401
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Hochachka WM, Dhondt AA, Dobson A, Hawley DM, Ley DH, Lovette IJ. Multiple host transfers, but only one successful lineage in a continent-spanning emergent pathogen. Proc Biol Sci 2013; 280:20131068. [PMID: 23843387 DOI: 10.1098/rspb.2013.1068] [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] [Indexed: 11/12/2022] Open
Abstract
Emergence of a new disease in a novel host is thought to be a rare outcome following frequent pathogen transfers between host species. However, few opportunities exist to examine whether disease emergence stems from a single successful pathogen transfer, and whether this successful lineage represents only one of several pathogen transfers between hosts. We examined the successful host transfer and subsequent evolution of the bacterial pathogen Mycoplasma gallisepticum, an emergent pathogen of house finches (Haemorhous (formerly Carpodacus) mexicanus). Our principal goals were to assess whether host transfer has been a repeated event between the original poultry hosts and house finches, whether only a single host transfer was ultimately responsible for the emergence of M. gallisepticum in these finches, and whether the spread of the pathogen from east to west across North America has resulted in spatial structuring in the pathogen. Using a phylogeny of M. gallisepticum based on 107 isolates from domestic poultry, house finches and other songbirds, we infer that the bacterium has repeatedly jumped between these two groups of hosts but with only a single lineage of M. gallisepticum persisting and evolving in house finches; bacterial evolution has produced monophyletic eastern and western North American subclades.
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402
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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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403
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Affiliation(s)
- Cadhla Firth
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032; ,
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032; ,
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404
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Niewiadomska AM, Gifford RJ. The extraordinary evolutionary history of the reticuloendotheliosis viruses. PLoS Biol 2013; 11:e1001642. [PMID: 24013706 PMCID: PMC3754887 DOI: 10.1371/journal.pbio.1001642] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 07/19/2013] [Indexed: 11/18/2022] Open
Abstract
The reticuloendotheliosis viruses (REVs) comprise several closely related amphotropic retroviruses isolated from birds. These viruses exhibit several highly unusual characteristics that have not so far been adequately explained, including their extremely close relationship to mammalian retroviruses, and their presence as endogenous sequences within the genomes of certain large DNA viruses. We present evidence for an iatrogenic origin of REVs that accounts for these phenomena. Firstly, we identify endogenous retroviral fossils in mammalian genomes that share a unique recombinant structure with REVs-unequivocally demonstrating that REVs derive directly from mammalian retroviruses. Secondly, through sequencing of archived REV isolates, we confirm that contaminated Plasmodium lophurae stocks have been the source of multiple REV outbreaks in experimentally infected birds. Finally, we show that both phylogenetic and historical evidence support a scenario wherein REVs originated as mammalian retroviruses that were accidentally introduced into avian hosts in the late 1930s, during experimental studies of P. lophurae, and subsequently integrated into the fowlpox virus (FWPV) and gallid herpesvirus type 2 (GHV-2) genomes, generating recombinant DNA viruses that now circulate in wild birds and poultry. Our findings provide a novel perspective on the origin and evolution of REV, and indicate that horizontal gene transfer between virus families can expand the impact of iatrogenic transmission events.
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Affiliation(s)
| | - Robert J. Gifford
- Aaron Diamond AIDS Research Center, New York, New York, United States of America
- * E-mail:
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405
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Abstract
Paleovirology is the study of ancient viruses. The existence of a paleovirus can sometimes be detected by virtue of its accidental insertion into the germline of different animal species, which allows one to date when the virus actually existed. However, the ancient and the modern often connect, as modern viruses have unexpected origins that can be traced to ancient infections. The genomes of two species of mongooses and an egg-laying mammal called an echidna show that a virus currently present in poultry, the reticuloendotheliosis virus (REV), is actually of ancient exotic mammalian origin. REV apparently spread to poultry through a circuitous route involving the isolation of malaria parasites from a pheasant from Borneo housed at the Bronx Zoo that was contaminated with REV. Repeated passage of this virus in poultry adapted the virus to its new host. At some point, the virus got inserted into another virus, called fowlpox virus, which has spread back into the wild. Although REV may still exist somewhere in a mammalian host, its modern form links an 8 million-year-old infection of the ancestor of a mongoose to a virus that now is circulating in wild birds through malaria studies in the mid-20th century. These lessons of ancient and modern viruses have implications for modern human pandemics from viral reservoirs and for human interventions that may come with unintended consequences.
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Affiliation(s)
- Lucie Etienne
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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406
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Absence of frequent herpesvirus transmission in a nonhuman primate predator-prey system in the wild. J Virol 2013; 87:10651-9. [PMID: 23885068 DOI: 10.1128/jvi.01104-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Emergence of viruses into the human population by transmission from nonhuman primates (NHPs) represents a serious potential threat to human health that is primarily associated with the increased bushmeat trade. Transmission of RNA viruses across primate species appears to be relatively frequent. In contrast, DNA viruses appear to be largely host specific, suggesting low transmission potential. Herein, we use a primate predator-prey system to study the risk of herpesvirus transmission between different primate species in the wild. The system was comprised of western chimpanzees (Pan troglodytes verus) and their primary (western red colobus, Piliocolobus badius badius) and secondary (black-and-white colobus, Colobus polykomos) prey monkey species. NHP species were frequently observed to be coinfected with multiple beta- and gammaherpesviruses (including new cytomegalo- and rhadinoviruses). However, despite frequent exposure of chimpanzees to blood, organs, and bones of their herpesvirus-infected monkey prey, there was no evidence for cross-species herpesvirus transmission. These findings suggest that interspecies transmission of NHP beta- and gammaherpesviruses is, at most, a rare event in the wild.
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407
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Lootvoet A, Blanchet S, Gevrey M, Buisson L, Tudesque L, Loot G. Patterns and processes of alternative host use in a generalist parasite: insights from a natural host-parasite interaction. Funct Ecol 2013. [DOI: 10.1111/1365-2435.12140] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Amélie Lootvoet
- Station d'Ecologie Expérimentale du CNRS à Moulis; USR 2936; Moulis 09 200 France
- Laboratoire Ecologie, Systématique, Evolution; UMR 8079; CNRS - Université Paris-Sud - ENGREF; Bâtiment 362 Orsay cedex F-91405 France
| | - Simon Blanchet
- Station d'Ecologie Expérimentale du CNRS à Moulis; USR 2936; Moulis 09 200 France
- CNRS; UMR 5174 EDB (Evolution et Diversité Biologique); Toulouse 31062 France
| | - Muriel Gevrey
- CNRS; UMR 5174 EDB (Evolution et Diversité Biologique); Toulouse 31062 France
- Chesapeake Biological Laboratory; University of Maryland Center for Environmental Science; P.O. Box 38 Solomons Maryland 20688 USA
| | - Laetitia Buisson
- CNRS; UMR 5245 EcoLab (Laboratoire Ecologie Fonctionnelle et Environnement); 118 Route de Narbonne Toulouse 31062 France
- INP, UPS, EcoLab; Université de Toulouse; Toulouse 31062 France
| | - Loïc Tudesque
- CNRS; UMR 5174 EDB (Evolution et Diversité Biologique); Toulouse 31062 France
- INP UPS EDB; Université de Toulouse; 118 Route de Narbonne Toulouse 31062 France
| | - Géraldine Loot
- Station d'Ecologie Expérimentale du CNRS à Moulis; USR 2936; Moulis 09 200 France
- INP UPS EDB; Université de Toulouse; 118 Route de Narbonne Toulouse 31062 France
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408
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Abstract
Influenza A viruses (IAV) are significant pathogens able to repeatedly switch hosts to infect multiple avian and mammalian species, including humans. The unpredictability of IAV evolution and interspecies movement creates continual public health challenges, such as the emergence of the 2009 pandemic H1N1 virus from swine, as well as pandemic threats from the ongoing H5N1 and the recent H7N9 epizootics. In the last decade there has been increased concern about the “dual use” nature of microbiology, and a set of guidelines covering “dual use research of concern” includes seven categories of potentially problematic scientific experiments. In this Perspective, we consider how in nature IAV continually undergo “dual use experiments” as a matter of evolution and selection, and we conclude that studying these properties of IAV is critical for mitigating and preventing future epidemics and pandemics.
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409
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Abstract
ABSTRACT The ongoing H7N9 influenza epizootic in China once again presents us questions about the origin of pandemics and how to recognize them in early stages of development. Over the past ~135 years, H7 influenza viruses have neither caused pandemics nor been recognized as having undergone human adaptation. Yet several unusual properties of these viruses, including their poultry epizootic potential, mammalian adaptation, and atypical clinical syndromes in rarely infected humans, suggest that they may be different from other avian influenza viruses, thus questioning any assurance that the likelihood of human adaptation is low. At the same time, the H7N9 epizootic provides an opportunity to learn more about the mammalian/human adaptational capabilities of avian influenza viruses and challenges us to integrate virologic and public health research and surveillance at the animal-human interface.
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410
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Affiliation(s)
- David M. Morens
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Anthony S. Fauci
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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411
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Cooperation: another mechanism of viral evolution. Trends Microbiol 2013; 21:320-4. [DOI: 10.1016/j.tim.2013.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/12/2013] [Accepted: 05/13/2013] [Indexed: 02/05/2023]
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412
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Chong YL, Lam TTY, Kim O, Lu H, Dunn P, Poss M. Successful establishment and global dispersal of genotype VI avian paramyxovirus serotype 1 after cross species transmission. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2013; 17:260-8. [PMID: 23628639 PMCID: PMC7106292 DOI: 10.1016/j.meegid.2013.04.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 04/08/2013] [Accepted: 04/22/2013] [Indexed: 02/02/2023]
Abstract
The evolutionary history of avian paramyxovirus serotype 1 (PMV1), which includes the agents of Newcastle disease (ND), is characterized by a series of strain emergence events since viruses in this family were first recognized in the 1920s. Despite the importance of ND to the poultry industry, little is known about PMV1 strain emergence events and the subsequent dispersal and evolution of new strains. The genotype VI-PMV1 was first identified in the 1980s and has been named pigeon paramyxovirus-1 (PPMV1) because of unusual host specificity with Columbiformes (Collins et al., 1996); it has been responsible for panzootics in both chickens and pigeons during that time. Here, we used evolutionary analyses to characterize the emergence of this contemporary PMV1 lineage. We demonstrate that GVI-PMV1 arose through cross-species transmission events from Galliformes (i.e. chicken) to Columbiformes, and quickly established in pigeon populations. Our studies revealed a close association between the time of viral emergence and panzootic events of this virus. The virus appeared first in Southeastern Europe and quickly spread across the European continent, which became the epicenter for global virus dissemination. With new viral gene sequences, we show that GVI-PMV1 viruses currently circulating in North America resulted from multiple invasion events from Europe, one associated with an exotic European Columbiformes species, and that extant lineages have diversified locally. This study extends our understanding of successful viral emergence subsequent to cross-species transmission and dispersal patterns of newly emerged avian viruses, which may improve surveillance awareness and disease control of this and other important avian pathogens.
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Affiliation(s)
- Yee Ling Chong
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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413
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Abrams AJ, Cannatella DC, Hillis DM, Sawyer SL. Recent host-shifts in ranaviruses: signatures of positive selection in the viral genome. J Gen Virol 2013; 94:2082-2093. [PMID: 23784445 DOI: 10.1099/vir.0.052837-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ranaviruses have been implicated in recent declines in global amphibian populations. Compared with the family Iridoviridae, to which the genus Ranavirus belongs, ranaviruses have a wide host range in that species/strains are known to infect fish, amphibians and reptiles, presumably due to recent host-switching events. We used eight sequenced ranavirus genomes and two selection-detection methods (site based and branch based) to identify genes that exhibited signatures of positive selection, potentially due to the selective pressures at play during host switching. We found evidence of positive selection acting on four genes via the site-based method, three of which were newly acquired genes unique to ranavirus genomes. Using the branch-based method, we identified eight additional candidate genes that exhibited signatures of dN/dS (non-synonymous/synonymous substitution rate) >1 in the clade where intense host switching had occurred. We found that these branch-specific patterns of elevated dN/dS were enriched in a small group of viral genes that have been acquired most recently in the ranavirus genome, compared with core genes that are shared among all members of the family Iridoviridae. Our results suggest that the group of newly acquired genes in the ranavirus genome may have undergone recent adaptive changes that have facilitated interspecies and interclass host switching.
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Affiliation(s)
- A Jeanine Abrams
- Section of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - David C Cannatella
- Section of Integrative Biology and Texas Memorial Museum, University of Texas, Austin, TX 78712, USA
| | - David M Hillis
- Section of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas, Austin, TX 78712, USA
| | - Sara L Sawyer
- Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
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414
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Corman VM, Rasche A, Diallo TD, Cottontail VM, Stöcker A, Souza BFDCD, Corrêa JI, Carneiro AJB, Franke CR, Nagy M, Metz M, Knörnschild M, Kalko EKV, Ghanem SJ, Morales KDS, Salsamendi E, Spínola M, Herrler G, Voigt CC, Tschapka M, Drosten C, Drexler JF. Highly diversified coronaviruses in neotropical bats. J Gen Virol 2013; 94:1984-1994. [PMID: 23761408 DOI: 10.1099/vir.0.054841-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Bats host a broad diversity of coronaviruses (CoVs), including close relatives of human pathogens. There is only limited data on neotropical bat CoVs. We analysed faecal, blood and intestine specimens from 1562 bats sampled in Costa Rica, Panama, Ecuador and Brazil for CoVs by broad-range PCR. CoV RNA was detected in 50 bats representing nine different species, both frugivorous and insectivorous. These bat CoVs were unrelated to known human or animal pathogens, indicating an absence of recent zoonotic spill-over events. Based on RNA-dependent RNA polymerase (RdRp)-based grouping units (RGUs) as a surrogate for CoV species identification, the 50 viruses represented five different alphacoronavirus RGUs and two betacoronavirus RGUs. Closely related alphacoronaviruses were detected in Carollia perspicillata and C. brevicauda across a geographical distance exceeding 5600 km. Our study expands the knowledge on CoV diversity in neotropical bats and emphasizes the association of distinct CoVs and bat host genera.
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Affiliation(s)
- Victor Max Corman
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Andrea Rasche
- University of Veterinary Medicine Hannover, Foundation, Hannover, Germany.,Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | | | | | - Andreas Stöcker
- Infectious Diseases Research Laboratory, University Hospital Professor Edgard Santos, Federal University of Bahia, Salvador, Brazil
| | | | - Jefferson Ivan Corrêa
- Infectious Diseases Research Laboratory, University Hospital Professor Edgard Santos, Federal University of Bahia, Salvador, Brazil
| | | | | | - Martina Nagy
- Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Berlin, Germany
| | - Markus Metz
- Fondazione Edmund Mach, Research and Innovation Centre, Department of Biodiversity and Molecular Ecology, S. Michele all'Adige, Italy
| | | | - Elisabeth K V Kalko
- Smithsonian Tropical Research Institute, Balboa, Panama.,Institute of Experimental Ecology, University of Ulm, Ulm, Germany
| | - Simon J Ghanem
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Karen D Sibaja Morales
- Instituto Internacional en Conservación y Manejo de Vida Silvestre, Universidad Nacional, Heredia, Costa Rica
| | - Egoitz Salsamendi
- Department of Zoology and Animal Cell Biology, University of the Basque Country, Bilbao, The Basque Country.,Institute of Experimental Ecology, University of Ulm, Ulm, Germany
| | - Manuel Spínola
- Instituto Internacional en Conservación y Manejo de Vida Silvestre, Universidad Nacional, Heredia, Costa Rica
| | - Georg Herrler
- University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | | | - Marco Tschapka
- Smithsonian Tropical Research Institute, Balboa, Panama.,Institute of Experimental Ecology, University of Ulm, Ulm, Germany
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
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415
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Loverdo C, Lloyd-Smith JO. Intergenerational phenotypic mixing in viral evolution. Evolution 2013; 67:1815-22. [PMID: 23730772 PMCID: PMC3676872 DOI: 10.1111/evo.12048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 12/25/2012] [Indexed: 01/12/2023]
Abstract
Viral particles (virions) are made of genomic material packaged with proteins, drawn from the pool of proteins in the parent cell. It is well known that when virion concentrations are high, cells can be coinfected with multiple viral strains that can complement each other. Viral genomes can then interact with proteins derived from different strains, in a phenomenon known as phenotypic mixing. But phenotypic mixing is actually far more common: viruses mutate very often, and each time a mutation occurs, the parent cell contains different types of viral genomes. Due to phenotypic mixing, changes in viral phenotypes can be shifted by a generation from the mutations that cause them. In the regime of evolutionary invasion and escape, when mutations are crucial for the virus to survive, this timing can have a large influence on the probability of emergence of an adapted strain. Modeling the dynamics of viral evolution in these contexts thus requires attention to the mutational mechanism and the determinants of fitness.
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Affiliation(s)
- Claude Loverdo
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, CA 90095, USA.
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416
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Demogines A, Abraham J, Choe H, Farzan M, Sawyer SL. Dual host-virus arms races shape an essential housekeeping protein. PLoS Biol 2013; 11:e1001571. [PMID: 23723737 PMCID: PMC3665890 DOI: 10.1371/journal.pbio.1001571] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 04/17/2013] [Indexed: 02/07/2023] Open
Abstract
Relentless selective pressures exerted by viruses trigger arms race dynamics that shape the evolution of even critical host genes like those involved in iron homeostasis. Transferrin Receptor (TfR1) is the cell-surface receptor that regulates iron uptake into cells, a process that is fundamental to life. However, TfR1 also facilitates the cellular entry of multiple mammalian viruses. We use evolutionary and functional analyses of TfR1 in the rodent clade, where two families of viruses bind this receptor, to mechanistically dissect how essential housekeeping genes like TFR1 successfully balance the opposing selective pressures exerted by host and virus. We find that while the sequence of rodent TfR1 is generally conserved, a small set of TfR1 residue positions has evolved rapidly over the speciation of rodents. Remarkably, all of these residues correspond to the two virus binding surfaces of TfR1. We show that naturally occurring mutations at these positions block virus entry while simultaneously preserving iron-uptake functionalities, both in rodent and human TfR1. Thus, by constantly replacing the amino acids encoded at just a few residue positions, TFR1 divorces adaptation to ever-changing viruses from preservation of key cellular functions. These dynamics have driven genetic divergence at the TFR1 locus that now enforces species-specific barriers to virus transmission, limiting both the cross-species and zoonotic transmission of these viruses. Genetic differences between mammalian species dictate the patterns of viral infection observed in nature. They also define how viruses must evolve in order to infect new mammalian hosts, giving rise to new and sometimes pandemic diseases. Because viruses must enter cells before they can replicate, new diseases often emerge when existing viruses evolve the ability to bind to the cell-surface receptor of a new species. At the same time, host cell receptors also evolve to counteract virus attacks. This back-and-forth evolution between virus and host can lead to an arms race that shapes the sequences of the proteins involved. In wild rodent populations, the retrovirus MMTV and New World arenaviruses both exploit Transferrin Receptor 1 (TfR1) to enter the cells of their hosts. Here we show that the physical interactions between these viruses and TfR1 have triggered evolutionary arms race dynamics that have directly modified the sequence of TfR1 and at least one of the viruses involved. Computational evolutionary analysis allowed us to identify specific residues in TfR1 that define patterns of viral infection in nature. The approach presented here can theoretically be applied to the study of any virus, through analysis of host genes known to be key to controlling viral infection. As such, this approach can expand our understanding of how viruses emerge from wildlife reservoirs, and how they drive the evolution of host genes.
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Affiliation(s)
- Ann Demogines
- Department of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Jonathan Abraham
- Department of Medicine, Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Hyeryun Choe
- Department of Medicine, Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael Farzan
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sara L. Sawyer
- Department of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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417
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Rocha CS, Castillo-Urquiza GP, Lima ATM, Silva FN, Xavier CAD, Hora-Júnior BT, Beserra-Júnior JEA, Malta AWO, Martin DP, Varsani A, Alfenas-Zerbini P, Mizubuti ESG, Zerbini FM. Brazilian begomovirus populations are highly recombinant, rapidly evolving, and segregated based on geographical location. J Virol 2013; 87:5784-99. [PMID: 23487451 PMCID: PMC3648162 DOI: 10.1128/jvi.00155-13] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 03/04/2013] [Indexed: 01/21/2023] Open
Abstract
The incidence of begomovirus infections in crop plants sharply increased in Brazil during the 1990s following the introduction of the invasive B biotype of the whitefly vector, Bemisia tabaci. It is believed that this biotype transmitted begomoviruses from noncultivated plants to crop species with greater efficiency than indigenous B. tabaci biotypes. Either through rapid host adaptation or selection pressure in genetically diverse populations of noncultivated hosts, over the past 20 years various previously unknown begomovirus species have became progressively more prevalent in cultivated species such as tomato. Here we assess the genetic structure of begomovirus populations infecting tomatoes and noncultivated hosts in southeastern Brazil. Between 2005 and 2010, we sampled and sequenced 126 DNA-A and 58 DNA-B full-length begomovirus components. We detected nine begomovirus species in tomatoes and eight in the noncultivated host samples, with four species common to both tomatoes and noncultivated hosts. Like many begomoviruses, most species are obvious interspecies recombinants. Furthermore, species identified in tomato have probable parental viruses from noncultivated hosts. While the population structures of five well-sampled viral species all displayed geographical subdivision, a noncultivated host-infecting virus was more genetically variable than the four predominantly tomato-infecting viruses.
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Affiliation(s)
- Carolina S. Rocha
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Gloria P. Castillo-Urquiza
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Alison T. M. Lima
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Fábio N. Silva
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Cesar A. D. Xavier
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Braz T. Hora-Júnior
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - José E. A. Beserra-Júnior
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Antonio W. O. Malta
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch, Cape Town, South Africa
- School of Biological Sciences, University of Canterbury, Ilam, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch, New Zealand
| | - Poliane Alfenas-Zerbini
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Eduardo S. G. Mizubuti
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - F. Murilo Zerbini
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
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418
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Lipkin WI, Firth C. Viral surveillance and discovery. Curr Opin Virol 2013; 3:199-204. [PMID: 23602435 DOI: 10.1016/j.coviro.2013.03.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 03/20/2013] [Indexed: 01/27/2023]
Abstract
The field of virus discovery has burgeoned with the advent of high throughput sequencing platforms and bioinformatics programs that enable rapid identification and molecular characterization of known and novel agents, investments in global microbial surveillance that include wildlife and domestic animals as well as humans, and recognition that viruses may be implicated in chronic as well as acute diseases. Here we review methods for viral surveillance and discovery, strategies and pitfalls in linking discoveries to disease, and identify opportunities for improvements in sequencing instrumentation and analysis, the use of social media and medical informatics that will further advance clinical medicine and public health.
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Affiliation(s)
- Walter Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health of Columbia University, 722 West 168th Street, New York, NY 10025, USA.
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419
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Farrell MJ, Berrang-Ford L, Davies TJ. The study of parasite sharing for surveillance of zoonotic diseases. ENVIRONMENTAL RESEARCH LETTERS : ERL [WEB SITE] 2013; 8:015036. [PMID: 32288780 PMCID: PMC7106949 DOI: 10.1088/1748-9326/8/1/015036] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 03/04/2013] [Indexed: 06/11/2023]
Abstract
Determining the factors that influence the transmission of parasites among hosts is important for directing surveillance of animal parasites before they successfully emerge in humans, and increasing the efficacy of programs for the control and management of zoonotic diseases. Here we present a review of recent advances in the study of parasite sharing, wildlife ecology, and epidemiology that could be extended and incorporated into proactive surveillance frameworks for multi-host infectious diseases. These methods reflect emerging interdisciplinary techniques with significant promise for the identification of future zoonotic parasites and unknown reservoirs of current zoonoses, strategies for the reduction of parasite prevalence and transmission among hosts, and decreasing the burden of infectious diseases.
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Affiliation(s)
- Maxwell J Farrell
- Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, QC, H3A 1B1,
- Department of Geography, McGill University, 805 Sherbrooke Street, West Montreal, QC, H3A 0B9, Canada
| | - Lea Berrang-Ford
- Department of Geography, McGill University, 805 Sherbrooke Street, West Montreal, QC, H3A 0B9, Canada
| | - T Jonathan Davies
- Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, QC, H3A 1B1,
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420
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Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs. BMC Genomics 2013; 14:96. [PMID: 23402258 PMCID: PMC3599684 DOI: 10.1186/1471-2164-14-96] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 02/06/2013] [Indexed: 01/06/2023] Open
Abstract
Backgound High throughput sequencing is beginning to make a transformative impact in the area of viral evolution. Deep sequencing has the potential to reveal the mutant spectrum within a viral sample at high resolution, thus enabling the close examination of viral mutational dynamics both within- and between-hosts. The challenge however, is to accurately model the errors in the sequencing data and differentiate real viral mutations, particularly those that exist at low frequencies, from sequencing errors. Results We demonstrate that overlapping read pairs (ORP) -- generated by combining short fragment sequencing libraries and longer sequencing reads -- significantly reduce sequencing error rates and improve rare variant detection accuracy. Using this sequencing protocol and an error model optimized for variant detection, we are able to capture a large number of genetic mutations present within a viral population at ultra-low frequency levels (<0.05%). Conclusions Our rare variant detection strategies have important implications beyond viral evolution and can be applied to any basic and clinical research area that requires the identification of rare mutations.
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421
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Gessain A, Rua R, Betsem E, Turpin J, Mahieux R. HTLV-3/4 and simian foamy retroviruses in humans: discovery, epidemiology, cross-species transmission and molecular virology. Virology 2013; 435:187-99. [PMID: 23217627 PMCID: PMC7111966 DOI: 10.1016/j.virol.2012.09.035] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 09/28/2012] [Indexed: 12/20/2022]
Abstract
Non-human primates are considered to be likely sources of viruses that can infect humans and thus pose a significant threat to human population. This is well illustrated by some retroviruses, as the simian immunodeficiency viruses and the simian T lymphotropic viruses, which have the ability to cross-species, adapt to a new host and sometimes spread. This leads to a pandemic situation for HIV-1 or an endemic one for HTLV-1. Here, we present the available data on the discovery, epidemiology, cross-species transmission and molecular virology of the recently discovered HTLV-3 and HTLV-4 deltaretroviruses, as well as the simian foamy retroviruses present in different human populations at risk, especially in central African hunters. We discuss also the natural history in humans of these retroviruses of zoonotic origin (magnitude and geographical distribution, possible inter-human transmission). In Central Africa, the increase of the bushmeat trade during the last decades has opened new possibilities for retroviral emergence in humans, especially in immuno-compromised persons.
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Affiliation(s)
- Antoine Gessain
- Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, France, Département de Virologie, Institut Pasteur, 25-28 rue du Dr Roux, 75724 Paris, Cedex 15, France.
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422
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Park M, Loverdo C, Schreiber SJ, Lloyd-Smith JO. Multiple scales of selection influence the evolutionary emergence of novel pathogens. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120333. [PMID: 23382433 DOI: 10.1098/rstb.2012.0333] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
When pathogens encounter a novel environment, such as a new host species or treatment with an antimicrobial drug, their fitness may be reduced so that adaptation is necessary to avoid extinction. Evolutionary emergence is the process by which new pathogen strains arise in response to such selective pressures. Theoretical studies over the last decade have clarified some determinants of emergence risk, but have neglected the influence of fitness on evolutionary rates and have not accounted for the multiple scales at which pathogens must compete successfully. We present a cross-scale theory for evolutionary emergence, which embeds a mechanistic model of within-host selection into a stochastic model for emergence at the population scale. We explore how fitness landscapes at within-host and between-host scales can interact to influence the probability that a pathogen lineage will emerge successfully. Results show that positive correlations between fitnesses across scales can greatly facilitate emergence, while cross-scale conflicts in selection can lead to evolutionary dead ends. The local genotype space of the initial strain of a pathogen can have disproportionate influence on emergence probability. Our cross-scale model represents a step towards integrating laboratory experiments with field surveillance data to create a rational framework to assess emergence risk.
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Affiliation(s)
- Miran Park
- Department of Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Dr. South, Los Angeles, CA 90095, USA.
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423
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Faria NR, Suchard MA, Rambaut A, Streicker DG, Lemey P. Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120196. [PMID: 23382420 DOI: 10.1098/rstb.2012.0196] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The factors that determine the origin and fate of cross-species transmission events remain unclear for the majority of human pathogens, despite being central for the development of predictive models and assessing the efficacy of prevention strategies. Here, we describe a flexible Bayesian statistical framework to reconstruct virus transmission between different host species based on viral gene sequences, while simultaneously testing and estimating the contribution of several potential predictors of cross-species transmission. Specifically, we use a generalized linear model extension of phylogenetic diffusion to perform Bayesian model averaging over candidate predictors. By further extending this model with branch partitioning, we allow for distinct host transition processes on external and internal branches, thus discriminating between recent cross-species transmissions, many of which are likely to result in dead-end infections, and host shifts that reflect successful onwards transmission in the new host species. Our approach corroborates genetic distance between hosts as a key determinant of both host shifts and cross-species transmissions of rabies virus in North American bats. Furthermore, our results indicate that geographical range overlap is a modest predictor for cross-species transmission, but not for host shifts. Although our evolutionary framework focused on the multi-host reservoir dynamics of bat rabies virus, it is applicable to other pathogens and to other discrete state transition processes.
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Affiliation(s)
- Nuno Rodrigues Faria
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.
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424
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Murray KA, Daszak P. Human ecology in pathogenic landscapes: two hypotheses on how land use change drives viral emergence. Curr Opin Virol 2013; 3:79-83. [PMID: 23415415 PMCID: PMC3713401 DOI: 10.1016/j.coviro.2013.01.006] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/23/2013] [Accepted: 01/26/2013] [Indexed: 11/20/2022]
Abstract
The emergence of novel viral diseases is driven by socioeconomic, demographic and environmental changes. These include land use changes such as deforestation, agricultural expansion and habitat degradation. However, the links between land use change and disease emergence are poorly understood and probably complex. In this review, we propose two hypotheses for the mechanisms by which land use change can lead to viral emergence: firstly, by perturbing disease dynamics in multihost disease systems via impacts on cross-species transmission rates (the 'perturbation' hypothesis); and secondly, by allowing exposure of novel hosts to a rich pool of pathogen diversity (the 'pathogen pool' hypothesis). We discuss ways by which these two hypotheses might be tested using a combination of ecological and virological approaches, and how this may provide novel control and prevention strategies.
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Affiliation(s)
- Kris. A. Murray
- EcoHealth Alliance, 460 W 34 St, 17 Floor, New York, 10001, NY, United States
| | - Peter Daszak
- EcoHealth Alliance, 460 W 34 St, 17 Floor, New York, 10001, NY, United States
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425
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Cooper N, Nunn CL. Identifying future zoonotic disease threats: Where are the gaps in our understanding of primate infectious diseases? EVOLUTION MEDICINE AND PUBLIC HEALTH 2013; 2013:27-36. [PMID: 24481184 PMCID: PMC3868449 DOI: 10.1093/emph/eot001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Across all primates, less than two thirds of primate viruses, protozoa and helminths have currently been recorded. Similar effects emerge in analyses of parasite sampling by country, and for individual primate species. Therefore a great deal more disease sampling is needed to understand zoonotic disease risks to humans. Background and objectives: Emerging infectious diseases often originate in wildlife, making it important to identify infectious agents in wild populations. It is widely acknowledged that wild animals are incompletely sampled for infectious agents, especially in developing countries, but it is unclear how much more sampling is needed, and where that effort should focus in terms of host species and geographic locations. Here, we identify these gaps in primate parasites, many of which have already emerged as threats to human health. Methodology: We obtained primate host–parasite records and other variables from existing databases. We then investigated sampling effort within primates relative to their geographic range size, and within countries relative to their primate species richness. We used generalized linear models, controlling for phylogenetic or spatial autocorrelation, to model variation in sampling effort across primates and countries. Finally, we used species richness estimators to extrapolate parasite species richness. Results: We found uneven sampling effort within all primate groups and continents. Sampling effort among primates was influenced by their geographic range size and substrate use, with terrestrial species receiving more sampling. Our parasite species richness estimates suggested that, among the best sampled primates and countries, almost half of primate parasites remain to be sampled; for most primate hosts, the situation is much worse. Conclusions and implications: Sampling effort for primate parasites is uneven and low. The sobering message is that we know little about even the best studied primates, and even less regarding the spatial and temporal distribution of parasitism within species.
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Affiliation(s)
- Natalie Cooper
- School of Natural Sciences; Trinity Centre for Biodiversity Research, Trinity College Dublin, Dublin 2, Ireland and Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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426
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Abstract
Infectious diseases continue to plague the modern world. In the evolutionary arms race of pathogen emergence, the rules of engagement appear to have suddenly changed. Human activities have collided with nature to hasten the emergence of more potent pathogens from natural microbial populations. This is evident in recent infectious disease outbreaks, the events that led to their origin, and lessons learned: influenza (2009), meningitis (Africa, 2009), cholera (Haiti, 2010), E. coli (Germany, 2011) and Salmonella (USA, 2012). Developing a comprehensive control plan requires an understanding of the genetics, epidemiology and evolution of emergent pathogens for which humans have little or no pre-existing immunity. As we plot our next move, nature's genetic lottery continues, providing the fuel to transform the most unlikely infectious disease scenarios into reality.
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Affiliation(s)
- Michael J Mahan
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA.
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427
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The new age of virus discovery: genomic analysis of a novel human betacoronavirus isolated from a fatal case of pneumonia. mBio 2013; 4:e00548-12. [PMID: 23300251 PMCID: PMC3546555 DOI: 10.1128/mbio.00548-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A new human betacoronavirus in lineage c, tentatively called HCoV-EMC, was isolated from a patient from the Kingdom of Saudi Arabia who died from acute severe pneumonia and renal failure. The viral RNA has been detected in eight additional cases. Sequencing and bioinformatic analysis of the viral genomic RNA showed that it is a novel virus not previously detected in any other species and that its closest relatives are two Asian bat coronaviruses. HCoV-EMC may represent a sporadic spillover to humans from an unknown animal reservoir. In a recent article, van Boheemen et al. demonstrated how state-of-the-art sequencing technology and bioinformatic analysis can quickly provide critical insight into the viral genome sequence, phylogeny, replication strategy, and potential drug and vaccine targets and generate tools to evaluate the possible epidemic risk associated with this novel human virus.
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428
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Drexler JF, Corman VM, Müller MA, Lukashev AN, Gmyl A, Coutard B, Adam A, Ritz D, Leijten LM, van Riel D, Kallies R, Klose SM, Gloza-Rausch F, Binger T, Annan A, Adu-Sarkodie Y, Oppong S, Bourgarel M, Rupp D, Hoffmann B, Schlegel M, Kümmerer BM, Krüger DH, Schmidt-Chanasit J, Setién AA, Cottontail VM, Hemachudha T, Wacharapluesadee S, Osterrieder K, Bartenschlager R, Matthee S, Beer M, Kuiken T, Reusken C, Leroy EM, Ulrich RG, Drosten C. Evidence for novel hepaciviruses in rodents. PLoS Pathog 2013; 9:e1003438. [PMID: 23818848 PMCID: PMC3688547 DOI: 10.1371/journal.ppat.1003438] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 04/22/2013] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) is among the most relevant causes of liver cirrhosis and hepatocellular carcinoma. Research is complicated by a lack of accessible small animal models. The systematic investigation of viruses of small mammals could guide efforts to establish such models, while providing insight into viral evolutionary biology. We have assembled the so-far largest collection of small-mammal samples from around the world, qualified to be screened for bloodborne viruses, including sera and organs from 4,770 rodents (41 species); and sera from 2,939 bats (51 species). Three highly divergent rodent hepacivirus clades were detected in 27 (1.8%) of 1,465 European bank voles (Myodes glareolus) and 10 (1.9%) of 518 South African four-striped mice (Rhabdomys pumilio). Bats showed anti-HCV immunoblot reactivities but no virus detection, although the genetic relatedness suggested by the serologic results should have enabled RNA detection using the broadly reactive PCR assays developed for this study. 210 horses and 858 cats and dogs were tested, yielding further horse-associated hepaciviruses but none in dogs or cats. The rodent viruses were equidistant to HCV, exceeding by far the diversity of HCV and the canine/equine hepaciviruses taken together. Five full genomes were sequenced, representing all viral lineages. Salient genome features and distance criteria supported classification of all viruses as hepaciviruses. Quantitative RT-PCR, RNA in-situ hybridisation, and histopathology suggested hepatic tropism with liver inflammation resembling hepatitis C. Recombinant serology for two distinct hepacivirus lineages in 97 bank voles identified seroprevalence rates of 8.3 and 12.4%, respectively. Antibodies in bank vole sera neither cross-reacted with HCV, nor the heterologous bank vole hepacivirus. Co-occurrence of RNA and antibodies was found in 3 of 57 PCR-positive bank vole sera (5.3%). Our data enable new hypotheses regarding HCV evolution and encourage efforts to develop rodent surrogate models for HCV.
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Affiliation(s)
- Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Victor Max Corman
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | | | | | - Anatoly Gmyl
- Chumakov Institute of Poliomyelitis and Viral Encephalitides, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Bruno Coutard
- Architectures et Fonctions des Macromolécules Biologiques, UMR 7257 CNRS and Aix-Marseille University, Marseille, France
| | - Alexander Adam
- Institute of Pathology, University of Cologne Medical Centre, Cologne, Germany
| | - Daniel Ritz
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | | | - Debby van Riel
- Erasmus MC, Department of Viroscience, Rotterdam, The Netherlands
| | - Rene Kallies
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Stefan M. Klose
- Institute of Experimental Ecology, University of Ulm, Ulm, Germany
| | - Florian Gloza-Rausch
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
- Noctalis, Centre for Bat Protection and Information, Bad Segeberg, Germany
| | - Tabea Binger
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Augustina Annan
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Yaw Adu-Sarkodie
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Samuel Oppong
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mathieu Bourgarel
- Centre de Cooperation Internationale de Recherche en Agronomie pour le Développement, UPR AGIRs, Montpellier, France
| | - Daniel Rupp
- Department of Infectious Diseases, Molecular Virology, Medical Facility, Heidelberg University, Heidelberg, Germany
| | - Bernd Hoffmann
- Friedrich-Loeffler-Institut, Institute for Virus Diagnostics, Greifswald–Insel Riems, Germany
| | - Mathias Schlegel
- Friedrich-Loeffler-Institut, Institute for Novel and Emerging Infectious Diseases, Greifswald–Insel Riems, Germany
| | - Beate M. Kümmerer
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Detlev H. Krüger
- Institute of Medical Virology (Helmut Ruska Haus), Charité Medical School, Berlin, Germany
| | - Jonas Schmidt-Chanasit
- Bernhard Nocht Institute for Tropical Medicine, Department of Virology, Hamburg, Germany
| | - Alvaro Aguilar Setién
- Unidad de Investigación Médica en Inmunología, Hospital de Pediatría, México DF, Mexico
| | | | - Thiravat Hemachudha
- Chulalongkorn University, Faculty of Medicine, Neuroscience Center for Research and Development, Bangkok, Thailand
| | - Supaporn Wacharapluesadee
- Chulalongkorn University, Faculty of Medicine, Neuroscience Center for Research and Development, Bangkok, Thailand
| | - Klaus Osterrieder
- Institute of Virology, Free University of Berlin, Department of Veterinary Medicine, Berlin, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Medical Facility, Heidelberg University, Heidelberg, Germany
| | - Sonja Matthee
- Department of Conservation Ecology and Entomology, Stellenbosch University, Stellenbosch, South Africa
| | - Martin Beer
- Friedrich-Loeffler-Institut, Institute for Virus Diagnostics, Greifswald–Insel Riems, Germany
| | - Thijs Kuiken
- Erasmus MC, Department of Viroscience, Rotterdam, The Netherlands
| | - Chantal Reusken
- Netherlands Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Eric M. Leroy
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
- Institut de Recherche pour le Développement, UMR 224 (MIVEGEC), IRD/CNRS/UM1, Montpellier, France
| | - Rainer G. Ulrich
- Friedrich-Loeffler-Institut, Institute for Novel and Emerging Infectious Diseases, Greifswald–Insel Riems, Germany
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
- * E-mail:
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429
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Degeling C, Kerridge I. Hendra in the news: public policy meets public morality in times of zoonotic uncertainty. Soc Sci Med 2012; 82:156-63. [PMID: 23294874 PMCID: PMC7116936 DOI: 10.1016/j.socscimed.2012.12.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 11/10/2022]
Abstract
Public discourses have influence on policymaking for emerging health issues. Media representations of unfolding events, scientific uncertainty, and real and perceived risks shape public acceptance of health policy and therefore policy outcomes. To characterize and track views in popular circulation on the causes, consequences and appropriate policy responses to the emergence of Hendra virus as a zoonotic risk, this study examines coverage of this issue in Australian mass media for the period 2007–2011. Results demonstrate the predominant explanation for the emergence of Hendra became the encroachment of flying fox populations on human settlement. Depictions of scientific uncertainty as to whom and what was at risk from Hendra virus promoted the view that flying foxes were a direct risk to human health. Descriptions of the best strategy to address Hendra have become polarized between recognized health authorities advocating individualized behaviour changes to limit risk exposure; versus populist calls for flying fox control and eradication. Less than a quarter of news reports describe the ecological determinants of emerging infectious disease or upstream policy solutions. Because flying foxes rather than horses were increasingly represented as the proximal source of human infection, existing policies of flying fox protection became equated with government inaction; the plight of those affected by flying foxes representative of a moral failure. These findings illustrate the potential for health communications for emerging infectious disease risks to become entangled in other political agendas, with implications for the public's likelihood of supporting public policy and risk management strategies that require behavioural change or seek to address the ecological drivers of incidence.
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Affiliation(s)
- Chris Degeling
- Centre for Values, Ethics and the Law in Medicine, Sydney School of Public Health, University of Sydney, Australia.
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430
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Holmes EC. What can we predict about viral evolution and emergence? Curr Opin Virol 2012; 3:180-4. [PMID: 23273851 PMCID: PMC3626763 DOI: 10.1016/j.coviro.2012.12.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 12/02/2012] [Accepted: 12/03/2012] [Indexed: 01/14/2023]
Abstract
Predicting the emergence of infectious diseases has been touted as one of the most important goals of biomedical science, with an array of funding schemes and research projects. However, evolutionary biology generally has a dim view of prediction, and there is a danger that erroneous predictions will mean a misuse of resources and undermine public confidence. Herein, I outline what can be realistically predicted about viral evolution and emergence, argue that any success in predicting what may emerge is likely to be limited, but that forecasting how viruses might evolve and spread following emergence is more tractable. I also emphasize that a properly grounded research program in disease prediction must involve a synthesis of ecological and genetic perspectives.
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Affiliation(s)
- Edward C Holmes
- Sydney Emerging Infections and Biosecurity Institute, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
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431
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Morens DM, Fauci AS. Emerging infectious diseases in 2012: 20 years after the institute of medicine report. mBio 2012; 3:e00494-12. [PMID: 23232716 PMCID: PMC3520107 DOI: 10.1128/mbio.00494-12] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 11/06/2012] [Indexed: 02/07/2023] Open
Abstract
Twenty years ago (1992), a landmark Institute of Medicine report entitled "Emerging Infections: Microbial Threats to Health in the United States" underscored the important but often underappreciated concept of emerging infectious diseases (EIDs). A review of the progress made and setbacks experienced over the past 2 decades suggests that even though many new diseases have emerged, such as SARS (severe acute respiratory syndrome) and the 2009 pandemic influenza, significant advances have occurred in EID control, prevention, and treatment. Among many elements of the increase in the capacity to control EIDs are genomics-associated advances in microbial detection and treatment, improved disease surveillance, and greater awareness of EIDs and the complicated variables that underlie emergence. In looking back over the past 20 years, it is apparent that we are in a time of great change in which both the challenge of EIDs and our responses to them are being transformed. Recent advances support guarded optimism that further breakthroughs lie ahead.
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Affiliation(s)
- David M Morens
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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432
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Abstract
Although parvoviruses are commonly described in domestic carnivores, little is known about their biodiversity in nondomestic species. A phylogenetic analysis of VP2 gene sequences from puma, coyote, gray wolf, bobcat, raccoon, and striped skunk revealed two major groups related to either feline panleukopenia virus ("FPV-like") or canine parvovirus ("CPV-like"). Cross-species transmission was commonplace, with multiple introductions into each host species but, with the exception of raccoons, relatively little evidence for onward transmission in nondomestic species.
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433
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Morse SS, Mazet JAK, Woolhouse M, Parrish CR, Carroll D, Karesh WB, Zambrana-Torrelio C, Lipkin WI, Daszak P. Prediction and prevention of the next pandemic zoonosis. Lancet 2012; 380:1956-65. [PMID: 23200504 PMCID: PMC3712877 DOI: 10.1016/s0140-6736(12)61684-5] [Citation(s) in RCA: 526] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Most pandemics--eg, HIV/AIDS, severe acute respiratory syndrome, pandemic influenza--originate in animals, are caused by viruses, and are driven to emerge by ecological, behavioural, or socioeconomic changes. Despite their substantial effects on global public health and growing understanding of the process by which they emerge, no pandemic has been predicted before infecting human beings. We review what is known about the pathogens that emerge, the hosts that they originate in, and the factors that drive their emergence. We discuss challenges to their control and new efforts to predict pandemics, target surveillance to the most crucial interfaces, and identify prevention strategies. New mathematical modelling, diagnostic, communications, and informatics technologies can identify and report hitherto unknown microbes in other species, and thus new risk assessment approaches are needed to identify microbes most likely to cause human disease. We lay out a series of research and surveillance opportunities and goals that could help to overcome these challenges and move the global pandemic strategy from response to pre-emption.
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Affiliation(s)
- Stephen S Morse
- Mailman School of Public Health; Columbia University, New York, NY, USA
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Jonna AK Mazet
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Mark Woolhouse
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Colin R Parrish
- College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Dennis Carroll
- US Agency for International Development, Washington, DC, USA
| | - William B Karesh
- EcoHealth Alliance, New York, NY, USA
- IUCN Species Survival Commission Wildlife Health Specialist Group, Gland, Switzerland
| | | | - W Ian Lipkin
- Center for Infection and Immunity; Columbia University, New York, NY, USA
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434
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Ostfeld RS, Keesing F. Effects of Host Diversity on Infectious Disease. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2012. [DOI: 10.1146/annurev-ecolsys-102710-145022] [Citation(s) in RCA: 301] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Felicia Keesing
- Cary Institute of Ecosystem Studies, Millbrook, New York 12545;
- Biology Program, Bard College, Annandale-on-Hudson, New York 12504
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435
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Variable evolutionary routes to host establishment across repeated rabies virus host shifts among bats. Proc Natl Acad Sci U S A 2012; 109:19715-20. [PMID: 23150575 DOI: 10.1073/pnas.1203456109] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Determining the genetic pathways that viruses traverse to establish in new host species is crucial to predict the outcome of cross-species transmission but poorly understood for most host-virus systems. Using sequences encoding 78% of the rabies virus genome, we explored the extent, repeatability and dynamic outcome of evolution associated with multiple host shifts among New World bats. Episodic bursts of positive selection were detected in several viral proteins, including regions associated with host cell interaction and viral replication. Host shifts involved unique sets of substitutions, and few sites exhibited repeated evolution across adaptation to many bat species, suggesting diverse genetic determinants over host range. Combining these results with genetic reconstructions of the demographic histories of individual viral lineages revealed that although rabies viruses shared consistent three-stage processes of emergence in each new bat species, host shifts involving greater numbers of positively selected substitutions had longer delays between cross-species transmission and enzootic viral establishment. Our results point to multiple evolutionary routes to host establishment in a zoonotic RNA virus that may influence the speed of viral emergence.
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436
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Abstract
Cucumber mosaic virus (CMV) comprises numerous isolates with various levels of in-host diversity. Subgroup-distinctive features of the Fny and LS strains provided us with a platform to genetically map the viral control elements for genetic variation in planta. We found that both RNAs 1 and 2 controlled levels of genetic diversity, and further fine mapping revealed that the control elements of mutation frequency reside within the first 596 amino acids (aa) of RNA 1. The 2a/2b overlapping region of the 2a protein also contributed to control of viral genetic variation. Furthermore, the 3' nontranslated region (NTR) of RNA 3 constituted a hot spot of polymorphism, where the majority of fixed mutations found in the population were clustered. The 2b gene of CMV, a viral suppressor of gene silencing, controls the abundance of the fixed mutants in the viral population via a host-dependent mechanism.
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437
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Abstract
Simian foamy viruses (SFVs) are retroviruses that are widespread among nonhuman primates (NHPs). SFVs actively replicate in their oral cavity and can be transmitted to humans after NHP bites, giving rise to a persistent infection even decades after primary infection. Very few data on the genetic structure of such SFVs found in humans are available. In the framework of ongoing studies searching for SFV-infected humans in south Cameroon rainforest villages, we studied 38 SFV-infected hunters whose times of infection had presumably been determined. By long-term cocultures of peripheral blood mononuclear cells with BHK-21 cells, we isolated five new SFV strains and obtained complete genomes of SFV strains from chimpanzee (Pan troglodytes troglodytes; strains BAD327 and AG15), monkey (Cercopithecus nictitans; strain AG16), and gorilla (Gorilla gorilla; strains BAK74 and BAD468). These zoonotic strains share a very high degree of similarity with their NHP counterparts and have a high degree of conservation of the genetic elements important for viral replication. Interestingly, analysis of FV DNA sequences obtained before cultivation revealed variants with deletions in both the U3 region and tas that may correlate with in vivo chronicity in humans. Genomic changes in bet (a premature stop codon) and gag were also observed. To determine if such changes were specific to zoonotic strains, we studied local SFV-infected chimpanzees and found the same genomic changes. Our study reveals that natural polymorphism of SFV strains does exist at both the intersubspecies level (gag, bet) and the intrasubspecies (U3, tas) levels but does not seem to reflect a viral adaptation specific to zoonotic SFV strains.
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438
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Lam TTY, Liu W, Bowden TA, Cui N, Zhuang L, Liu K, Zhang YY, Cao WC, Pybus OG. Evolutionary and molecular analysis of the emergent severe fever with thrombocytopenia syndrome virus. Epidemics 2012; 5:1-10. [PMID: 23438426 PMCID: PMC4330987 DOI: 10.1016/j.epidem.2012.09.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 09/13/2012] [Indexed: 01/08/2023] Open
Abstract
In 2009, a novel Bunyavirus, called severe fever with thrombocytopenia syndrome virus (SFTSV) was identified in the vicinity of Huaiyangshan, China. Clinical symptoms of this zoonotic virus included severe fever, thrombocytopenia, and leukocytopenia, with a mortality rate of ∼10%. By the end of 2011 the disease associated with this pathogen had been reported from eleven Chinese provinces and human-to-human transmission suspected. However, current understanding of the evolution and molecular epidemiology of SFTSV before and after its identification is limited. To address this we undertake phylogenetic, evolutionary and structural analyses of all available SFTSV genetic sequences, including a new SFTSV complete genome isolated from a patient from Henan in 2011. Our discovery of a mosaic L segment sequence, which is descended from two major circulating lineages of SFTSV in China, represents the first evidence that homologous recombination plays a role in SFTSV evolution. Selection analyses indicate that negative selection is predominant in SFTSV genes, yet differences in selective forces among genes are consistent between Phlebovirus species. Further analysis reveals structural conservation between SFTSV and Rift Valley fever virus in the residues of their nucleocapsids that are responsible for oligomerisation and RNA-binding, suggesting the viruses share similar modes of higher-order assembly. We reconstruct the epidemic history of SFTSV using molecular clock and coalescent-based methods, revealing that the extant SFTSV lineages originated 50–150 years ago, and that the viral population experienced a recent growth phase that concurs with and extends the earliest serological reports of SFTSV infection. Taken together, our combined structural and phylogenetic analyses shed light into the evolutionary behaviour of SFTSV in the context of other, better-known, pathogenic Phleboviruses.
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439
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Louz D, Bergmans HE, Loos BP, Hoeben RC. Animal models in virus research: their utility and limitations. Crit Rev Microbiol 2012; 39:325-61. [PMID: 22978742 DOI: 10.3109/1040841x.2012.711740] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Viral diseases are important threats to public health worldwide. With the number of emerging viral diseases increasing the last decades, there is a growing need for appropriate animal models for virus studies. The relevance of animal models can be limited in terms of mimicking human pathophysiology. In this review, we discuss the utility of animal models for studies of influenza A viruses, HIV and SARS-CoV in light of viral emergence, assessment of infection and transmission risks, and regulatory decision making. We address their relevance and limitations. The susceptibility, immune responses, pathogenesis, and pharmacokinetics may differ between the various animal models. These complexities may thwart translating results from animal experiments to the humans. Within these constraints, animal models are very informative for studying virus immunopathology and transmission modes and for translation of virus research into clinical benefit. Insight in the limitations of the various models may facilitate further improvements of the models.
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Affiliation(s)
- Derrick Louz
- National Institute for Public Health and the Environment (RIVM), GMO Office , Bilthoven , The Netherlands
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440
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Cooper N, Griffin R, Franz M, Omotayo M, Nunn CL, Fryxell J. Phylogenetic host specificity and understanding parasite sharing in primates. Ecol Lett 2012; 15:1370-7. [PMID: 22913776 DOI: 10.1111/j.1461-0248.2012.01858.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/04/2012] [Accepted: 07/30/2012] [Indexed: 12/15/2022]
Abstract
Understanding how parasites are transmitted to new species is of great importance for human health, agriculture and conservation. However, it is still unclear why some parasites are shared by many species, while others have only one host. Using a new measure of 'phylogenetic host specificity', we find that most primate parasites with more than one host are phylogenetic generalists, infecting less closely related primates than expected. Evolutionary models suggest that phylogenetic host generalism is driven by a mixture of host-parasite cospeciation and lower rates of parasite extinction. We also show that phylogenetic relatedness is important in most analyses, but fails to fully explain patterns of parasite sharing among primates. Host ecology and geographical distribution emerged as key additional factors that influence contacts among hosts to facilitate sharing. Greater understanding of these factors is therefore crucial to improve our ability to predict future infectious disease risks.
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Affiliation(s)
- Natalie Cooper
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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441
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Wallau GL, Ortiz MF, Loreto ELS. Horizontal transposon transfer in eukarya: detection, bias, and perspectives. Genome Biol Evol 2012; 4:689-99. [PMID: 22798449 PMCID: PMC3516303 DOI: 10.1093/gbe/evs055] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The genetic similarity observed among species is normally attributed to the existence of
a common ancestor. However, a growing body of evidence suggests that the exchange of
genetic material is not limited to the transfer from parent to offspring but can also
occur through horizontal transfer (HT). Transposable elements (TEs) are DNA fragments with
an innate propensity for HT; they are mobile and possess parasitic characteristics that
allow them to exist and proliferate within host genomes. However, horizontal transposon
transfer (HTT) is not easily detected, primarily because the complex TE life cycle can
generate phylogenetic patterns similar to those expected for HTT events. The increasingly
large number of new genome projects, in all branches of life, has provided an
unprecedented opportunity to evaluate the TE content and HTT events in these species,
although a standardized method of HTT detection is required before trends in the HTT rates
can be evaluated in a wide range of eukaryotic taxa and predictions about these events can
be made. Thus, we propose a straightforward hypothesis test that can be used by TE
specialists and nonspecialists alike to discriminate between HTT events and natural TE
life cycle patterns. We also discuss several plausible explanations and predictions for
the distribution and frequency of HTT and for the inherent biases of HTT detection.
Finally, we discuss some of the methodological concerns for HTT detection that may result
in the underestimation and overestimation of HTT rates during eukaryotic genome
evolution.
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Affiliation(s)
- Gabriel Luz Wallau
- Programa de Pós-Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Brazil.
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442
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Pizzatto L, Shine R. Typhoid Mary in the frogpond: can we use native frogs to disseminate a lungworm biocontrol for invasive cane toads? Anim Conserv 2012. [DOI: 10.1111/j.1469-1795.2012.00564.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- L. Pizzatto
- School of Biological Sciences; The University of Sydney; Sydney; NSW; Australia
| | - R. Shine
- School of Biological Sciences; The University of Sydney; Sydney; NSW; Australia
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443
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Analysis by single-gene reassortment demonstrates that the 1918 influenza virus is functionally compatible with a low-pathogenicity avian influenza virus in mice. J Virol 2012; 86:9211-20. [PMID: 22718825 DOI: 10.1128/jvi.00887-12] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The 1918-1919 "Spanish" influenza pandemic is estimated to have caused 50 million deaths worldwide. Understanding the origin, virulence, and pathogenic properties of past pandemic influenza viruses, including the 1918 virus, is crucial for current public health preparedness and future pandemic planning. The origin of the 1918 pandemic virus has not been resolved, but its coding sequences are very like those of avian influenza virus. The proteins encoded by the 1918 virus differ from typical low-pathogenicity avian influenza viruses at only a small number of amino acids in each open reading frame. In this study, a series of chimeric 1918 influenza viruses were created in which each of the eight 1918 pandemic virus gene segments was replaced individually with the corresponding gene segment of a prototypical low-pathogenicity avian influenza (LPAI) H1N1 virus in order to investigate functional compatibility of the 1918 virus genome with gene segments from an LPAI virus and to identify gene segments and mutations important for mammalian adaptation. This set of eight "7:1" chimeric viruses was compared to the parental 1918 and LPAI H1N1 viruses in intranasally infected mice. Seven of the 1918 LPAI 7:1 chimeric viruses replicated and caused disease equivalent to the fully reconstructed 1918 virus. Only the chimeric 1918 virus containing the avian influenza PB2 gene segment was attenuated in mice. This attenuation could be corrected by the single E627K amino acid change, further confirming the importance of this change in mammalian adaptation and mouse pathogenicity. While the mechanisms of influenza virus host switch, and particularly mammalian host adaptation are still only partly understood, these data suggest that the 1918 virus, whatever its origin, is very similar to avian influenza virus.
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444
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Abstract
Two studies of H5N1 avian influenza viruses that had been genetically engineered to render them transmissible between ferrets have proved highly controversial. Divergent opinions exist about the importance of these studies of influenza transmission and about potential 'dual use' research implications. No consensus has developed yet about how to balance these concerns. After not recommending immediate full publication of earlier, less complete versions of the studies, the United States National Science Advisory Board for Biosecurity subsequently recommended full publication of more complete manuscripts; however, controversy about this and similar research remains.
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445
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Evolutionary reconstructions of the transferrin receptor of Caniforms supports canine parvovirus being a re-emerged and not a novel pathogen in dogs. PLoS Pathog 2012; 8:e1002666. [PMID: 22570610 PMCID: PMC3342950 DOI: 10.1371/journal.ppat.1002666] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 03/09/2012] [Indexed: 12/12/2022] Open
Abstract
Parvoviruses exploit transferrin receptor type-1 (TfR) for cellular entry in carnivores, and specific interactions are key to control of host range. We show that several key mutations acquired by TfR during the evolution of Caniforms (dogs and related species) modified the interactions with parvovirus capsids by reducing the level of binding. These data, along with signatures of positive selection in the TFRC gene, are consistent with an evolutionary arms race between the TfR of the Caniform clade and parvoviruses. As well as the modifications of amino acid sequence which modify binding, we found that a glycosylation site mutation in the TfR of dogs which provided resistance to the carnivore parvoviruses which were in circulation prior to about 1975 predates the speciation of coyotes and dogs. Because the closely-related black-backed jackal has a TfR similar to their common ancestor and lacks the glycosylation site, reconstructing this mutation into the jackal TfR shows the potency of that site in blocking binding and infection and explains the resistance of dogs until recent times. This alters our understanding of this well-known example of viral emergence by indicating that canine parvovirus emergence likely resulted from the re-adaptation of a parvovirus to the resistant receptor of a former host. Parvoviruses in cats and dogs have been studied as a model system to understand how viruses gain the ability to infect new host species. By studying the evolution of the transferrin receptor, which the virus uses to enter a cell, we discovered that the ancestors of dogs were likely infected by a parvovirus millions of years ago until they evolved and became resistant; this was caused by their transferrin receptor changing so it no longer bound the virus. When a variant virus that infects dogs emerged in the 1970s, it had adapted to overcome this block. This story suggests that diseases which were once eliminated from a species can evolve and regain the infectivity for that host, therefore having high potential to be emerging diseases. We identified features of the receptor that were important to the evolution of this host-virus interaction and confirmed their role in regulating virus binding in cell culture.
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446
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Chen XP, Yu J, Li MH, Zhao GY, Wang W, Guo WP, Deng XZ, Zhang Y, Fu ZF, Qin XC, Zhang YZ. Pathogenicity of a natural reassortant hantavirus CGRn9415 in newborn rats and newborn mice. J Gen Virol 2012; 93:1017-1022. [DOI: 10.1099/vir.0.038703-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To better understand the pathogenicity and infectivity of a natural reassortant CGRn9415 generated from Hantaan virus (HTNV) and Seoul virus (SEOV), CGRn9415, HTNV 76–118 and SEOV L99 were used to infect newborn Kunming (KM) mice and newborn Wistar rats. In KM mice, there was no statistical difference between the death rate with CGRn9415 and that of L99, while 76–118 killed all mice even at low dosage; CGRn9415 killed all infected rats similar to L99 at the dosage of 105 f.f.u., while no death occurred in rats infected with 76–118 even as high as 2×105 f.f.u., suggesting that the reassortant CGRn9415 possesses similar pathogenicity as L99. Furthermore, the reassortant CGRn9415 could establish a persistent infection in both KM mice and Wistar rats more easily than 76–118 or L99. These data suggest that the reassorted hantavirus behaves more like SEOV as far as the pathogenicity is concerned.
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Affiliation(s)
- Xiao-Ping Chen
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Liuzi 5, 102206 Beijing, PR China
| | - Juan Yu
- Medical Institute of Nanjing Army, Nanjing, PR China
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Liuzi 5, 102206 Beijing, PR China
| | - Ming-Hui Li
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Liuzi 5, 102206 Beijing, PR China
| | - Gao-Yu Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Liuzi 5, 102206 Beijing, PR China
| | - Wen Wang
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Liuzi 5, 102206 Beijing, PR China
| | - Wen-Ping Guo
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Liuzi 5, 102206 Beijing, PR China
| | | | - Yun Zhang
- Medical Institute of Nanjing Army, Nanjing, PR China
| | - Zhen F. Fu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, PR China
- Department of Pathology, University of Georgia, Athens, GA 30602, USA
| | - Xin-Cheng Qin
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Liuzi 5, 102206 Beijing, PR China
| | - Yong-Zhen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Liuzi 5, 102206 Beijing, PR China
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447
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Drexler JF, Corman VM, Müller MA, Maganga GD, Vallo P, Binger T, Gloza-Rausch F, Cottontail VM, Rasche A, Yordanov S, Seebens A, Knörnschild M, Oppong S, Sarkodie YA, Pongombo C, Lukashev AN, Schmidt-Chanasit J, Stöcker A, Carneiro AJB, Erbar S, Maisner A, Fronhoffs F, Buettner R, Kalko EKV, Kruppa T, Franke CR, Kallies R, Yandoko ER, Herrler G, Reusken C, Hassanin A, Krüger DH, Matthee S, Ulrich RG, Leroy EM, Drosten C. Bats host major mammalian paramyxoviruses. Nat Commun 2012; 3:796. [PMID: 22531181 PMCID: PMC3343228 DOI: 10.1038/ncomms1796] [Citation(s) in RCA: 468] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 03/19/2012] [Indexed: 12/12/2022] Open
Abstract
The large virus family Paramyxoviridae includes some of the most significant human and livestock viruses, such as measles-, distemper-, mumps-, parainfluenza-, Newcastle disease-, respiratory syncytial virus and metapneumoviruses. Here we identify an estimated 66 new paramyxoviruses in a worldwide sample of 119 bat and rodent species (9,278 individuals). Major discoveries include evidence of an origin of Hendra- and Nipah virus in Africa, identification of a bat virus conspecific with the human mumps virus, detection of close relatives of respiratory syncytial virus, mouse pneumonia- and canine distemper virus in bats, as well as direct evidence of Sendai virus in rodents. Phylogenetic reconstruction of host associations suggests a predominance of host switches from bats to other mammals and birds. Hypothesis tests in a maximum likelihood framework permit the phylogenetic placement of bats as tentative hosts at ancestral nodes to both the major Paramyxoviridae subfamilies (Paramyxovirinae and Pneumovirinae). Future attempts to predict the emergence of novel paramyxoviruses in humans and livestock will have to rely fundamentally on these data.
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Affiliation(s)
- Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, 53127 Germany
| | - Victor Max Corman
- Institute of Virology, University of Bonn Medical Centre, Bonn, 53127 Germany
| | | | - Gael Darren Maganga
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Peter Vallo
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, v.v.i., Brno, Czech Republic
| | - Tabea Binger
- Institute of Virology, University of Bonn Medical Centre, Bonn, 53127 Germany
| | - Florian Gloza-Rausch
- Institute of Virology, University of Bonn Medical Centre, Bonn, 53127 Germany
- Noctalis, Centre for Bat Protection and Information, Bad Segeberg, Germany
| | | | - Andrea Rasche
- Institute of Virology, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
| | - Stoian Yordanov
- Forestry Board Directorate of Strandja Natural Park, Malko Tarnovo, Bulgaria
| | - Antje Seebens
- Noctalis, Centre for Bat Protection and Information, Bad Segeberg, Germany
| | | | - Samuel Oppong
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Yaw Adu Sarkodie
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | | | - Jonas Schmidt-Chanasit
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Andreas Stöcker
- Infectious Diseases Research Laboratory, University Hospital Professor Edgard Santos, Federal University of Bahia, Salvador, Brazil
| | | | - Stephanie Erbar
- Institute of Virology, Philipps University of Marburg, Marburg, Germany
| | - Andrea Maisner
- Institute of Virology, Philipps University of Marburg, Marburg, Germany
| | - Florian Fronhoffs
- Institute of Pathology, University of Bonn Medical Centre, Bonn, Germany
| | - Reinhard Buettner
- Institute of Pathology, University of Bonn Medical Centre, Bonn, Germany
- Institute of Pathology, University of Cologne Medical Centre, Cologne, Germany
| | - Elisabeth K. V. Kalko
- Institute of Experimental Ecology, University of Ulm, Ulm, Germany
- Smithsonian Tropical Research Institute, Balboa, Panama
| | - Thomas Kruppa
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | | | - René Kallies
- Institute of Virology, University of Bonn Medical Centre, Bonn, 53127 Germany
| | | | - Georg Herrler
- Institute of Virology, University of Veterinary Medicine Hannover Foundation, Hannover, Germany
| | - Chantal Reusken
- Netherlands Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Alexandre Hassanin
- Muséum National d'Histoire Naturelle/Centre National de la Recherche Scientifique, UMR 7205, Paris, France
| | - Detlev H. Krüger
- Institute of Medical Virology (Helmut Ruska Haus), Charité Medical School, Berlin, Germany
| | - Sonja Matthee
- Department of Conservation Ecology and Entomology, Stellenbosch University, Stellenbosch, South Africa
| | - Rainer G. Ulrich
- Institute for Novel and Emerging Infections Diseases, Friedrich-Loeffler-Institut, Institute for Novel and Emerging Infectious Diseases, Greifswald–Insel Riems, Germany
| | - Eric M. Leroy
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
- Institut de Recherche pour le Développement, UMR 224 (MIVEGEC), IRD/CNRS/UM1, Montpellier, France
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, 53127 Germany
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448
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Cross-species transmission of simian retroviruses: how and why they could lead to the emergence of new diseases in the human population. AIDS 2012; 26:659-73. [PMID: 22441170 DOI: 10.1097/qad.0b013e328350fb68] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The HIV-1 group M epidemic illustrates the extraordinary impact and consequences resulting from a single zoonotic transmission. Exposure to blood or other secretions of infected animals, through hunting and butchering of bushmeat, or through bites and scratches inflicted by pet nonhuman primates (NHPs), represent the most plausible source for human infection with simian immunodeficiency virus (SIV), simian T-cell lymphotropic virus (STLV) and simian foamy virus. The chance for cross-species transmissions could increase when frequency of exposure and retrovirus prevalence is high. According to the most recent data, human exposure to SIV or STLV appears heterogeneous across the African countries surveyed. Exposure is not sufficient to trigger disease: viral and host molecular characteristics and compatibility are fundamental factors to establish infection. A successful species jump is achieved when the pathogen becomes transmissible between individuals within the new host population. To spread efficiently, HIV likely required changes in human behavior. Given the increasing exposure to NHP pathogens through hunting and butchering, it is likely that SIV and other simian viruses are still transmitted to the human population. The behavioral and socio-economic context of the twenty-first century provides favorable conditions for the emergence and spread of new epidemics. Therefore, it is important to evaluate which retroviruses the human population is exposed to and to better understand how these viruses enter, infect, adapt and spread to its new host.
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449
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Calvignac-Spencer S, Leendertz SAJ, Gillespie TR, Leendertz FH. Wild great apes as sentinels and sources of infectious disease. Clin Microbiol Infect 2012; 18:521-7. [PMID: 22448813 DOI: 10.1111/j.1469-0691.2012.03816.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Emerging zoonotic infectious diseases pose a serious threat to global health. This is especially true in relation to the great apes, whose close phylogenetic relationship with humans results in a high potential for microorganism exchange. In this review, we show how studies of the microorganisms of wild great apes can lead to the discovery of novel pathogens of importance for humans. We also illustrate how these primates, living in their natural habitats, can serve as sentinels for outbreaks of human disease in regions with a high likelihood of disease emergence. Greater sampling efforts and improvements in sample preservation and diagnostic capacity are rapidly improving our understanding of the diversity and distribution of microorganisms in wild great apes. Linking non-invasive diagnostic data with observational health data from great apes habituated to human presence is a promising approach for the discovery of pathogens of high relevance for humans.
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450
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Evidence for ACE2-utilizing coronaviruses (CoVs) related to severe acute respiratory syndrome CoV in bats. J Virol 2012; 86:6350-3. [PMID: 22438550 DOI: 10.1128/jvi.00311-12] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In 2002, severe acute respiratory syndrome (SARS)-coronavirus (CoV) appeared as a novel human virus with high similarity to bat coronaviruses. However, while SARS-CoV uses the human angiotensin-converting enzyme 2 (ACE2) receptor for cellular entry, no coronavirus isolated from bats appears to use ACE2. Here we show that signatures of recurrent positive selection in the bat ACE2 gene map almost perfectly to known SARS-CoV interaction surfaces. Our data indicate that ACE2 utilization preceded the emergence of SARS-CoV-like viruses from bats.
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