DOCSLIB.ORG

Classify Viruses — the Gain Is Worth the Pain Viruses Hold Solutions to a Lot of Problems, So Let’S Fund and Reward Cataloguing, Urge Jens H

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Classify Viruses — the Gain Is Worth the Pain Viruses Hold Solutions to a Lot of Problems, So Let’S Fund and Reward Cataloguing, Urge Jens H COMMENT Viruses that infect humans, such as Ebola, are a tiny fraction of what needs to be characterized. Classify viruses — the gain is worth the pain Viruses hold solutions to a lot of problems, so let’s fund and reward cataloguing, urge Jens H. Kuhn and colleagues. arth probably harbours a million been formally described. Comparative anal- single-stranded negative-sense RNA viruses times more virus particles than there yses of the genomes of these and numerous (see ‘Branching out’). Similar high-rank are stars in the observable Universe. unclassified viruses show that the current taxa could be established for other major EThese viruses could hold solutions to many taxonomy is vastly incomplete and, in places, virus groups. of humanity’s current problems. even wrong. Comprehensive classification of the Phage therapy could someday be used to Last month a momentous step was entire virosphere now seems within reach. treat diseases caused by multidrug-resistant announced by the International Commit- But major changes are needed to make that bacteria, for instance. Enzymes encoded by tee on Taxonomy of Viruses (ICTV), which happen. new viruses could help researchers to develop authorizes and organizes the classifica- OF HEALTH/SPL INSTITUTE NATIONAL pharmaceuticals. Or viruses that kill algal tion and naming of virus species. (Five of HIDDEN DIVERSITY cells could be used to control harmful blooms. us have roles in this organization: J.H.K., There are probably billions of distinct viruses. Tapping into the benefits — and threats — M.K., Y.-Z.Z., P.M. and V.V.D.) The com- Viruses depend on host cells to replicate, as do requires describing and cataloguing viruses mittee endorsed the establishment of taxa other ‘selfish’ genetic elements, such as viroids and mapping their evolutionary relationships. above the rank of order1. It introduced the and plasmids. The same host (say, humans or But, so far, just 4,958 virus species have first-ever virus phylum, Negarnaviricota, for the Escherichia coli bacterium) can be infected 318 | NATURE | VOL 566 | 21 FEBRUARY 2019©2019 Spri nger Nature Li mited. All ri ghts reserved. ©2019 Spri nger Nature Li mited. All ri ghts reserved. COMMENT by many, very different viruses. However, most of the viruses that have been described BRANCHING OUT infect only a few hosts. In fact, bacterial viruses (bacteriophages) often infect mem- A first for viruses bers of just one species, so are sometimes used to identify the bacteria in a sample. In other Higher taxonomic ranks of RNA viruses for single-stranded, negative-sense RNA words, the diversity of viruses is probably at can be established on the basis of a viruses. This single branch splits into two least as great as that of their available hosts. phylogeny of a universal marker. (In a subbranches, the subphyla Haploviricotina Only around 5,500 species of mammal and similar way, the taxonomy of cellular and Polyploviricotina (see ‘Classifying RNA about 391,000 species of vascular plant have organisms is based largely on the viruses’ and supplementary information). been established. But the smaller the organ- phylogenetic trees of universally conserved The need for two subphyla is also ism, the higher the numbers typically get. genes, such as those for ribosomal RNA.) supported by another major molecular There are 1 million to 10 million species of For RNA viruses, this marker is the RNA- marker. Haploviricotines synthesize a arthropod and probably more than 5.1 mil- dependent RNA polymerase (RdRp), the cap structure on virus messenger RNAs lion distinct fungi. And all bets are off when it only protein shared by all bona fide RNA that is required for protein synthesis comes to prokaryotes (bacteria and archaea). viruses. In the RdRp tree6, all negative- using a virus enzyme. Polyploviricotines, Estimates differ widely, but an analysis pub- sense RNA viruses form a single branch, by contrast, ‘snatch’ this cap from host lished earlier this month suggests that there justifying the phylum Negarnaviricota mRNAs. J.H.K. et al. could be as many as 1.6 million distinct 2 microbes on Earth . Each of these microbes CLASSIFYING RNA VIRUSES is almost certainly associated with at least Phylogenetic tree determined using RNA-dependent RNA polymerases. one virus. During one of the Tara Oceans expeditions BRANCH 2 (between 2009 and 2013), investigators iden- Includes poliovirus and BRANCH 4 SARS coronavirus. Includes Giardia tified 5,476 populations of double-stranded lamblia virus DNA viruses in 43 samples taken from 26 sta- and Colorado SOURCE: ADAPTED FROM REF. 6 FROM REF. SOURCE: ADAPTED BRANCH tick fever virus. tions. And only 39 of these populations were Includes Escherichia virus Qβ and found to closely resemble lineages recog- Ourmia melon virus. nized by the ICTV3. Only last year, a study of marine microbial metagenomes revealed more phylogenetic diversity in one proposed family of large DNA viruses (‘Megaviridae’) than currently exists in bacteria and archaea, Mobile genetic elements, 4 including non-long combined . terminal repeat (non-LTR) In short, the planet hosts massive virus retrotransposons. diversity. Subphylum UNTAPPED POTENTIAL BRANCH 3 Haploviricotina “So what?” some might ask. Only a few Includes hepatitis C virus Includes Ebola and tobacco mosaic virus. virus and hundred viruses are known to cause animal rabies virus. or plant diseases, and although more patho- genic viruses will certainly be discovered, they will probably number only in the hundreds. In our view, limiting analyses only to poten- Subphylum Polyploviricotina tially pathogenic viruses is short-sighted and BRANCH 5 Includes Lassa virus Phylum Negarnaviricota and inuenza A virus. ultimately negligent. Most antibiotics in The rst ever phylum is for single-stranded, clinical use were discovered from harmless negative-sense RNA viruses. soil bacteria. A key component of commer- cial detergents — heat-resistant proteases — was discovered in deep-sea prokaryotes not different from those they have access to today. fungi and worms that inhabit human bodies; known to harm any eukaryotes. Most influ- And bacterial and archaeal viruses encode those in our close associates — pets, pests ential biotechnological breakthroughs of the an enormous diversity of proteins that could and farm animals; and the viruses in the twentieth and twenty-first centuries are based enable geneticists to fine-tune their use of microfauna that inhabit these animals. on enzymes from seemingly ‘unimportant’ CRISPR to engineer organisms. Ultimately, we must decipher patterns in bacteria. Examples include: the restriction We cannot know what the trove of the virosphere — for instance, how viruses enzymes that launched genetic engineering ‘unimportant’ viruses could possibly amount interact with each other and with microbes, in the 1970s; the polymerase chain reaction to until we have examined them. as well as the triggers that cause them to jump (PCR) used to make many copies of a DNA What’s more, virologists are discovering hosts. Then, we might be able to predict the segment; and the CRISPR technology now that the phenomenon of switching hosts is emergence of the next HIV-1, Ebola virus, or revolutionizing genome engineering. Indeed, not as random and rare as was thought. Given influenza A virus that is capable of causing CRISPR–Cas systems were discovered the growing threat of emerging virus diseases another deadly pandemic. Antiviral therapy through the study of prokaryotic immune in the face of human-induced changes such could even be feasible for a person infected responses against viruses that no clinician as population growth, urbanization and cli- with a new virus, if researchers have a deep could name. mate change, describing and cataloguing the understanding of the virus’s closest relatives. It is quite possible that the proteases and viromes of healthy and sick humans is crucial. (A similar approach is now routinely used to polymerases encoded by the viruses of deep- Cataloguing should include all the viruses in treat bacterial infections.) sea organisms will offer researchers qualities human tissues; those in the bacteria, protists, Last but not least, comprehensive ©2019 Spri nger Nature Li mited. All ri ghts reserved. ©2019 Spri nger Nature Li mited. All ri ghts reserve21d. FEBRUARY 2019 | VOL 566 | NATURE | 319 COMMENT classification is essential for understanding functions almost exclusively through the as formal publications in their own right. Or how viruses and their cellular hosts have efforts of a few hundred volunteers who publishers could make submitting a proposal shaped each other, as well as how life on Earth advance virus taxonomy using their free to the ICTV a condition of publishing papers began and has evolved. time and, very often, personal funds. Thus, on newly described viruses (much of the the classification of viruses is somewhat information required for both is the same). MANY CHALLENGES neglected — especially for ones that do In principle, the classification of viruses could Classifying millions of viruses into not obviously fall under the purview of become routine, much the same as the depo- hierarchically organized taxa requires a the existing study groups or are discovered sition of gene-sequence information to public huge, community-wide effort and a broad through metagenomics surveys. databases such as GenBank has become com- array of researchers — including virologists, In 2017, the ICTV greatly eased the monplace in genomics. microbiologists, ecologists, veterinary sur- process by allowing viruses to be classified If more virologists joined ICTV study geons and zoologists. These scientists will on the basis of genome-sequence informa- groups, and all discoverers submitted taxo- need incentives. Changes should also be tion alone5. Before this, researchers had to nomic proposals and manuscripts in tandem, made to the classification process itself. grow and study them the specialists on the new viruses would rou- Currently, for a newly discovered virus or “The in the laboratory — a tinely join the ICTV volunteers in prepar- group of viruses to be classified, research- classification process that is feasible ing taxonomic proposals.
Load more

Recommended publications
  • Imaging, Tracking and Computational Analyses of Virus Entry and Egress
    1 Review 2 Imaging, Tracking and Computational Analyses of 3 Virus Entry and Egress with the Cytoskeleton 4 I-Hsuan Wang 1,†, Christoph J. Burckhardt 2,†, A. Yakimovich 3 and Urs F. Greber 4,* 5 1 Division of Virology, Institute of Medical Science, tHe University of ToKyo, ToKyo 108-8639, Japan 6 2 UT SoutHwestern Medical Center, Lyda Hill Department of Bioinformatics, Dallas TX 75390, USA 7 3 MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom 8 4 Department of Molecular Life Sciences, University of ZuricH, WintertHurerstrasse 190, CH-8057 ZuricH, 9 Switzerland 10 * Correspondence: [email protected], Telephone: +41 44 635 4841, Fax: +41 44 635 6817 11 † These autHors contributed equally to tHis work. 12 Received: date; Accepted: date; PublisHed: date 13 Abstract: Viruses Have a dual nature - particles are ‘passive substances’ lacKing chemical energy 14 transformation, wHereas infected cells are ‘active substances’ turning-over energy. How passive 15 viral substances convert to active substances, comprising viral replication and assembly 16 compartments Has been of intense interest to virologists, cell and molecular biologists and 17 immunologists. Infection starts witH virus entry into a susceptible cell and delivers tHe viral 18 genome to the replication site. THis is a multi-step process, and involves tHe cytosKeleton and 19 associated motor proteins. LiKewise, the egress of progeny virus particles from the replication site 20 to the extracellular space is enHanced by tHe cytosKeleton and associated motor proteins. THis 21 overcomes tHe limitation of tHermal diffusion, and transports virions and virion components, 22 often in association witH cellular organelles.
    [Show full text]
  • An Expanded View of Viruses
    An Expanded View of Viruses Urs F. Greber 1) & Ralf Bartenschlager 2) 1) Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland 2) Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69198 Heidelberg, Germany Correspondence to: [email protected] [email protected] 1 figure Keywords: Zoonosis; Pandemics; Dengue, Ebola; Influenza; Entry; Endocytosis; Uncoating; Transport; Filovirus; Comparative genomics; Computational analyses; Virus-host interactions; Filamentous virus; Bacterial biofilm; Phage; Bacteriophage; Glycan; Immunity; Infection; Disease; Evolution; Variability; Giant virus; Ferret; Guinea pig; Emerging disease; Pandemic; Host range; Enveloped virus; 1 Viruses are ubiquitous, and are important in medicine, biology, biotechnology and ecology. All kinds of cells can be infected with viruses, and sometimes, a particular cell is infected with different viruses at the same time. The virus particle, ‘virion’ is composed of the viral coat proteins sheltering the viral genome, and is often surrounded by a lipid “envelope”. A virion is small compared to cells, and when it enters cells gives rise to infection distinct from an intracellular bacterial pathogen (Lwoff, 1957). A virus-infected cell has a profoundly altered homeostasis due to numerous interactions between cellular and viral components. This leads to evolutionary pressure on both virus and host, and argues that viruses are a part of life (Ludmir & Enquist, 2009). Our cells can be infected by viruses causing acute disease, such as respiratory disease by Influenza virus or rhinoviruses, or chronic disease, such as hepatitis or immune deficiency. However, most viral attacks on cells are fend off, or the spread of viruses in an infected organism is restricted, and infection abrogated.
    [Show full text]
  • 10.2.2 Nomenclature of Viruses and Taxonomic Groups Bacterial Viruses Such As T1, T2 and Φx174
    Classification and nomenclature of viruses History of virus classification • Type of host • Type of disease • Transmition by an arthropod vector • Nucleic acid type • SS or DS • Segmented • Size of the virion • Capsid simmetry • Envelope Nomenclature • Small, icosahedral, single-stranded DNA viruses of animals were called parvoviruses (Latin parvus = small) • Nematode-transmitted polyhedral (icosahedral) viruses of plants were called nepoviruses • Phages T2, T4 and T6 were called T even phages • Serological relationships between viruses were investigated • Distinct strains (serotypes) could be distinguished in serological tests • Antisera against purified virions • Serotypes reflect differences in virus proteins International Committee on Taxonomy of Viruses • Order had to be brought • ICTV was formed in 1966 • Many working groups and is advised by virologists around the world • Rules for the nomenclature and classification of viruses • Considers proposals for new taxonomic groups and virus names • Approved are published in book form and on the web Modern virus classification and nomenclature • Each order, family, subfamily and genus is defined by viral characteristics that are necessary for membership of that group. Classification based on genome sequences • Similarity is represented in diagrams known as phylogenetic trees. • Rooted- the tree begins at a root which is assumed to be the ancestor of the viruses in the tree. • Unrooted- no assumption is made about the ancestor of the viruses in the tree. 10.2.2 Nomenclature of viruses and taxonomic groups Bacterial viruses such as T1, T2 and ϕX174. Viruses of humans and other vertebrates diseases that they cause Examples: measles virus, smallpox virus, foot and mouth disease virus Some viruses city, town or river Examples: Newcastle disease virus, Norwalk virus, Ebola virus Insect viruses Many insect viruses were named after the insect, with an indication of the effect of infection on the host.
    [Show full text]
  • WHO Immunological Basis for Immunization Series
    WHO Immunological Basis for Immunization Series Module 21: Rotavirus Update 2019 Department of Immunization, Vaccines and Biologicals World Health Organization 20, Avenue Appia CH-1211 Geneva 27, Switzerland [email protected] http://www.who.int/immunization/en/ Immunization, Vaccines and Biologicals WHO Immunological Basis for Immunization Series Module 21: Rotavirus Update 2019 Immunization, Vaccines and Biologicals The immunological basis for immunization series: module 21: Rotavirus Vaccines (Immunological basis for immunization series; module 21) ISBN 978-92-4-000235-7 © World Health Organization 2020 Some rights reserved. This work is available under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 IGO licence (CC BY-NC-SA 3.0 IGO; https://creativecommons.org/licenses/by-nc-sa/3.0/igo). Under the terms of this licence, you may copy, redistribute and adapt the work for non-commercial purposes, provided the work is appropriately cited, as indicated below. In any use of this work, there should be no suggestion that WHO endorses any specific organization, products or services. The use of the WHO logo is not permitted. If you adapt the work, then you must license your work under the same or equivalent Creative Commons licence. If you create a translation of this work, you should add the following disclaimer along with the suggested citation: “This translation was not created by the World Health Organization (WHO). WHO is not responsible for the content or accuracy of this translation. The original English edition shall be the binding and authentic edition”. Any mediation relating to disputes arising under the licence shall be conducted in accordance with the mediation rules of the World Intellectual Property Organization.
    [Show full text]
  • Persistent Virus and Addiction Modules: an Engine of Symbiosis
    UC Irvine UC Irvine Previously Published Works Title Persistent virus and addiction modules: an engine of symbiosis. Permalink https://escholarship.org/uc/item/5ck1g026 Journal Current opinion in microbiology, 31 ISSN 1369-5274 Author Villarreal, Luis P Publication Date 2016-06-01 DOI 10.1016/j.mib.2016.03.005 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Available online at www.sciencedirect.com ScienceDirect Persistent virus and addiction modules: an engine of symbiosis Luis P Villarreal The giant DNA viruses are highly prevalent and have a particular host would occasionally survive but still retain a bit of affinity for the lytic infection of unicellular eukaryotic host. The the selfish virus DNA. Thus although parasitic selfish giant viruses can also be infected by inhibitory virophage which (virus-like) information is common in the genomes of all can provide lysis protection to their host. The combined life forms, its presence was explained as mostly defective protective and destructive action of such viruses can define a remnants of past plague sweeps that provides no func- general model (PD) of virus-mediated host survival. Here, I tional benefit to the host (e.g. junk). Until recently, this present a general model for role such viruses play in the explanation seemed satisfactory. In the last twenty years, evolution of host symbiosis. By considering how virus mixtures however, various observation-based developments have can participate in addiction modules, I provide a functional compelled us to re-evaluate this stance. Both comparative explanation for persistence of virus derived genetic ‘junk’ in genomics and metagenomics (sequencing habitats) has their host genomic habitats.
    [Show full text]
  • Structural Variability and Complexity of the Giant Pithovirus Sibericum
    www.nature.com/scientificreports OPEN Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high- Received: 29 March 2017 Accepted: 22 September 2017 voltage electron cryo-tomography Published: xx xx xxxx and energy-fltered electron cryo- microscopy Kenta Okamoto1, Naoyuki Miyazaki2, Chihong Song2, Filipe R. N. C. Maia1, Hemanth K. N. Reddy1, Chantal Abergel 3, Jean-Michel Claverie3,4, Janos Hajdu1,5, Martin Svenda1 & Kazuyoshi Murata2 The Pithoviridae giant virus family exhibits the largest viral particle known so far, a prolate spheroid up to 2.5 μm in length and 0.9 μm in diameter. These particles show signifcant variations in size. Little is known about the structure of the intact virion due to technical limitations with conventional electron cryo-microscopy (cryo-EM) when imaging thick specimens. Here we present the intact structure of the giant Pithovirus sibericum particle at near native conditions using high-voltage electron cryo- tomography (cryo-ET) and energy-fltered cryo-EM. We detected a previously undescribed low-density outer layer covering the tegument and a periodical structuring of the fbres in the striated apical cork. Energy-fltered Zernike phase-contrast cryo-EM images show distinct substructures inside the particles, implicating an internal compartmentalisation. The density of the interior volume of Pithovirus particles is three quarters lower than that of the Mimivirus. However, it is remarkably high given that the 600 kbp Pithovirus genome is only half the size of the Mimivirus genome and is packaged in a volume up to 100 times larger. These observations suggest that the interior is densely packed with macromolecules in addition to the genomic nucleic acid.
    [Show full text]
  • Structural Variability and Complexity of the Giant Pithovirus Sibericum
    Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy Kenta Okamoto, Naoyuki Miyazaki, Chihong Song, Filipe Maia, Hemanth Reddy, Chantal Abergel, Jean-Michel Claverie, Janos Hajdu, Martin Svenda, Kazuyoshi Murata To cite this version: Kenta Okamoto, Naoyuki Miyazaki, Chihong Song, Filipe Maia, Hemanth Reddy, et al.. Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy. Scientific Reports, Nature Publishing Group, 2017, 7 (1), pp.13291. 10.1038/s41598-017-13390-4. hal-01785112 HAL Id: hal-01785112 https://hal-amu.archives-ouvertes.fr/hal-01785112 Submitted on 4 May 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. www.nature.com/scientificreports OPEN Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high- Received: 29 March 2017 Accepted: 22 September 2017 voltage electron cryo-tomography Published: xx xx xxxx and energy-fltered electron cryo- microscopy Kenta Okamoto1, Naoyuki Miyazaki2, Chihong Song2, Filipe R. N. C. Maia1, Hemanth K. N. Reddy1, Chantal Abergel 3, Jean-Michel Claverie3,4, Janos Hajdu1,5, Martin Svenda1 & Kazuyoshi Murata2 The Pithoviridae giant virus family exhibits the largest viral particle known so far, a prolate spheroid up to 2.5 μm in length and 0.9 μm in diameter.
    [Show full text]
  • Introduction to Viroids and Prions
    Harriet Wilson, Lecture Notes Bio. Sci. 4 - Microbiology Sierra College Introduction to Viroids and Prions Viroids – Viroids are plant pathogens made up of short, circular, single-stranded RNA molecules (usually around 246-375 bases in length) that are not surrounded by a protein coat. They have internal base-pairs that cause the formation of folded, three-dimensional, rod-like shapes. Viroids apparently do not code for any polypeptides (proteins), but do cause a variety of disease symptoms in plants. The mechanism for viroid replication is not thoroughly understood, but is apparently dependent on plant enzymes. Some evidence suggests they are related to introns, and that they may also infect animals. Disease processes may involve RNA-interference or activities similar to those involving mi-RNA. Prions – Prions are proteinaceous infectious particles, associated with a number of disease conditions such as Scrapie in sheep, Bovine Spongiform Encephalopathy (BSE) or Mad Cow Disease in cattle, Chronic Wasting Disease (CWD) in wild ungulates such as muledeer and elk, and diseases in humans including Creutzfeld-Jacob disease (CJD), Gerstmann-Straussler-Scheinker syndrome (GSS), Alpers syndrome (in infants), Fatal Familial Insomnia (FFI) and Kuru. These diseases are characterized by loss of motor control, dementia, paralysis, wasting and eventually death. Prions can be transmitted through ingestion, tissue transplantation, and through the use of comtaminated surgical instruments, but can also be transmitted from one generation to the next genetically. This is because prion proteins are encoded by genes normally existing within the brain cells of various animals. Disease is caused by the conversion of normal cell proteins (glycoproteins) into prion proteins.
    [Show full text]
  • Type D Primate Retroviruses: a Review1
    [CANCER RESEARCH 38, 3123-3139, October 1978] Type D Primate Retroviruses: A Review1 Donald Fine and Gerald Schochetman Viral Oncology Program, Frederick Cancer Research Center. Frederick, Maryland 21701 Abstract The prototype virus of the type D retroviruses is the techniques. The retrovirus associated with the induction of Mason-Pfizer monkey virus (MPMV). MPMV was originally mammary cancer in mice, MMTV,2 is morphologically dis isolated from a breast carcinoma of a female rhesus tinct from the type C viruses and is the prototype of the type monkey (an Old World monkey). MPMV is of obvious B virus group (30). A retrovirus group of primate origin, importance in that it is the only retrovirus thus far isolated which has properties similar to the type C and type B from a mammary tumor of a primate and has been shown viruses but is morphologically distinct from them, has been to have transforming potential for primate cells in vitro. designated genus Oncornavirus D (30). The prototype virus Subsequent to the isolation of MPMV, viruses morpholog of this genus is the MPMV. MPMV was originally isolated ically and ¡mmunologicallyindistinguishable from MPMV from a mammary carcinoma of a female rhesus monkey (an have been isolated from normal placenta and lactating Old World monkey) (19, 60). Because mammary carcinomas mammary glands of other rhesus monkeys in captivity. represent the most prevalent form of neoplasia in humans Recently, viruses morphologically resembling MPMV have and, furthermore, because the incidence of mammary tu been isolated from a langur monkey (another Old World mors in subhuman primates is rare (61, 62, 70, 78), MPMV monkey) and from squirrel monkeys (a New World mon is of obvious potential importance because it is the only key).
    [Show full text]
  • Basic Properties of Viruses and Virus–Cell Interaction
    WBV5 6/27/03 10:28 PM Page 49 Basic Properties of Viruses and Virus–Cell II Interaction PART ✷ VIRUS STRUCTURE AND CLASSIFICATION ✷ CLASSIFICATION SCHEMES ✷ THE BEGINNING AND END OF THE VIRUS REPLICATION CYCLE ✷ LATE EVENTS IN VIRAL INFECTION: CAPSID ASSEMBLY AND VIRION RELEASE ✷ HOST IMMUNE RESPONSE TO VIRAL INFECTION: THE NATURE OF THE VERTEBRATE IMMUNE RESPONSE ✷ PRESENTATION OF VIRAL ANTIGENS TO IMMUNE REACTIVE CELLS ✷ CONTROL AND DYSFUNCTION OF IMMUNITY ✷ MEASUREMENT OF THE IMMUNE REACTION ✷ STRATEGIES TO PROTECT AGAINST AND COMBAT VIRAL INFECTION ✷ VACCINATION — INDUCTION OF IMMUNITY TO PREVENT VIRUS INFECTION ✷ EUKARYOTIC CELL-BASED DEFENSES AGAINST VIRAL REPLICATION ✷ ANTIVIRAL DRUGS ✷ BACTERIAL ANTIVIRAL SYSTEMS — RESTRICTION ENDONUCLEASES ✷ PROBLEMS FOR PART II ✷ ADDITIONAL READING FOR PART II WBV5 6/27/03 10:28 PM Page 50 WBV5 6/27/03 3:35 PM Page 51 Virus Structure and Classification ✷ 5 Viral genomes ✷ Viral capsids ✷ Viral membrane envelopes ✷ CLASSIFICATION SCHEMES CHAPTER ✷ The Baltimore scheme of virus classification ✷ Disease-based classification schemes for viruses ✷ QUESTIONS FOR CHAPTER 5 Viruses are small compared to the wavelength of visible light; indeed, while the largest virus can be discerned in a good light microscope, viruses can only be visualized in detail using an electron microscope. A size scale with some important landmarks is shown in Fig. 5.1. Viruses are composed of a nucleic acid genomeor core, which is the genetic material of the virus, surrounded by a capsid made up of virus-encoded proteins. Viral genetic material encodes the structural proteins of the capsid and other viral proteins essential for other functions in initiating virus replication. The entire structure of the virus (the genome, the capsid, and — where present — the envelope) make up the virion or virus particle.
    [Show full text]
  • 30,000 Year-Old Giant Virus Found in Siberia
    NATIONAL PRESS RELEASE I PARIS I MARCH 3, 2014 30,000 year-old giant virus found in Siberia A new type of giant virus called “Pithovirus” has been discovered in the frozen ground of extreme north-eastern Siberia by researchers from the Information Génomique et Structurale laboratory (CNRS/AMU), in association with teams from the Biologie à Grande Echelle laboratory (CEA/INSERM/Université Joseph Fourier), Génoscope (CEA/CNRS) and the Russian Academy of Sciences. Buried underground, this giant virus, which is harmless to humans and animals, has survived being frozen for more than 30,000 years. Although its size and amphora shape are reminiscent of Pandoravirus, analysis of its genome and replication mechanism proves that Pithovirus is very different. This work brings to three the number of distinct families of giant viruses. It is published on the website of the journal PNAS in the week of March 3, 2014. In the families Megaviridae (represented in particular by Mimivirus, discovered in 2003) and Pandoraviridae1, researchers thought they had classified the diversity of giant viruses (the only viruses visible under optical microscopy, since their diameter exceeds 0.5 microns). These viruses, which infect amoeba such as Acanthamoeba, contain a very large number of genes compared to common viruses (like influenza or AIDS, which only contain about ten genes). Their genome is about the same size or even larger than that of many bacteria. By studying a sample from the frozen ground of extreme north-eastern Siberia, in the Chukotka autonomous region, researchers were surprised to discover a new giant virus more than 30,000 years old (contemporaneous with the extinction of Neanderthal man), which they have named “Pithovirus sibericum”.
    [Show full text]
  • Estimating Evolutionary Rates in Giant Viruses Using Ancient Genomes Sebastia´N Ducheˆne1 and Edward C
    Virus Evolution, 2018, 4(1): vey006 doi: 10.1093/ve/vey006 Reflections Estimating evolutionary rates in giant viruses using ancient genomes Sebastia´n Ducheˆne1 and Edward C. Holmes2,*,† 1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3020, Australia and 2Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia *Corresponding author: E-mail: [email protected] †http://orcid.org/0000-0001-9596-3552 Abstract Pithovirus sibericum is a giant (610 Kpb) double-stranded DNA virus discovered in a purportedly 30,000-year-old permafrost sample. A closely related virus, Pithovirus massiliensis, was recently isolated from a sewer in southern France. An initial comparison of these two virus genomes assumed that P. sibericum was directly ancestral to P. massiliensis and gave a maximum evolutionary rate of 2.60 Â 10À5 nucleotide substitutions per site per year (subs/site/year). If correct, this would make pithoviruses among the fastest-evolving DNA viruses, with rates close to those seen in some RNA viruses. To help determine whether this unusually high rate is accurate we utilized the well-known negative association between evolution- ary rate and genome size in DNA microbes. This revealed that a more plausible rate estimate for Pithovirus evolution is 2.23 Â 10À6 subs/site/year, with even lower estimates obtained if evolutionary rates are assumed to be time-dependent. Hence, we estimate that Pithovirus has evolved at least an order of magnitude more slowly than previously suggested.
    [Show full text]