DOCSLIB.ORG

A Proposed New Order for Eukaryotic Nucleocytoplasmic Large DNA Viruses Philippe Colson Aix-Marseille Universite

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A Proposed New Order for Eukaryotic Nucleocytoplasmic Large DNA Viruses Philippe Colson Aix-Marseille Universite University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Virology Papers Virology, Nebraska Center for 2013 ‘‘Megavirales’’, a proposed new order for eukaryotic nucleocytoplasmic large DNA viruses Philippe Colson Aix-Marseille Universite Xavier De Lamballerie EHSP French School of Public Health, Aix-Marseille Universite Natalya Yutin National Institutes of Health Sassan Asgari The University of Queensland Yves Bigot International Committee on Taxonomy of Viruses See next page for additional authors Follow this and additional works at: http://digitalcommons.unl.edu/virologypub Part of the Biological Phenomena, Cell Phenomena, and Immunity Commons, Cell and Developmental Biology Commons, Genetics and Genomics Commons, Infectious Disease Commons, Medical Immunology Commons, Medical Pathology Commons, and the Virology Commons Colson, Philippe; De Lamballerie, Xavier; Yutin, Natalya; Asgari, Sassan; Bigot, Yves; Bideshi, Dennis K.; Cheng, Xiao-Wen; Federici, Brian A.; Van Etten, James L.; Koonin, Eugene V.; La Scola, Bernard; and Raoult, Didier, "‘‘Megavirales’’, a proposed new order for eukaryotic nucleocytoplasmic large DNA viruses" (2013). Virology Papers. 268. http://digitalcommons.unl.edu/virologypub/268 This Article is brought to you for free and open access by the Virology, Nebraska Center for at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Virology Papers by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Philippe Colson, Xavier De Lamballerie, Natalya Yutin, Sassan Asgari, Yves Bigot, Dennis K. Bideshi, Xiao- Wen Cheng, Brian A. Federici, James L. Van Etten, Eugene V. Koonin, Bernard La Scola, and Didier Raoult This article is available at DigitalCommons@University of Nebraska - Lincoln: http://digitalcommons.unl.edu/virologypub/268 Arch Virol (2013) 158:2517–2521 DOI 10.1007/s00705-013-1768-6 ORIGINAL ARTICLE ‘‘Megavirales’’, a proposed new order for eukaryotic nucleocytoplasmic large DNA viruses Philippe Colson • Xavier De Lamballerie • Natalya Yutin • Sassan Asgari • Yves Bigot • Dennis K. Bideshi • Xiao-Wen Cheng • Brian A. Federici • James L. Van Etten • Eugene V. Koonin • Bernard La Scola • Didier Raoult Received: 3 August 2012 / Accepted: 7 May 2013 / Published online: 29 June 2013 Ó Springer-Verlag Wien 2013 Abstract The nucleocytoplasmic large DNA viruses replication and virion formation to the last common (NCLDVs) comprise a monophyletic group of viruses that ancestor of all these viruses. Taken together, these char- infect animals and diverse unicellular eukaryotes. The acteristics lead us to propose assigning an official taxo- NCLDV group includes the families Poxviridae, Asfarvir- nomic rank to the NCLDVs as the order ‘‘Megavirales’’, in idae, Iridoviridae, Ascoviridae, Phycodnaviridae, Mimi- reference to the large size of the virions and genomes of viridae and the proposed family ‘‘Marseilleviridae’’. The these viruses. family Mimiviridae includes the largest known viruses, with genomes in excess of one megabase, whereas the genome size in the other NCLDV families varies from 100 Introduction to 400 kilobase pairs. Most of the NCLDVs replicate in the cytoplasm of infected cells, within so-called virus factories. The nucleocytoplasmic large DNA viruses (NCLDVs) are The NCLDVs share a common ancient origin, as demon- an apparently monophyletic group of viruses infecting strated by evolutionary reconstructions that trace approxi- eukaryotes that was first described in 2001 [1]. The mately 50 genes encoding key proteins involved in viral NCLDVs encompass the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, and Phycodnaviridae [1–3] and two groups of distinct giant viruses that have been isolated S. Asgari, Y. Bigot, D. K. Bideshi, X.-W. Cheng and B. A. Federici from Acanthamoeba, giving rise to the now established belong to the Ascoviridae study group of the International Committee family Mimiviridae [4–7] and the proposed family ‘‘Mar- on Taxonomy of Viruses (ICTV). seilleviridae’’ [8–10] (Table 1). P. Colson Á B. La Scola Á D. Raoult (&) N. Yutin Á E. V. Koonin Unite´ des Rickettsies, URMITE UMR CNRS 7278 IRD 198 National Center for Biotechnology Information (NCBI), INSERM U1095, Faculte´sdeMe´decine et de Pharmacie, IHU National Library of Medicine, National Institutes of Health, Me´diterrane´e Infection, Aix-Marseille Universite´, 27 Boulevard Bldg. 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA Jean Moulin, 13385 Marseille Cedex 05, France e-mail: [email protected] S. Asgari School of Biological Sciences, The University of Queensland, P. Colson Á X. De Lamballerie Á B. La Scola Á D. Raoult St Lucia, QLD 4072, Australia Poˆle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fe´de´ration de Bacte´riologie-Hygie`ne-Virologie, Y. Bigot IHU Me´diterrane´e Infection, Assistance Publique, Hoˆpitaux de UMR INRA-CNRS 7247, PRC, Centre INRA de Nouzilly, Marseille, Centre Hospitalo-Universitaire Timone, 264 Rue 37380 Nouzilly, France Saint-Pierre, 13385 Marseille Cedex 05, France D. K. Bideshi X. De Lamballerie Molecular and Developmental Biology, University of California, Unite´ des Virus Emergents, UMR190 Emergence des Riverside, CA 92521, USA pathologies virales, Faculte´ de Me´decine, Institut de Recherche pour le De´veloppement, EHSP French School of Public Health, Aix-Marseille Universite´, Marseille, France 123 2518 P. Colson et al. The viruses of the family Mimiviridae possess by far the the entire group [3]. The maximum-likelihood evolutionary largest virions and genomes among all currently known reconstruction that led to this conclusion relied upon a viruses. Strikingly, mimivirus genomes are larger than phylogenetic tree of the universally conserved NCLDV those of many parasitic and symbiotic bacteria and genes and the patterns of presence-absence of other genes approach the size and complexity of the smallest known as derived from the clusters of orthologous genes of the free-living bacteria and archaea. Moreover, mimiviruses NCLDVs (NCVOGs). Although a comprehensive phylo- encode many genes that have not been found in other genetic analysis of the putative ancestral NCLDV genes viruses, in particular multiple components of the translation revealed a complex picture of evolution that involved system such as aminoacyl-tRNA synthetases [4, 11, 12]. A multiple non-orthologous gene displacements, on the distant relative of mimiviruses, Cafeteria roenbergensis whole, the results of this analysis were compatible with the virus (CroV), has been isolated from a marine stramenopile descent of (nearly) all of these genes from an ancestral [13], and numerous homologs of mimivirus genes have virus [19]. Moreover, the inferred ancestral NCLDV genes been detected in metagenomic samples [14–17], indicating encode proteins that perform key functions in virus genome that the actual diversity of the giant viruses remains largely replication and expression as well as virion morphogenesis untapped. These unusual features of the mimiviruses have and structure, suggesting that the putative ancestral virus attracted strong interest of many researchers and revitalized already possessed the main biological features of the extant the study of molecular biology and biochemistry of the NCLDVs. NCLDVs. Importantly, the set of the approximately 50 ancestral A reclassification of the members of the NCLDV fam- genes sharply partitions the NCLDVs from all other groups ilies into a new virus order ‘‘Megavirales’’ has been sug- of viruses, including large DNA viruses infecting eukary- gested recently [18], based upon several defining features. otes, such as nudiviruses, herpesviruses and baculoviruses, In the present proposal, we succinctly summarize these as well as large DNA viruses of bacteria and archaea. unique traits of the NCLDV and make the formal case for Although some of these viruses share with the NCLDVs the distinctness of the NCLDVs from other large DNA one or more of the ‘‘virus hallmark genes’’, such as the viruses. DNA polymerase, the helicase-primase or the packaging ATPase, none come close to possessing the entire set of the ancestral NCLDV genes [20]. The defining features of the NCLDVs The apparent origin of the NCLDVs from a common ancestral virus is buttressed by shared genomic, structural The monophyly of the NCLDVs, i.e., the common origin of and biological features. With the exception of the members all these viruses from the same ancestral virus, was inferred of the virus families Poxviridae and Ascoviridae, all the from the results of phylogenetic and phyletic analyses [1–3, NCLDVs form large, icosahedral capsids (more than 19]. All of the NCLDVs share five core genes, namely 100 nm in diameter) that are comprised of a single, those encoding the major capsid protein (poxvirus D13 homologous double b barrel jelly roll protein [21] and gene), helicase-primase (D5), DNA polymerase elongation encapsidate a single double-stranded DNA molecule subunit family B, DNA-packaging ATPase (A32), and viral ranging in size from 100 kilobase pairs to over one meg- late transcription factor 3 (A2L). Moreover, approximately abase pairs (Table 1). The exceptions to this conserved 50 genes, although missing in some of the NCLDVs, were virion architecture are the poxviruses and the ascoviruses, assigned, with high confidence, to the common ancestor of with their unique brick-shaped virions and allantoid caps- ids, respectively [22, 23]. However, at least in poxviruses, this appears to be a derived
Load more

Recommended publications
  • Adams Hawii 0085O 10232.Pdf
    ANALYSIS AND DEVELOPMENT OF MANAGEMENT TOOLS FOR ORYCTES RHINOCEROS (COLEOPTERA: SCARABAEIDAE) A THESIS SUBMITTED TO THE GRAUDATE DIVISION OF THE UNIVERSITY OF HAWAIʻI AT MĀNOA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE IN TROPICAL PLANT PATHOLOGY MAY 2019 By Brandi-Leigh H. Adams Thesis Committee: Michael Melzer, Chairperson Zhiqiang Cheng Brent Sipes ACKNOWLEDGEMENTS It is with deep gratitude that I thank the members of my committee, Dr. Michael Melzer, Dr. Zhiqiang Cheng, and Dr. Brent Sipes for their expert advice and knowledge, to which I have constantly deferred to during my time as a graduate student. A very special thank you goes to Dr. Michael Melzer, who took me in as an undergraduate lab assistant, and saw enough potential in me that he felt I deserved the opportunity to learn, travel, and grow under his guidance. I would also like to give special thanks to Dr. Shizu Watanabe, who always made time to answer even the smallest, most O.C.D. of my questions, who gave me words of encouragement when experiments did not go as planned or when I would find myself in doubt, and who has become a mentor and friend along the way. To my very first mentors in science; Dr. Wendy Kuntz, Dr. Matthew Tuthill, and Keolani Noa; thank you for encouraging me to pursue a major and career in STEM in the first place. I would also like to thank my lab mates, Nelson Masang Jr., Alexandra Kong, Alejandro Olmedo Velarde, Tomie Vowell, Asoka De Silva, Megan Manley, Jarin Loristo, and Cheyenne Barela for their support with experiments, and the knowledge and skills they have passed on to me.
    [Show full text]
  • Changes to Virus Taxonomy 2004
    Arch Virol (2005) 150: 189–198 DOI 10.1007/s00705-004-0429-1 Changes to virus taxonomy 2004 M. A. Mayo (ICTV Secretary) Scottish Crop Research Institute, Invergowrie, Dundee, U.K. Received July 30, 2004; accepted September 25, 2004 Published online November 10, 2004 c Springer-Verlag 2004 This note presents a compilation of recent changes to virus taxonomy decided by voting by the ICTV membership following recommendations from the ICTV Executive Committee. The changes are presented in the Table as decisions promoted by the Subcommittees of the EC and are grouped according to the major hosts of the viruses involved. These new taxa will be presented in more detail in the 8th ICTV Report scheduled to be published near the end of 2004 (Fauquet et al., 2004). Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U., and Ball, L.A. (eds) (2004). Virus Taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp. 1258. Recent changes to virus taxonomy Viruses of vertebrates Family Arenaviridae • Designate Cupixi virus as a species in the genus Arenavirus • Designate Bear Canyon virus as a species in the genus Arenavirus • Designate Allpahuayo virus as a species in the genus Arenavirus Family Birnaviridae • Assign Blotched snakehead virus as an unassigned species in family Birnaviridae Family Circoviridae • Create a new genus (Anellovirus) with Torque teno virus as type species Family Coronaviridae • Recognize a new species Severe acute respiratory syndrome coronavirus in the genus Coro- navirus, family Coronaviridae, order Nidovirales
    [Show full text]
  • Recombinant and Chimeric Viruses
    Recombinant and chimeric viruses: Evaluation of risks associated with changes in tropism Ben P.H. Peeters Animal Sciences Group, Wageningen University and Research Centre, Division of Infectious Diseases, P.O. Box 65, 8200 AB Lelystad, The Netherlands. May 2005 This report represents the personal opinion of the author. The interpretation of the data presented in this report is the sole responsibility of the author and does not necessarily represent the opinion of COGEM or the Animal Sciences Group. Dit rapport is op persoonlijke titel door de auteur samengesteld. De interpretatie van de gepresenteerde gegevens komt geheel voor rekening van de auteur en representeert niet de mening van de COGEM, noch die van de Animal Sciences Group. Advisory Committee Prof. dr. R.C. Hoeben (Chairman) Leiden University Medical Centre Dr. D. van Zaane Wageningen University and Research Centre Dr. C. van Maanen Animal Health Service Drs. D. Louz Bureau Genetically Modified Organisms Ing. A.M.P van Beurden Commission on Genetic Modification Recombinant and chimeric viruses 2 INHOUDSOPGAVE RECOMBINANT AND CHIMERIC VIRUSES: EVALUATION OF RISKS ASSOCIATED WITH CHANGES IN TROPISM Executive summary............................................................................................................................... 5 Introduction............................................................................................................................................ 7 1. Genetic modification of viruses .................................................................................................9
    [Show full text]
  • 25 May 7, 2014
    Joint Pathology Center Veterinary Pathology Services Wednesday Slide Conference 2013-2014 Conference 25 May 7, 2014 ______________________________________________________________________________ CASE I: 3121206023 (JPC 4035610). Signalment: 5-week-old mixed breed piglet, (Sus domesticus). History: Two piglets from the faculty farm were found dead, and another piglet was weak and ataxic and, therefore, euthanized. Gross Pathology: The submitted piglet was in good body condition. It was icteric and had a diffusely pale liver. Additionally, petechial hemorrhages were found on the kidneys, and some fibrin was present covering the abdominal organs. Laboratory Results: The intestine was PCR positive for porcine circovirus (>9170000). Histopathologic Description: Mesenteric lymph node: Diffusely, there is severe lymphoid depletion with scattered karyorrhectic debris (necrosis). Also scattered throughout the section are large numbers of macrophages and eosinophils. The macrophages often contain botryoid basophilic glassy intracytoplasmic inclusion bodies. In fewer macrophages, intranuclear basophilic inclusions can be found. Liver: There is massive loss of hepatocytes, leaving disrupted liver lobules and dilated sinusoids engorged with erythrocytes. The remaining hepatocytes show severe swelling, with micro- and macrovesiculation of the cytoplasm and karyomegaly. Some swollen hepatocytes have basophilic intranuclear, irregular inclusions (degeneration). Throughout all parts of the liver there are scattered moderate to large numbers of macrophages (without inclusions). Within portal areas there is multifocally mild to moderate fibrosis and bile duct hyperplasia. Some bile duct epithelial cells show degeneration and necrosis, and there is infiltration of neutrophils within the lumen. The limiting plate is often obscured mainly by infiltrating macrophages and eosinophils, and fewer neutrophils, extending into the adjacent parenchyma. Scattered are small areas with extra medullary hematopoiesis.
    [Show full text]
  • And Γ- Cytoplasmic Actin in Vaccinia Virus Infection
    Lights, Camera, Actin: Divergent roles of β- and γ- cytoplasmic actin in vaccinia virus infection NOORUL BISHARA MARZOOK A thesis submitted in fulfillment of requirements for the degree of Doctor of Philosophy FACULTY OF SCIENCE SCHOOL OF MOLECULAR BIOSCIENCE UNIVERSITY OF SYDNEY 2017 i TABLE OF CONTENTS Table of Contents ........................................................................................................... ii Acknowledgements ....................................................................................................... v Declaration ................................................................................................................... vii Abstract ....................................................................................................................... viii List of Figures ................................................................................................................ x List of Publications Arising From This Work.............................................................. xi Abbreviations Used ..................................................................................................... xii Chapter 1: Introduction ............................................................................................... 1 1.1 The Cytoskeleton ............................................................................................................ 2 1.1.1 The Eukaryotic Cytoskeleton .....................................................................................
    [Show full text]
  • Diversity of Large DNA Viruses of Invertebrates ⇑ Trevor Williams A, Max Bergoin B, Monique M
    Journal of Invertebrate Pathology 147 (2017) 4–22 Contents lists available at ScienceDirect Journal of Invertebrate Pathology journal homepage: www.elsevier.com/locate/jip Diversity of large DNA viruses of invertebrates ⇑ Trevor Williams a, Max Bergoin b, Monique M. van Oers c, a Instituto de Ecología AC, Xalapa, Veracruz 91070, Mexico b Laboratoire de Pathologie Comparée, Faculté des Sciences, Université Montpellier, Place Eugène Bataillon, 34095 Montpellier, France c Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands article info abstract Article history: In this review we provide an overview of the diversity of large DNA viruses known to be pathogenic for Received 22 June 2016 invertebrates. We present their taxonomical classification and describe the evolutionary relationships Revised 3 August 2016 among various groups of invertebrate-infecting viruses. We also indicate the relationships of the Accepted 4 August 2016 invertebrate viruses to viruses infecting mammals or other vertebrates. The shared characteristics of Available online 31 August 2016 the viruses within the various families are described, including the structure of the virus particle, genome properties, and gene expression strategies. Finally, we explain the transmission and mode of infection of Keywords: the most important viruses in these families and indicate, which orders of invertebrates are susceptible to Entomopoxvirus these pathogens. Iridovirus Ó Ascovirus 2016 Elsevier Inc. All rights reserved. Nudivirus Hytrosavirus Filamentous viruses of hymenopterans Mollusk-infecting herpesviruses 1. Introduction in the cytoplasm. This group comprises viruses in the families Poxviridae (subfamily Entomopoxvirinae) and Iridoviridae. The Invertebrate DNA viruses span several virus families, some of viruses in the family Ascoviridae are also discussed as part of which also include members that infect vertebrates, whereas other this group as their replication starts in the nucleus, which families are restricted to invertebrates.
    [Show full text]
  • A Scoping Review of Viral Diseases in African Ungulates
    veterinary sciences Review A Scoping Review of Viral Diseases in African Ungulates Hendrik Swanepoel 1,2, Jan Crafford 1 and Melvyn Quan 1,* 1 Vectors and Vector-Borne Diseases Research Programme, Department of Veterinary Tropical Disease, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa; [email protected] (H.S.); [email protected] (J.C.) 2 Department of Biomedical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium * Correspondence: [email protected]; Tel.: +27-12-529-8142 Abstract: (1) Background: Viral diseases are important as they can cause significant clinical disease in both wild and domestic animals, as well as in humans. They also make up a large proportion of emerging infectious diseases. (2) Methods: A scoping review of peer-reviewed publications was performed and based on the guidelines set out in the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) extension for scoping reviews. (3) Results: The final set of publications consisted of 145 publications. Thirty-two viruses were identified in the publications and 50 African ungulates were reported/diagnosed with viral infections. Eighteen countries had viruses diagnosed in wild ungulates reported in the literature. (4) Conclusions: A comprehensive review identified several areas where little information was available and recommendations were made. It is recommended that governments and research institutions offer more funding to investigate and report viral diseases of greater clinical and zoonotic significance. A further recommendation is for appropriate One Health approaches to be adopted for investigating, controlling, managing and preventing diseases. Diseases which may threaten the conservation of certain wildlife species also require focused attention.
    [Show full text]
  • University of Florida Thesis Or Dissertation Formatting
    THE ROLE OF CELL SIGNALING IN POXVIRUS TROPISM: THE CASE OF THE M-T5 HOST-RANGE PROTEIN OF MYXOMA VIRUS By STEVEN JAMES WERDEN A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2009 1 © 2009 Steven James Werden 2 To my family 3 ACKNOWLEDGMENTS I would like to thank Dr. Grant McFadden for continuous support, encouragement and advice during the course of my PhD. I am truly grateful for all the time and energy he has spent training me to become a better scientist and critical thinker. Without his guidance and persistent help this dissertation would not have been possible. In addition, I am appreciative to my committee members, Drs. Richard Condit, Greg Schultz and Dave Bloom for their encouraging words, fruitful discussion and most importantly, their commitment to helping me succeed. During the past five years, I have had the opportunity and privilege to work with many talented individuals. I would like to acknowledge all members of the McFadden laboratory, both past and present, for creating a work environment that fostered creativity. Special thanks go to Drs.Gen Wang, Steve Nazarian, Marianne Stanford and Fuan Wang for providing technical training. Dr. John Barrett deserves a special mention for his continued mentorship and support. I must not forget to thank those who attended the weekly “Poxaholics” meetings, for providing constructive criticism and a wonderful atmosphere to present data. Thanks go out to Doug Smith for assistance with the confocal microscope and to all who contributed reagents that were used in this dissertation.
    [Show full text]
  • Whole-Proteome Phylogeny of Large Dsdna Virus Families by an Alignment-Free Method
    Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method Guohong Albert Wua,b, Se-Ran Juna, Gregory E. Simsa,b, and Sung-Hou Kima,b,1 aDepartment of Chemistry, University of California, Berkeley, CA 94720; and bPhysical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 Contributed by Sung-Hou Kim, May 15, 2009 (sent for review February 22, 2009) The vast sequence divergence among different virus groups has self-organizing maps (18) have also been used to understand the presented a great challenge to alignment-based sequence com- grouping of viruses. parison among different virus families. Using an alignment-free In the previous alignment-free phylogenomic studies using l-mer comparison method, we construct the whole-proteome phylogeny profiles, 3 important issues were not properly addressed: (i) the for a population of viruses from 11 viral families comprising 142 selection of the feature length, l, appears to be without logical basis; large dsDNA eukaryote viruses. The method is based on the feature (ii) no statistical assessment of the tree branching support was frequency profiles (FFP), where the length of the feature (l-mer) is provided; and (iii) the effect of HGT on phylogenomic relationship selected to be optimal for phylogenomic inference. We observe was not considered. HGT in LDVs has been documented by that (i) the FFP phylogeny segregates the population into clades, alignment-based methods (19–22), but these studies have mostly the membership of each has remarkable agreement with current searched for HGT from host to a single family of viruses, and there classification by the International Committee on the Taxonomy of has not been a study of interviral family HGT among LDVs.
    [Show full text]
  • ICTV Code Assigned: 2011.001Ag Officers)
    This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document “Help with completing a taxonomic proposal” Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc (to be completed by ICTV Code assigned: 2011.001aG officers) Short title: Change existing virus species names to non-Latinized binomials (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 9 are required) 6 7 8 9 Author(s) with e-mail address(es) of the proposer: Van Regenmortel Marc, [email protected] Burke Donald, [email protected] Calisher Charles, [email protected] Dietzgen Ralf, [email protected] Fauquet Claude, [email protected] Ghabrial Said, [email protected] Jahrling Peter, [email protected] Johnson Karl, [email protected] Holbrook Michael, [email protected] Horzinek Marian, [email protected] Keil Guenther, [email protected] Kuhn Jens, [email protected] Mahy Brian, [email protected] Martelli Giovanni, [email protected] Pringle Craig, [email protected] Rybicki Ed, [email protected] Skern Tim, [email protected] Tesh Robert, [email protected] Wahl-Jensen Victoria, [email protected] Walker Peter, [email protected] Weaver Scott, [email protected] List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at http://www.ictvonline.org/subcommittees.asp .
    [Show full text]
  • Whole-Proteome Phylogeny of Large Dsdna Viruses and Parvoviruses
    Yu et al. BMC Evolutionary Biology 2010, 10:192 http://www.biomedcentral.com/1471-2148/10/192 RESEARCH ARTICLE Open Access Whole-proteomeResearch article phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model Zu-Guo Yu1,2, Ka Hou Chu*3, Chi Pang Li3, Vo Anh1, Li-Qian Zhou2 and Roger Wei Wang4 Abstract Background: The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes. Results: In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV). Conclusions: The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size.
    [Show full text]
  • JOURNAL of VIROLOGY VOLUME 63 * DECEMBER 1989 NUMBER 12 Arnold J
    JOURNAL OF VIROLOGY VOLUME 63 * DECEMBER 1989 NUMBER 12 Arnold J. Levine, Editor in Chief Robert A. Lamb Editor (1992) (1994) Northwestern University Princeton University Stephen P. Goff, Editor (1994) Evanston, Ill. Princeton, N.J. Columbia University Michael B. A. Oldstone, Editor (1993) Joan S. Brugge, Editor (1994) New York, N. Y. Scripps Clinic & Research University ofPennsylvania Peter M. Howley, Editor (1993) Foundation Philadelphia, Pa. National Cancer Institute La Jolla, Calif. Bernard N. Fields, Editor (1993) Bethesda, Md. Thomas E. Shenk, Editor (1994) Harvard Medical School Princeton University Boston, Mass. Princeton, N.J. EDITORIAL BOARD Rafi Ahmed (1991) Emanuel A. Faust (1990) Robert A. Lazzarini (1990) William S. Robinson (1989) James Alwine (1991) S. Jane Flint (1990) Jonathan Leis (1991) Bernard Roizman (1991) David Baltimore (1990) William R. Folk (1991) Myron Levine (1991) John K. Rose (1991) Amiya K. Banerjee (1990) Donald Ganem (1991) Arthur D. Levinson (1991) Naomi Rosenberg (1989) Tamar Ben-Porat (1990) Costa Georgopolous (1989) Maxine Linial (1991) Roland R. Rueckert (1991) Kenneth I. Berns (1991) Walter Gerhard (1989) David M. Livingston (1991) Norman P. Salzman (1990) Joseph B. Bolen (1991) Mary-Jane Gething (1990) Douglas R. Lowy (1989) Charles E. Samuel (1989) Michael Botchan (1989) Joseph C. Glorioso (1989) Malcohm Martin (1989) Priscilla A. Schaffer (1990) Thomas J. Braciale (1991) Larry M. Gold (1991) Robert Martin (1990) Sondra Schlesinger (1989) Dalius J. Briedis (1991) Hidesaburo Hanafusa (1989) Warren Masker (1990) Robert J. Schneider (1991) Michael J. Buchmeier (1989) John Hassell (1989) James McDougall (1990) Bart Sefton (1991) Robert Callahan (1991) William S. Hayward (1990) Thomas Merigan (1989) Bert L.
    [Show full text]