characterizing both sides of the host-virus dynamic has presented a challenge for ecologists and virologists alike, despite the potential for this approach to provide insights into which conditions destabilize the equilibrium state resulting in outbreaks or mortality of hosts in extreme cases. The use of different methods that are either host-centric or virus-centric has made it difficult to reconcile the disparate fields of host ecology and virology for investigating and ultimately predicting wild bird-mediated transmission of IAV. This review distills some of the key lessons learned from virological and ecological studies and explores the promises and pitfalls of both approaches. Ultimately, reconciling ecological and virological approaches hinges on integrating scales for measuring host-virus interactions. We argue that prospects for finding common scales for measuring wild bird-influenza dynamics are improving due to advances in genomic sequencing, host-tracking technology and remote sensing data, with the unit of time (months, year, or seasons) providing a starting point for crossover.
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Affiliation(s)
- Nichola J Hill
- Massachusetts Institute of Technology, Division of Comparative Medicine & Department of Biological Engineering, 77 Massachusetts Ave, Cambridge 02139
| | - Jonathan A Runstadler
- Massachusetts Institute of Technology, Division of Comparative Medicine & Department of Biological Engineering, 77 Massachusetts Ave, Cambridge 02139
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71
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Hillung J, García-García F, Dopazo J, Cuevas JM, Elena SF. The transcriptomics of an experimentally evolved plant-virus interaction. Sci Rep 2016; 6:24901. [PMID: 27113435 PMCID: PMC4845063 DOI: 10.1038/srep24901] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/07/2016] [Indexed: 01/14/2023] Open
Abstract
Models of plant-virus interaction assume that the ability of a virus to infect a host genotype depends on the matching between virulence and resistance genes. Recently, we evolved tobacco etch potyvirus (TEV) lineages on different ecotypes of Arabidopsis thaliana, and found that some ecotypes selected for specialist viruses whereas others selected for generalists. Here we sought to evaluate the transcriptomic basis of such relationships. We have characterized the transcriptomic responses of five ecotypes infected with the ancestral and evolved viruses. Genes and functional categories differentially expressed by plants infected with local TEV isolates were identified, showing heterogeneous responses among ecotypes, although significant parallelism existed among lineages evolved in the same ecotype. Although genes involved in immune responses were altered upon infection, other functional groups were also pervasively over-represented, suggesting that plant resistance genes were not the only drivers of viral adaptation. Finally, the transcriptomic consequences of infection with the generalist and specialist lineages were compared. Whilst the generalist induced very similar perturbations in the transcriptomes of the different ecotypes, the perturbations induced by the specialist were divergent. Plant defense mechanisms were activated when the infecting virus was specialist but they were down-regulated when infecting with generalist.
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Affiliation(s)
- Julia Hillung
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain
| | - Francisco García-García
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Eduardo Primo Yúfera 3, 46012 València, Spain
| | - Joaquín Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Eduardo Primo Yúfera 3, 46012 València, Spain
- Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), 46012 València, Spain
- Functional Genomics Node, INB at CIPF, 46012 València, Spain
| | - José M. Cuevas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain
| | - Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM 87501, USA
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72
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Reddy KE, Yoo MS, Kim YH, Kim NH, Ramya M, Jung HN, Thao LTB, Lee HS, Kang SW. Homology differences between complete Sacbrood virus genomes from infected Apis mellifera and Apis cerana honeybees in Korea. Virus Genes 2016; 52:281-9. [PMID: 26810400 DOI: 10.1007/s11262-015-1268-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/01/2015] [Indexed: 11/27/2022]
Abstract
Sacbrood virus (SBV) represents a serious threat to the health of managed honeybees. We determined four complete SBV genomic sequences (AmSBV-Kor1, AmSBV-Kor2, AcSBV-Kor3, and AcSBV-Kor4) isolated from Apis mellifera and Apis cerana in various regions of South Korea. A phylogenetic tree was constructed from the complete genomic sequences of these Korean SBVs (KSBVs) and 21 previously reported SBV sequences from other countries. Three KSBVs (not AmSBV-Kor1) clustered with previously reported Korean genomes, but separately from SBV genomes from other countries. The KSBVs shared 90-98 % identity, and 89-97 % identity with the genomes from other countries. AmSBV-Kor1 was least similar (~90 % identity) to the other KSBVs, and was most similar to previously reported strains AmSBV-Kor21 (97 %) and AmSBV-UK (93 %). Phylogenetic analysis of the partial VP1 region sequences indicated that SBVs clustered by host species and country of origin. The KSBVs were aligned with nine previously reported complete SBV genomes and compared. The KSBVs were most different from the other genomes at the end of the 5' untranslated region and in the entire open reading frame. A SimPlot graph of the VP1 region confirmed its high variability, especially between the SBVs infecting A. mellifera and A. cerana. In this genomic region, SBVs from A. mellifera species contain an extra continuous 51-nucleotide sequence relative to the SBVs from A. cerana. This genomic diversity may reflect the adaptation of SBV to specific hosts, viral cross-infections, and the spatial distances separating the KSBVs from other SBVs.
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Affiliation(s)
- Kondreddy Eswar Reddy
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea.
- Plant Molecular Biology Lab, Department of Botany, S. K. University, Anantapur, Andhrapradesh, India.
| | - Mi Sun Yoo
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
| | - Young-Ha Kim
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
| | - Nam-Hee Kim
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
| | - Mummadireddy Ramya
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
- Plant Molecular Biology Lab, Department of Botany, S. K. University, Anantapur, Andhrapradesh, India
| | - Ha-Na Jung
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
| | - Le Thi Bich Thao
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Hee-Soo Lee
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
| | - Seung-Won Kang
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea.
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Weber de Melo V, Sheikh Ali H, Freise J, Kühnert D, Essbauer S, Mertens M, Wanka KM, Drewes S, Ulrich RG, Heckel G. Spatiotemporal dynamics of Puumala hantavirus associated with its rodent host, Myodes glareolus. Evol Appl 2015; 8:545-59. [PMID: 26136821 PMCID: PMC4479511 DOI: 10.1111/eva.12263] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 03/23/2015] [Indexed: 12/15/2022] Open
Abstract
Many viruses significantly impact human and animal health. Understanding the population dynamics of these viruses and their hosts can provide important insights for epidemiology and virus evolution. Puumala virus (PUUV) is a European hantavirus that may cause regional outbreaks of hemorrhagic fever with renal syndrome in humans. Here, we analyzed the spatiotemporal dynamics of PUUV circulating in local populations of its rodent reservoir host, the bank vole (Myodes glareolus) during eight years. Phylogenetic and population genetic analyses of all three genome segments of PUUV showed strong geographical structuring at a very local scale. There was a high temporal turnover of virus strains in the local bank vole populations, but several virus strains persisted through multiple years. Phylodynamic analyses showed no significant changes in the local effective population sizes of PUUV, although vole numbers and virus prevalence fluctuated widely. Microsatellite data demonstrated also a temporally persisting subdivision between local vole populations, but these groups did not correspond to the subdivision in the virus strains. We conclude that restricted transmission between vole populations and genetic drift play important roles in shaping the genetic structure and temporal dynamics of PUUV in its natural host which has several implications for zoonotic risks of the human population.
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Affiliation(s)
- Vanessa Weber de Melo
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of BernBern, Switzerland
| | - Hanan Sheikh Ali
- Institute for Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal HealthGreifswald-Insel Riems, Germany
- College of Veterinary Medicine, Sudan University of Science and TechnologyKhartoum, Sudan
| | - Jona Freise
- Fachbereich Schädlingsbekämpfung, Niedersächsisches Landesamt für Verbraucherschutz und LebensmittelsicherheitWardenburg, Germany
| | - Denise Kühnert
- Department of Environmental Systems Science, Eidgenössische Technische Hochschule ZürichZürich, Switzerland
| | - Sandra Essbauer
- Department of Virology & Rickettsiology, Bundeswehr Institute of MicrobiologyMunich, Germany
| | - Marc Mertens
- Institute for Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal HealthGreifswald-Insel Riems, Germany
| | - Konrad M Wanka
- Institute for Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal HealthGreifswald-Insel Riems, Germany
| | - Stephan Drewes
- Institute for Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal HealthGreifswald-Insel Riems, Germany
| | - Rainer G Ulrich
- Institute for Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal HealthGreifswald-Insel Riems, Germany
| | - Gerald Heckel
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of BernBern, Switzerland
- Swiss Institute of BioinformaticsLausanne, Switzerland
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Rodelo-Urrego M, García-Arenal F, Pagán I. The effect of ecosystem biodiversity on virus genetic diversity depends on virus species: A study of chiltepin-infecting begomoviruses in Mexico. Virus Evol 2015; 1:vev004. [PMID: 27774278 PMCID: PMC5014474 DOI: 10.1093/ve/vev004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Current declines in biodiversity put at risk ecosystem services that are fundamental for human welfare. Increasing evidence indicates that one such service is the ability to reduce virus emergence. It has been proposed that the reduction of virus emergence occurs at two levels: through a reduction of virus prevalence/transmission and, as a result of these epidemiological changes, through a limitation of virus genetic diversity. Although the former mechanism has been studied in a few host-virus interactions, very little is known about the association between ecosystem biodiversity and virus genetic diversity. To address this subject, we estimated genetic diversity, synonymous and non-synonymous nucleotide substitution rates, selection pressures, and frequency of recombinants and re-assortants in populations of Pepper golden mosaic virus (PepGMV) and Pepper huasteco yellow vein virus (PHYVV) that infect chiltepin plants in Mexico. We then analyzed how these parameters varied according to the level of habitat anthropization, which is the major cause of biodiversity loss. Our results indicated that genetic diversity of PepGMV (but not of PHYVV) populations increased with the loss of biodiversity at higher levels of habitat anthropization. This was mostly the consequence of higher rates of synonymous nucleotide substitutions, rather than of adaptive selection. The frequency of recombinants and re-assortants was higher in PepGMV populations infecting wild chiltepin than in those infecting cultivated ones, suggesting that genetic exchange is not the main mechanism for generating genetic diversity in PepGMV populations. These findings provide evidence that biodiversity may modulate the genetic diversity of plant viruses, but it may differentially affect even two closely related viruses. Our analyses may contribute to understanding the factors involved in virus emergence.
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Affiliation(s)
- Manuel Rodelo-Urrego
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and Dpto. de Biotecnología, Campus Montegancedo, Universidad Politécnica de Madrid, Autopista M40 (Km. 38), 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and Dpto. de Biotecnología, Campus Montegancedo, Universidad Politécnica de Madrid, Autopista M40 (Km. 38), 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and Dpto. de Biotecnología, Campus Montegancedo, Universidad Politécnica de Madrid, Autopista M40 (Km. 38), 28223, Pozuelo de Alarcón, Madrid, Spain
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75
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Fries AC, Nolting JM, Bowman AS, Lin X, Halpin RA, Wester E, Fedorova N, Stockwell TB, Das SR, Dugan VG, Wentworth DE, Gibbs HL, Slemons RD. Spread and persistence of influenza A viruses in waterfowl hosts in the North American Mississippi migratory flyway. J Virol 2015; 89:5371-81. [PMID: 25741003 PMCID: PMC4442537 DOI: 10.1128/jvi.03249-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 02/23/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED While geographic distance often restricts the spread of pathogens via hosts, this barrier may be compromised when host species are mobile. Migratory waterfowl in the order Anseriformes are important reservoir hosts for diverse populations of avian-origin influenza A viruses (AIVs) and are assumed to spread AIVs during their annual continental-scale migrations. However, support for this hypothesis is limited, and it is rarely tested using data from comprehensive surveillance efforts incorporating both the temporal and spatial aspects of host migratory patterns. We conducted intensive AIV surveillance of waterfowl using the North American Mississippi Migratory Flyway (MMF) over three autumn migratory seasons. Viral isolates (n = 297) from multiple host species were sequenced and analyzed for patterns of gene dispersal between northern staging and southern wintering locations. Using a phylogenetic and nucleotide identity framework, we observed a larger amount of gene dispersal within this flyway rather than between the other three longitudinally identified North American flyways. Across seasons, we observed patterns of regional persistence of diversity for each genomic segment, along with limited survival of dispersed AIV gene lineages. Reassortment increased with both time and distance, resulting in transient AIV constellations. This study shows that within the MMF, AIV gene flow favors spread along the migratory corridor within a season, and also that intensive surveillance during bird migration is important for identifying virus dispersal on time scales relevant to pandemic responsiveness. In addition, this study indicates that comprehensive monitoring programs to capture AIV diversity are critical for providing insight into AIV evolution and ecology in a major natural reservoir. IMPORTANCE Migratory birds are a reservoir for antigenic and genetic diversity of influenza A viruses (AIVs) and are implicated in the spread of virus diversity that has contributed to previous pandemic events. Evidence for dispersal of avian-origin AIVs by migratory birds is rarely examined on temporal scales relevant to pandemic or panzootic threats. Therefore, characterizing AIV movement by hosts within a migratory season is important for implementing effective surveillance strategies. We conducted surveillance following birds along a major North American migratory route and observed that within a migratory season, AIVs rapidly reassorted and gene lineages were dispersed primarily within the migratory corridor. Patterns of regional persistence were observed across seasons for each gene segment. We show that dispersal of AIV gene lineages by migratory birds occurs quickly along migratory routes and that surveillance for AIVs threatening human and animal health should focus attention on these routes.
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Affiliation(s)
- Anthony C Fries
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
| | - Jacqueline M Nolting
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Andrew S Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Xudong Lin
- J. Craig Venter Institute, Virology, Rockville, Maryland, USA
| | | | - Eric Wester
- J. Craig Venter Institute, Virology, Rockville, Maryland, USA
| | - Nadia Fedorova
- J. Craig Venter Institute, Virology, Rockville, Maryland, USA
| | | | - Suman R Das
- J. Craig Venter Institute, Virology, Rockville, Maryland, USA
| | - Vivien G Dugan
- J. Craig Venter Institute, Virology, Rockville, Maryland, USA
| | | | - H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, Ohio, USA Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
| | - Richard D Slemons
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
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76
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Affiliation(s)
- Antoine Gessain
- Unit of Epidemiology and Physiopathology of Oncogenic Viruses, Institut Pasteur, and Centre National de la Recherche Scientifique, UMR 356928 rue du Docteur Roux, F75015 Paris, France.
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, Campus de Montegancedo, and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Madrid, Spain.
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Cheung PPH, Rogozin IB, Choy KT, Ng HY, Peiris JSM, Yen HL. Comparative mutational analyses of influenza A viruses. RNA (NEW YORK, N.Y.) 2015; 21:36-47. [PMID: 25404565 PMCID: PMC4274636 DOI: 10.1261/rna.045369.114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The error-prone RNA-dependent RNA polymerase (RdRP) and external selective pressures are the driving forces for RNA viral diversity. When confounded by selective pressures, it is difficult to assess if influenza A viruses (IAV) that have a wide host range possess comparable or distinct spontaneous mutational frequency in their RdRPs. We used in-depth bioinformatics analyses to assess the spontaneous mutational frequencies of two RdRPs derived from human seasonal (A/Wuhan/359/95; Wuhan) and H5N1 (A/Vietnam/1203/04; VN1203) viruses using the mini-genome system with a common firefly luciferase reporter serving as the template. High-fidelity reverse transcriptase was applied to generate high-quality mutational spectra which allowed us to assess and compare the mutational frequencies and mutable motifs along a target sequence of the two RdRPs of two different subtypes. We observed correlated mutational spectra (τ correlation P < 0.0001), comparable mutational frequencies (H3N2:5.8 ± 0.9; H5N1:6.0 ± 0.5), and discovered a highly mutable motif "(A)AAG" for both Wuhan and VN1203 RdRPs. Results were then confirmed with two recombinant A/Puerto Rico/8/34 (PR8) viruses that possess RdRP derived from Wuhan or VN1203 (RG-PR8×Wuhan(PB2, PB1, PA, NP) and RG-PR8×VN1203(PB2, PB1, PA, NP)). Applying novel bioinformatics analysis on influenza mutational spectra, we provide a platform for a comprehensive analysis of the spontaneous mutation spectra for an RNA virus.
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Affiliation(s)
- Peter Pak-Hang Cheung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894-6075, USA
| | - Ka-Tim Choy
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Hoi Yee Ng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Joseph Sriyal Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Hui-Ling Yen
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
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Cassone BJ, Cisneros Carter FM, Michel AP, Stewart LR, Redinbaugh MG. Genetic insights into Graminella nigrifrons Competence for maize fine streak virus infection and transmission. PLoS One 2014; 9:e113529. [PMID: 25420026 PMCID: PMC4242632 DOI: 10.1371/journal.pone.0113529] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 10/29/2014] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Most plant-infecting rhabdoviruses are transmitted by one or a few closely related insect species. Additionally, intraspecific differences in transmission efficacy often exist among races/biotypes within vector species and among strains within a virus species. The black-faced leafhopper, Graminella nigrifrons, is the only known vector of the persistent propagative rhabdovirus Maize fine streak virus (MFSV). Only a small percentage of leafhoppers are capable of transmitting the virus, although the mechanisms underlying vector competence are not well understood. METHODOLOGY RNA-Seq was carried out to explore transcript expression changes and sequence variation in G. nigrifrons and MFSV that may be associated with the ability of the vector to acquire and transmit the virus. RT-qPCR assays were used to validate differential transcript accumulation. RESULTS/SIGNIFICANCE Feeding on MFSV-infected maize elicited a considerable transcriptional response in G. nigrifrons, with increased expression of cytoskeleton organization and immunity transcripts in infected leafhoppers. Differences between leafhoppers capable of transmitting MFSV, relative to non-transmitting but infected leafhoppers were more limited, which may reflect difficulties discerning between the two groups and/or the likelihood that the transmitter phenotype results from one or a few genetic differences. The ability of infected leafhoppers to transmit MFSV did not appear associated with virus transcript accumulation in the infected leafhoppers or sequence polymorphisms in the viral genome. However, the non-structural MFSV 3 gene was expressed at unexpectedly high levels in infected leafhoppers, suggesting it plays an active role in the infection of the insect host. The results of this study begin to define the functional roles of specific G. nigrifrons and MFSV genes in the viral transmission process.
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Affiliation(s)
- Bryan J. Cassone
- United States Department of Agriculture- Agricultural Research Service, Corn, Soybean and Wheat Quality Research Unit, Ohio Agricultural Research and Development Center (OARDC), Wooster, Ohio, United States of America
| | - Fiorella M. Cisneros Carter
- Department of Plant Pathology, Ohio Agricultural Research and Development Center (OARDC), The Ohio State University, Wooster, Ohio, United States of America
| | - Andrew P. Michel
- Department of Entomology, The Ohio State University, Ohio Agricultural Research and Development Center (OARDC), The Ohio State University, Wooster, Ohio, United States of America
| | - Lucy R. Stewart
- United States Department of Agriculture- Agricultural Research Service, Corn, Soybean and Wheat Quality Research Unit, Ohio Agricultural Research and Development Center (OARDC), Wooster, Ohio, United States of America
- Department of Plant Pathology, Ohio Agricultural Research and Development Center (OARDC), The Ohio State University, Wooster, Ohio, United States of America
| | - Margaret G. Redinbaugh
- United States Department of Agriculture- Agricultural Research Service, Corn, Soybean and Wheat Quality Research Unit, Ohio Agricultural Research and Development Center (OARDC), Wooster, Ohio, United States of America
- Department of Plant Pathology, Ohio Agricultural Research and Development Center (OARDC), The Ohio State University, Wooster, Ohio, United States of America
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79
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Bedhomme S, Hillung J, Elena SF. Emerging viruses: why they are not jacks of all trades? Curr Opin Virol 2014; 10:1-6. [PMID: 25467278 DOI: 10.1016/j.coviro.2014.10.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/27/2014] [Accepted: 10/28/2014] [Indexed: 12/21/2022]
Abstract
In order to limit the impact of the recent pandemics ignited by viral host jumps, it is necessary to better understand the ecological and evolutionary factors influencing the early steps of emergence and the interactions between them. Antagonistic pleiotropy, that is, the negative fitness effect in the primary host of mutations allowing the infection of and the multiplication in a new host, has long been thought to be the main limitation to the evolution of generalist viruses and thus to emergence. However, the accumulation of experimental examples contradicting the hypothesis of antagonistic pleiotropy has highlighted the importance of other factors such as the epistasis between mutations increasing the adaptation to a new host. Epistasis is pervasive in viruses, affects the shape of the adaptive landscape and consequently the accessibility of evolutionary pathways. Finally, recent studies have gone steps further in the complexity of viral fitness determinism and stressed the potential importance of the epistatic pleiotropy and of the impact of host living conditions.
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Affiliation(s)
- Stéphanie Bedhomme
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022 Valencia, Spain.
| | - Julia Hillung
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022 Valencia, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022 Valencia, Spain; The Santa Fe Institute, Santa Fe, NM 87501, USA
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80
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Viral biocontrol: grand experiments in disease emergence and evolution. Trends Microbiol 2014; 23:83-90. [PMID: 25455418 DOI: 10.1016/j.tim.2014.10.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 10/08/2014] [Accepted: 10/10/2014] [Indexed: 02/05/2023]
Abstract
Although viral emergence is commonly associated with cross-species transmission, the processes and determinants of viral evolution in a novel host environment are poorly understood. We address key questions in virus emergence and evolution using data generated from two unique natural experiments: the deliberate release of myxoma virus (MYXV) and rabbit hemorrhagic disease virus (RHDV) as biological control (biocontrol) agents against the European rabbit in Australia, and which have been of enormous benefit to Australia's ecosystem and agricultural industries. Notably, although virulence evolution in MYXV and RHDV followed different trajectories, a strongly parallel evolutionary process was observed in Australia and Europe. These biocontrol agents were also characterized by a lack of transmission to nontarget host species, suggesting that there are major barriers to successful emergence.
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81
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Dunham JP, Simmons HE, Holmes EC, Stephenson AG. Analysis of viral (zucchini yellow mosaic virus) genetic diversity during systemic movement through a Cucurbita pepo vine. Virus Res 2014; 191:172-179. [PMID: 25107623 PMCID: PMC4176823 DOI: 10.1016/j.virusres.2014.07.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/23/2014] [Accepted: 07/26/2014] [Indexed: 01/04/2023]
Abstract
Determining the extent and structure of intra-host genetic diversity and the magnitude and impact of population bottlenecks is central to understanding the mechanisms of viral evolution. To determine the nature of viral evolution following systemic movement through a plant, we performed deep sequencing of 23 leaves that grew sequentially along a single Cucurbita pepo vine that was infected with zucchini yellow mosaic virus (ZYMV), and on a leaf that grew in on a side branch. Strikingly, of 112 genetic (i.e. sub-consensus) variants observed in the data set as a whole, only 22 were found in multiple leaves. Similarly, only three of the 13 variants present in the inoculating population were found in the subsequent leaves on the vine. Hence, it appears that systemic movement is characterized by sequential population bottlenecks, although not sufficient to reduce the population to a single virion as multiple variants were consistently transmitted between leaves. In addition, the number of variants within a leaf increases as a function of distance from the inoculated (source) leaf, suggesting that the circulating sap may serve as a continual source of virus. Notably, multiple mutational variants were observed in the cylindrical inclusion (CI) protein (known to be involved in both cell-to-cell and systemic movement of the virus) that were present in multiple (19/24) leaf samples. These mutations resulted in a conformational change, suggesting that they might confer a selective advantage in systemic movement within the vine. Overall, these data reveal that bottlenecks occur during systemic movement, that variants circulate in the phloem sap throughout the infection process, and that important conformational changes in CI protein may arise during individual infections.
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Affiliation(s)
- J P Dunham
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90033, USA
| | - H E Simmons
- Seed Science Center, Iowa State University, Ames, IA 50011, USA
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - E C Holmes
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Marie Bashir Institute for Emerging Diseases & Biosecurity, Charles Perkins Centre, School of Biological Sciences and Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - A G Stephenson
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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An evolutionary analysis of the Secoviridae family of viruses. PLoS One 2014; 9:e106305. [PMID: 25180860 PMCID: PMC4152289 DOI: 10.1371/journal.pone.0106305] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/04/2014] [Indexed: 01/03/2023] Open
Abstract
The plant-infecting Secoviridae family of viruses forms part of the Picornavirales order, an important group of non-enveloped viruses that infect vertebrates, arthropods, plants and algae. The impact of the secovirids on cultivated crops is significant, infecting a wide range of plants from grapevine to rice. The overwhelming majority are transmitted by ecdysozoan vectors such as nematodes, beetles and aphids. In this study, we have applied a variety of computational methods to examine the evolutionary traits of these viruses. Strong purifying selection pressures were calculated for the coat protein (CP) sequences of nine species, although for two species evidence of both codon specific and episodic diversifying selection were found. By using Bayesian phylogenetic reconstruction methods CP nucleotide substitution rates for four species were estimated to range from between 9.29×10−3 to 2.74×10−3 (subs/site/year), values which are comparable with the short-term estimates of other related plant- and animal-infecting virus species. From these data, we were able to construct a time-measured phylogeny of the subfamily Comovirinae that estimated divergence of ninety-four extant sequences occurred less than 1,000 years ago with present virus species diversifying between 50 and 250 years ago; a period coinciding with the intensification of agricultural practices in industrial societies. Although recombination (modularity) was limited to closely related taxa, significant and often unique similarities in the protein domains between secovirid and animal infecting picorna-like viruses, especially for the protease and coat protein, suggested a shared ancestry. We discuss our results in a wider context and find tentative evidence to indicate that some members of the Secoviridae might have their origins in insects, possibly colonizing plants in a number of founding events that have led to speciation. Such a scenario; virus infection between species of different taxonomic kingdoms, has significant implications for virus emergence.
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83
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Zheng N, Whalen CC, Handel A. Modeling the potential impact of host population survival on the evolution of M. tuberculosis latency. PLoS One 2014; 9:e105721. [PMID: 25157958 PMCID: PMC4144956 DOI: 10.1371/journal.pone.0105721] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 07/28/2014] [Indexed: 02/01/2023] Open
Abstract
Tuberculosis (TB) is an infectious disease with a peculiar feature: Upon infection with the causative agent, Mycobacterium Tuberculosis (MTB), most hosts enter a latent state during which no transmission of MTB to new hosts occurs. Only a fraction of latently infected hosts develop TB disease and can potentially infect new hosts. At first glance, this seems like a waste of transmission potential and therefore an evolutionary suboptimal strategy for MTB. It might be that the human immune response keeps MTB in check in most hosts, thereby preventing it from achieving its evolutionary optimum. Another possible explanation is that long latency and progression to disease in only a fraction of hosts are evolutionary beneficial to MTB by allowing it to persist better in small host populations. Given that MTB has co-evolved with human hosts for millenia or longer, it likely encountered small host populations for a large share of its evolutionary history and had to evolve strategies of persistence. Here, we use a mathematical model to show that indeed, MTB persistence is optimal for an intermediate duration of latency and level of activation. The predicted optimal level of activation is above the observed value, suggesting that human co-evolution has lead to host immunity, which keeps MTB below its evolutionary optimum.
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Affiliation(s)
- Nibiao Zheng
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Christopher C. Whalen
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, Georgia, United States of America
| | - Andreas Handel
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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84
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Arnaud-Haond S, Moalic Y, Barnabé C, Ayala FJ, Tibayrenc M. Discriminating micropathogen lineages and their reticulate evolution through graph theory-based network analysis: the case of Trypanosoma cruzi, the agent of Chagas disease. PLoS One 2014; 9:e103213. [PMID: 25148574 PMCID: PMC4141739 DOI: 10.1371/journal.pone.0103213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 06/28/2014] [Indexed: 12/02/2022] Open
Abstract
Micropathogens (viruses, bacteria, fungi, parasitic protozoa) share a common trait, which is partial clonality, with wide variance in the respective influence of clonality and sexual recombination on the dynamics and evolution of taxa. The discrimination of distinct lineages and the reconstruction of their phylogenetic history are key information to infer their biomedical properties. However, the phylogenetic picture is often clouded by occasional events of recombination across divergent lineages, limiting the relevance of classical phylogenetic analysis and dichotomic trees. We have applied a network analysis based on graph theory to illustrate the relationships among genotypes of Trypanosoma cruzi, the parasitic protozoan responsible for Chagas disease, to identify major lineages and to unravel their past history of divergence and possible recombination events. At the scale of T. cruzi subspecific diversity, graph theory-based networks applied to 22 isoenzyme loci (262 distinct Multi-Locus-Enzyme-Electrophoresis -MLEE) and 19 microsatellite loci (66 Multi-Locus-Genotypes -MLG) fully confirms the high clustering of genotypes into major lineages or "near-clades". The release of the dichotomic constraint associated with phylogenetic reconstruction usually applied to Multilocus data allows identifying putative hybrids and their parental lineages. Reticulate topology suggests a slightly different history for some of the main "near-clades", and a possibly more complex origin for the putative hybrids than hitherto proposed. Finally the sub-network of the near-clade T. cruzi I (28 MLG) shows a clustering subdivision into three differentiated lesser near-clades ("Russian doll pattern"), which confirms the hypothesis recently proposed by other investigators. The present study broadens and clarifies the hypotheses previously obtained from classical markers on the same sets of data, which demonstrates the added value of this approach. This underlines the potential of graph theory-based network analysis for describing the nature and relationships of major pathogens, thereby opening stimulating prospects to unravel the organization, dynamics and history of major micropathogen lineages.
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Affiliation(s)
- Sophie Arnaud-Haond
- IFREMER (Institut Français de Recherche pour l'Exploitation de la Mer) - Département Ecosystèmes Marins Exploités, Sète, France
| | - Yann Moalic
- IFREMER (Institut Français de Recherche pour l'Exploitation de la Mer) - Département Ecosystèmes Marins Exploités, Sète, France
| | - Christian Barnabé
- Interactions hôte-vecteur-parasite dans les maladies dues aux Trypanosomatidés, INTERTRYP (IRD-CIRAD), Montpellier, France
| | - Francisco José Ayala
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
| | - Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Montpellier, France
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85
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Qin L, Ma Y, Liang P, Tan Z, Li S. Differential distributions of mononucleotide repeat sequences in 256 viral genomes and its potential implications. Gene 2014; 544:159-64. [PMID: 24786215 DOI: 10.1016/j.gene.2014.04.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/14/2014] [Accepted: 04/26/2014] [Indexed: 11/18/2022]
Abstract
Mononucleotide repeats (MNRs) have been systematically investigated in the genomes of eukaryotic and prokaryotic organisms. However, detailed information on the distribution of MNRs in viral genomes is limited. In this study, we examined the distributions of MNRs in 256 fully sequenced virus genomes which showed extensive variations across viral genomes, and is significantly influenced by both genome size and CG content. Furthermore, the ratio of the observed to the expected number of MNRs (O/E ratio) appears to be influenced by both the host range and genome type of a particular virus. Additionally, the densities and frequencies of MNRs in genic regions are lower than in non-coding regions, suggesting that selective pressure acts on viral genomes. We also discuss the potential functional roles that these MNR loci could play in virus genomes. To our knowledge, this is the first analysis focusing on MNRs in viruses, and our study could have potential implications for a deeper understanding of virus genome stability and the co-evolution that occurs between a virus and its host.
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Affiliation(s)
- Lü Qin
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; College of Biology, State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
| | - Yuxin Ma
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Pengbo Liang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, China
| | - Zhongyang Tan
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; College of Biology, State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China.
| | - Shifang Li
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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86
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Waxman D, Weinert LA, Welch JJ. Inferring host range dynamics from comparative data: the protozoan parasites of new world monkeys. Am Nat 2014; 184:65-74. [PMID: 24921601 DOI: 10.1086/676589] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Uncovering the ecological determinants of parasite host range is a central goal of comparative parasitology and infectious disease ecology. But while parasites are often distributed nonrandomly across the host phylogeny, such patterns are difficult to interpret without a genealogy for the parasite samples and without knowing what sorts of ecological dynamics might lead to what sorts of nonrandomness. We investigated inferences from comparative data, using presence/absence records from protozoan parasites of the New World monkeys. We first demonstrate several distinct types of phylogenetic signal in these data, showing, for example, that parasite species are clustered on the host tree and that closely related host species harbor similar numbers of parasite species. We then show that all of these patterns can be generated by a single, simple dynamical model, in which parasite host range changes more rapidly than host speciation/extinction and parasites preferentially colonize uninfected host species that are closely related to their existing hosts. Fitting this model to data, we then estimate its parameters. Finally, we caution that quite different ecological processes can lead to similar signatures but show how phylogenetic variation in host susceptibility can be distinguished from a tendency for parasites to colonize closely related hosts. Our new process-based analyses, which estimate meaningful parameters, should be useful for inferring the determinants of parasite host range and transmission success.
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Affiliation(s)
- David Waxman
- Centre for Computational Systems Biology, Fudan University, Shanghai 200433, People's Republic of China
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87
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Abstract
ABSTRACT: It is well established that RNA viruses show extremely high mutation rates, but less attention has been paid to the fact that their mutation rates also vary strongly, from 10-6 to 10-4 substitutions per nucleotide per cell infection. The causes explaining this variability are still poorly understood, but candidate factors are the viral genome size and polarity, host-specific gene expression patterns, or the intracellular environment. Differences between animal and plant viruses, or between arthropod-borne and directly transmitted viruses have also been postulated. Finally, RNA viruses may be able to regulate the rate at which new mutations spread in the population by modifying features of the viral infection cycle, such as lysis time.
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Affiliation(s)
- Marine Combe
- Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Valencia, Spain
| | - Rafael Sanjuán
- Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Valencia, Spain
- Departament de Genetica, Universitat de Valencia, Valencia, Spain
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88
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Miras M, Sempere RN, Kraft JJ, Miller WA, Aranda MA, Truniger V. Interfamilial recombination between viruses led to acquisition of a novel translation-enhancing RNA element that allows resistance breaking. THE NEW PHYTOLOGIST 2014; 202:233-246. [PMID: 24372390 PMCID: PMC4337425 DOI: 10.1111/nph.12650] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/19/2013] [Indexed: 05/04/2023]
Abstract
Many plant viruses depend on functional RNA elements, called 3'-UTR cap-independent translation enhancers (3'-CITEs), for translation of their RNAs. In this manuscript we provide direct proof for the existing hypothesis that 3'-CITEs are modular and transferable by recombination in nature, and that this is associated with an advantage for the created virus. By characterizing a newly identified Melon necrotic spot virus (MNSV; Tombusviridae) isolate, which is able to overcome eukaryotic translation initiation factor 4E (eIF4E)-mediated resistance, we found that it contains a 55 nucleotide insertion in its 3'-UTR. We provide strong evidence that this insertion was acquired by interfamilial recombination with the 3'-UTR of an Asiatic Cucurbit aphid-borne yellows virus (CABYV; Luteoviridae). By constructing chimeric viruses, we showed that this recombined sequence is responsible for resistance breaking. Analysis of the translational efficiency of reporter constructs showed that this sequence functions as a novel 3'-CITE in both resistant and susceptible plants, being essential for translation control in resistant plants. In conclusion, we showed that a recombination event between two clearly identified viruses from different families led to the transfer of exactly the sequence corresponding to a functional RNA element, giving rise to a new isolate with the capacity to infect an otherwise nonsusceptible host.
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Affiliation(s)
- Manuel Miras
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
| | - Raquel N. Sempere
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
| | - Jelena J. Kraft
- Department of Plant Pathology and Microbiology, Iowa State University, 351 Bessey Hall, Ames, IA 50011, USA
| | - W. Allen Miller
- Department of Plant Pathology and Microbiology, Iowa State University, 351 Bessey Hall, Ames, IA 50011, USA
| | - Miguel A. Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
| | - Veronica Truniger
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Apdo. Correos 164, 30100 Espinardo, Murcia, Spain
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89
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Zanardo LG, Silva FN, Lima ATM, Milanesi DF, Castilho-Urquiza GP, Almeida AMR, Zerbini FM, Carvalho CM. Molecular variability of cowpea mild mottle virus infecting soybean in Brazil. Arch Virol 2014; 159:727-37. [PMID: 24142270 DOI: 10.1007/s00705-013-1879-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 10/03/2013] [Indexed: 11/26/2022]
Abstract
Molecular variability was assessed for 18 isolates of cowpea mild mottle virus (CPMMV, genus Carlavirus, family Betaflexiviridae) found infecting soybean in various Brazilian states (Bahia, Goiás, Maranhão, Mato Grosso, Minas Gerais, Pará) in 2001 and 2010. A variety of symptoms was expressed in soybean cv. CD206, ranging from mild (crinkle/blistering leaves, mosaic and vein clearing) to severe (bud blight, dwarfing, leaf and stem necrosis). Recombination analysis revealed only one CPMMV isolate to be recombinant. Pairwise comparisons and phylogenetic analysis were performed for partial genomes (ORF 2 to the 3' terminus) and for each ORF individually (ORFs 2 to 6), showing the isolates to be distinct. The topology of the phylogenetic tree could be related to symptoms, but not to the year of collection or geographical origin. Additionally, the phylogenetic analysis supported the existence of two distinct strains of the virus, designated CPMMV-BR1 and CPMMV-BR2, with molecular variations between them.
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Affiliation(s)
- L G Zanardo
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
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90
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Kao RR, Haydon DT, Lycett SJ, Murcia PR. Supersize me: how whole-genome sequencing and big data are transforming epidemiology. Trends Microbiol 2014; 22:282-91. [PMID: 24661923 PMCID: PMC7125769 DOI: 10.1016/j.tim.2014.02.011] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 02/17/2014] [Accepted: 02/24/2014] [Indexed: 01/08/2023]
Abstract
Whole-genome sequencing is used for forensic epidemiology. Big data can transform forensic epidemiology. Clustering, biases, wildlife reservoirs, and emerging infections can all be addressed. Phylodynamics approaches to integrate epidemiological and evolutionary data have been highly successful but still face scientific challenges.
In epidemiology, the identification of ‘who infected whom’ allows us to quantify key characteristics such as incubation periods, heterogeneity in transmission rates, duration of infectiousness, and the existence of high-risk groups. Although invaluable, the existence of many plausible infection pathways makes this difficult, and epidemiological contact tracing either uncertain, logistically prohibitive, or both. The recent advent of next-generation sequencing technology allows the identification of traceable differences in the pathogen genome that are transforming our ability to understand high-resolution disease transmission, sometimes even down to the host-to-host scale. We review recent examples of the use of pathogen whole-genome sequencing for the purpose of forensic tracing of transmission pathways, focusing on the particular problems where evolutionary dynamics must be supplemented by epidemiological information on the most likely timing of events as well as possible transmission pathways. We also discuss potential pitfalls in the over-interpretation of these data, and highlight the manner in which a confluence of this technology with sophisticated mathematical and statistical approaches has the potential to produce a paradigm shift in our understanding of infectious disease transmission and control.
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Affiliation(s)
- Rowland R Kao
- Boyd Orr Centre for Population and Ecosystem Health, College of Medical Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK.
| | - Daniel T Haydon
- Boyd Orr Centre for Population and Ecosystem Health, College of Medical Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
| | - Samantha J Lycett
- Boyd Orr Centre for Population and Ecosystem Health, College of Medical Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
| | - Pablo R Murcia
- Medical Research Council (MRC) Centre for Virus Research, College of Medical, Veterinary and Life Sciences, University of Glasgow, G61 1QH, UK
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91
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Moreno-Pérez MG, Pagán I, Aragón-Caballero L, Cáceres F, Fraile A, García-Arenal F. Ecological and genetic determinants of Pepino Mosaic Virus emergence. J Virol 2014; 88:3359-68. [PMID: 24390328 PMCID: PMC3957916 DOI: 10.1128/jvi.02980-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/29/2013] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Virus emergence is a complex phenomenon, which generally involves spread to a new host from a wild host, followed by adaptation to the new host. Although viruses account for the largest fraction of emerging crop pathogens, knowledge about their emergence is incomplete. We address here the question of whether Pepino Mosaic Virus (PepMV) emergence as a major tomato pathogen worldwide could have involved spread from wild to cultivated plant species and host adaptation. For this, we surveyed natural populations of wild tomatoes in southern Peru for PepMV infection. PepMV incidence, genetic variation, population structure, and accumulation in various hosts were analyzed. PepMV incidence in wild tomatoes was high, and a strain not yet reported in domestic tomato was characterized. This strain had a wide host range within the Solanaceae, multiplying efficiently in most assayed Solanum species and being adapted to wild tomato hosts. Conversely, PepMV isolates from tomato crops showed evidence of adaptation to domestic tomato, possibly traded against adaptation to wild tomatoes. Phylogenetic reconstructions indicated that the most probable ancestral sequence came from a wild Solanum species. A high incidence of PepMV in wild tomato relatives would favor virus spread to crops and its efficient multiplication in different Solanum species, including tomato, allowing its establishment as an epidemic pathogen. Later, adaptation to tomato, traded off against adaptation to other Solanum species, would isolate tomato populations from those in other hosts. IMPORTANCE Virus emergence is a complex phenomenon involving multiple ecological and genetic factors and is considered to involve three phases: virus encounter with the new host, virus adaptation to the new host, and changes in the epidemiological dynamics. We analyze here if this was the case in the recent emergence of Pepino Mosaic Virus (PepMV) in tomato crops worldwide. We characterized a new strain of PepMV infecting wild tomato populations in Peru. Comparison of this strain with PepMV isolates from tomato crops, plus phylogenetic reconstructions, supports a scenario in which PepMV would have spread to crops from wild tomato relatives, followed by adaptation to the new host and eventually leading to population isolation. Our data, which derive from the analysis of field isolates rather than from experimental evolution approaches, significantly contribute to understanding of plant virus emergence, which is necessary for its anticipation and prevention.
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Affiliation(s)
- Manuel G. Moreno-Pérez
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Madrid, Spain
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Fátima Cáceres
- Facultad de Ciencias Biológicas y Agropecuarias, Universidad Nacional de San Agustín, Arequipa, Peru
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Madrid, Spain
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92
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Cell tropism predicts long-term nucleotide substitution rates of mammalian RNA viruses. PLoS Pathog 2014; 10:e1003838. [PMID: 24415935 PMCID: PMC3887100 DOI: 10.1371/journal.ppat.1003838] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 11/04/2013] [Indexed: 02/05/2023] Open
Abstract
The high rates of RNA virus evolution are generally attributed to replication with error-prone RNA-dependent RNA polymerases. However, these long-term nucleotide substitution rates span three orders of magnitude and do not correlate well with mutation rates or selection pressures. This substitution rate variation may be explained by differences in virus ecology or intrinsic genomic properties. We generated nucleotide substitution rate estimates for mammalian RNA viruses and compiled comparable published rates, yielding a dataset of 118 substitution rates of structural genes from 51 different species, as well as 40 rates of non-structural genes from 28 species. Through ANCOVA analyses, we evaluated the relationships between these rates and four ecological factors: target cell, transmission route, host range, infection duration; and three genomic properties: genome length, genome sense, genome segmentation. Of these seven factors, we found target cells to be the only significant predictors of viral substitution rates, with tropisms for epithelial cells or neurons (P<0.0001) as the most significant predictors. Further, one-tailed t-tests showed that viruses primarily infecting epithelial cells evolve significantly faster than neurotropic viruses (P<0.0001 and P<0.001 for the structural genes and non-structural genes, respectively). These results provide strong evidence that the fastest evolving mammalian RNA viruses infect cells with the highest turnover rates: the highly proliferative epithelial cells. Estimated viral generation times suggest that epithelial-infecting viruses replicate more quickly than viruses with different cell tropisms. Our results indicate that cell tropism is a key factor in viral evolvability. RNA viruses are the fastest evolving human pathogens, making their treatment and control difficult. Compared to DNA viruses, RNA viruses replicate with much lower fidelity, which can explain why RNA viruses evolve significantly faster than most DNA viruses. However, there is tremendous variation among the evolutionary rates of different RNA viruses, which is not explained by variation in mutation rates. Here we present a survey of mammalian RNA virus rates of evolution, and a comprehensive comparison of these rates to different properties of virus genomic architecture and ecology. We found that cell tropism is the most significant predictor of long-term rates of mammalian RNA virus evolution. For instance, viruses targeting epithelial cells evolve significantly faster than viruses that target neurons. Our results provide mechanistic insight into why viruses that infect respiratory and gastrointestinal epithelia have been difficult to control.
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93
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Phylogenetic Analysis of Viral Haemorrhagic Septicaemia Virus (VHSV) Isolates from Asia. ACTA ACUST UNITED AC 2013. [DOI: 10.7847/jfp.2013.26.3.149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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94
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Kovaliski J, Sinclair R, Mutze G, Peacock D, Strive T, Abrantes J, Esteves PJ, Holmes EC. Molecular epidemiology of Rabbit Haemorrhagic Disease Virus in Australia: when one became many. Mol Ecol 2013; 23:408-20. [PMID: 24251353 DOI: 10.1111/mec.12596] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 11/06/2013] [Accepted: 11/13/2013] [Indexed: 12/20/2022]
Abstract
Rabbit Haemorrhagic Disease Virus (RHDV) was introduced into Australia in 1995 as a biological control agent against the wild European rabbit (Oryctolagus cuniculus). We evaluated its evolution over a 16-year period (1995-2011) by examining 50 isolates collected throughout Australia, as well as the original inoculum strains. Phylogenetic analysis of capsid protein VP60 sequences of the Australian isolates, compared with those sampled globally, revealed that they form a monophyletic group with the inoculum strains (CAPM V-351 and RHDV351INOC). Strikingly, despite more than 3000 rereleases of RHDV351INOC since 1995, only a single viral lineage has sustained its transmission in the long-term, indicative of a major competitive advantage. In addition, we find evidence for widespread viral gene flow, in which multiple lineages entered individual geographic locations, resulting in a marked turnover of viral lineages with time, as well as a continual increase in viral genetic diversity. The rate of RHDV evolution recorded in Australia -4.0 (3.3-4.7) × 10(-3) nucleotide substitutions per site per year - was higher than previously observed in RHDV, and evidence for adaptive evolution was obtained at two VP60 residues. Finally, more intensive study of a single rabbit population (Turretfield) in South Australia provided no evidence for viral persistence between outbreaks, with genetic diversity instead generated by continual strain importation.
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Affiliation(s)
- John Kovaliski
- NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide, SA, 5001, Australia.,Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia
| | - Ron Sinclair
- NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide, SA, 5001, Australia.,Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia
| | - Greg Mutze
- NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide, SA, 5001, Australia.,Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia
| | - David Peacock
- NRM Biosecurity, Biosecurity South Australia, PO Box 1671, Adelaide, SA, 5001, Australia.,Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia
| | - Tanja Strive
- Invasive Animals Cooperative Research Centre, University of Canberra, Canberra, ACT, 2601, Australia.,CSIRO Ecosystem Sciences, Black Mountain Laboratories, Clunies Ross Street, Black Mountain, ACT, 2601, Australia
| | - Joana Abrantes
- CIBIO/UP Centro de Investigação em Biodiversidade e Recursos Genéticos/Universidade do Porto, InBio, Laboratório Associado, Campus Agrário de Vairão, R. Padre Armando Quintas, 4485-661, Vairão, Portugal.,INSERM, U892, Université de Nantes, Nantes, France
| | - Pedro J Esteves
- INSERM, U892, Université de Nantes, Nantes, France.,CITS, Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra, Portugal
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
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95
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Allison AB, Mead DG, Palacios GF, Tesh RB, Holmes EC. Gene duplication and phylogeography of North American members of the Hart Park serogroup of avian rhabdoviruses. Virology 2013; 448:284-92. [PMID: 24314659 PMCID: PMC3873333 DOI: 10.1016/j.virol.2013.10.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 06/11/2013] [Accepted: 10/17/2013] [Indexed: 12/28/2022]
Abstract
Flanders virus (FLAV) and Hart Park virus (HPV) are rhabdoviruses that circulate in mosquito–bird cycles in the eastern and western United States, respectively, and constitute the only two North American representatives of the Hart Park serogroup. Previously, it was suggested that FLAV is unique among the rhabdoviruses in that it contains two pseudogenes located between the P and M genes, while the cognate sequence for HPV has been lacking. Herein, we demonstrate that FLAV and HPV do not contain pseudogenes in this region, but encode three small functional proteins designated as U1–U3 that apparently arose by gene duplication. To further investigate the U1–U3 region, we conducted the first large-scale evolutionary analysis of a member of the Hart Park serogroup by analyzing over 100 spatially and temporally distinct FLAV isolates. Our phylogeographic analysis demonstrates that although FLAV appears to be slowly evolving, phylogenetically divergent lineages co-circulate sympatrically. Flanders virus (FLAV) does not contain pseudogenes as previously reported. The FLAV U1–U3 proteins arose by gene duplication. The SH protein of FLAV is tentatively expressed by coupled translation. Distinct lineages of FLAV circulate sympatrically in the United States. Histone H4 and cyclophilin A are apparently incorporated into FLAV particles.
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Affiliation(s)
- Andrew B Allison
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
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96
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Levitt AL, Singh R, Cox-Foster DL, Rajotte E, Hoover K, Ostiguy N, Holmes EC. Cross-species transmission of honey bee viruses in associated arthropods. Virus Res 2013; 176:232-40. [DOI: 10.1016/j.virusres.2013.06.013] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 06/25/2013] [Accepted: 06/26/2013] [Indexed: 11/17/2022]
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97
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Yin X, Zheng FQ, Tang W, Zhu QQ, Li XD, Zhang GM, Liu HT, Liu BS. Genetic structure of rice black-streaked dwarf virus populations in China. Arch Virol 2013; 158:2505-15. [DOI: 10.1007/s00705-013-1766-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/06/2013] [Indexed: 01/21/2023]
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98
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Lalić J, Elena SF. Epistasis between mutations is host-dependent for an RNA virus. Biol Lett 2013; 9:20120396. [PMID: 22809724 PMCID: PMC3565478 DOI: 10.1098/rsbl.2012.0396] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 06/21/2012] [Indexed: 11/12/2022] Open
Abstract
How, and to what extent, does the environment influence the way mutations interact? Do environmental changes affect both the sign and the magnitude of epistasis? Are there any correlations between environments in the variability, sign or magnitude of epistasis? Very few studies have tackled these questions. Here, we addressed them in the context of viral emergence. Most emerging viruses are RNA viruses with small genomes, overlapping reading frames and multifunctional proteins for which epistasis is abundant. Understanding the effect of host species in the sign and magnitude of epistasis will provide insights into the evolutionary ecology of infectious diseases and the predictability of viral emergence.
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Affiliation(s)
- Jasna Lalić
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, 46022 València, Spain
| | - Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, 46022 València, Spain
- Santa Fe Institute, Santa Fe NM 87501, USA
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99
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Rodelo-Urrego M, Pagán I, González-Jara P, Betancourt M, Moreno-Letelier A, Ayllón MA, Fraile A, Piñero D, García-Arenal F. Landscape heterogeneity shapes host-parasite interactions and results in apparent plant-virus codivergence. Mol Ecol 2013; 22:2325-40. [DOI: 10.1111/mec.12232] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 12/12/2012] [Accepted: 12/20/2012] [Indexed: 12/22/2022]
Affiliation(s)
- M. Rodelo-Urrego
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos; Campus de Montegancedo; Universidad Politécnica de Madrid; Pozuelo de Alarcón Madrid 28223 Spain
| | - I. Pagán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos; Campus de Montegancedo; Universidad Politécnica de Madrid; Pozuelo de Alarcón Madrid 28223 Spain
| | - P. González-Jara
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos; Campus de Montegancedo; Universidad Politécnica de Madrid; Pozuelo de Alarcón Madrid 28223 Spain
| | - M. Betancourt
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos; Campus de Montegancedo; Universidad Politécnica de Madrid; Pozuelo de Alarcón Madrid 28223 Spain
| | - A. Moreno-Letelier
- Departamento de Ecología Evolutiva; Instituto de Ecología; Universidad Nacional Autónoma de México; Apartado Postal 70-275 México DF 04510 México
| | - M. A. Ayllón
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos; Campus de Montegancedo; Universidad Politécnica de Madrid; Pozuelo de Alarcón Madrid 28223 Spain
| | - A. Fraile
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos; Campus de Montegancedo; Universidad Politécnica de Madrid; Pozuelo de Alarcón Madrid 28223 Spain
| | - D. Piñero
- Departamento de Ecología Evolutiva; Instituto de Ecología; Universidad Nacional Autónoma de México; Apartado Postal 70-275 México DF 04510 México
| | - F. García-Arenal
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos; Campus de Montegancedo; Universidad Politécnica de Madrid; Pozuelo de Alarcón Madrid 28223 Spain
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100
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Li Y, Liu R, Zhou T, Fan Z. Genetic diversity and population structure of Sugarcane mosaic virus. Virus Res 2013; 171:242-6. [DOI: 10.1016/j.virusres.2012.10.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Revised: 10/12/2012] [Accepted: 10/22/2012] [Indexed: 11/16/2022]
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