Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names

Viruses

Mark S. Lever¹  Sophie J. Smither¹  Janusz T. Paweska²  Eric M. Leroy³  Rachel Sealfon⁴  Christian T. Happi⁵  Erica Ollmann Saphire⁶  Sunday A. Omilabu⁷  Kartik Chandran⁸  Robert F. Garry⁹  Elke Mühlberger^1,10  Clarence J. Peters^1,11  Alexander Bukreyev^1,11  Alexander N. Freiberg^1,11  Robert A. Davey^1,12  Anthony Griffiths^1,12  Jean L. Patterson^1,12  Ayato Takada^1,13  Kristian G. Andersen^1,14  Pardis C. Sabeti^1,14  Stephen K. Gire^1,14  Georgy M. Ignatyev^1,15  Olga Blinkova^1,16  J. Rodney Brister^1,16  Yīmíng Bào^1,16  Olga Dolnik^1,17  Hans-Dieter Klenk^1,17  Stephan Becker^1,17  Manfred Weidmann^1,18  Elena I. Ryabchikova^1,19  Alexander A. Chepurnov^2,20  Sven Enterlein^2,21  James Pettitt^2,22  Lisa E. Hensley^2,22  Matthew G. Lackemeyer^2,22  Gene G. Olinger^2,22  Jens H. Kuhn^2,22  Anna N. Honko^2,22  Jason Kindrachuk^2,22  Peter B. Jahrling^2,22  Joshua C. Johnson^2,22  Thomas Hoenen^2,23  Valentina A. Volchkova^2,24  Viktor E. Volchkov^2,24  Norman A. Doggett^2,25  Paul W. Fenimore^2,25  Jean-Paul Gonzalez^2,26  Richard S. Bennett^2,27  Tadeusz J. Kochel^2,27  Daniel F. Lackner^2,27  Victoria Wahl-Jensen^2,27  Nicholas H. Bergman^2,27  Michael C. Hevey^2,27  Karl M. Johnson^2,28  Guido van der Groen^2,29  Ralf G. Dietzgen^3,30  Sergey V. Netesov^3,31  Aleksandr M. Shestopalov^3,31  Gary Kobinger^3,32  Daniel J. Park^3,33  Rekha G. Panchal^3,34  Sina Bavari^3,34  Andrew S. Herbert^3,34  Sheli R. Radoshitzky^3,34  Louise Pitt^3,34  John M. Dye^3,34  Nicole L. Garza^3,34  Travis K. Warren^3,34  Gustavo Palacios^3,34  Kelly L. Warfield^3,35  Steven Bradfute^3,36  Nancy J. Sullivan^3,37  Stuart T. Nichol^3,38  Jonathan S. Towner^3,38  Pierre Formenty^3,39  Robert Swanepoel^4,40 

[1] Biomedical Sciences Department, Dstl, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK;Center for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg 2192, Gauteng, South Africa;Centre International de Recherches Médicales de Franceville, B. P. 769, Franceville, Gabon;Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;Department of Biological Sciences, College of Natural Sciences, and African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Lagos-Ibadan,Ogun State, Nigeria;Department of Immunology and Microbial Science and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA;Department of Medical Microbiology and Parasitology, College of Medicine of the University of Lagos, Idi-Araba, Private Mail Bag 12003, Lagos, Nigeria;Department of Microbiology and Immunology, Albert Einstein College of Medicine,Bronx, NY 10461, USA;Department of Microbiology and Immunology, Tulane University School of Medicine,New Orleans, LA 70112, USA;Department of Microbiology and National Emerging Infectious Diseases Laboratory,Boston University School of Medicine, Boston, MA 02118, USA;Department of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA;Department of Virology and Immunology, Texas Biomedical Research Institute,San Antonio, TX 78227, USA;Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Kita-ku, Sapporo, Japan;FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA;Federal State Unitary Company "Microgen Scientific Industrial Company for Immunobiological Medicines", Ministry of Health of the Russian Federation, Moscow,115088,Russia;Information Engineering Branch, National Center for Biotechnology Information,National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA;Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany;Institute of Aquaculture, University of Stirling FK9 4LA, UK;Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Novosibirsk Region, 630090, Russia;Institute of Clinical Immunology, Russian Academy of Science, Siberian Branch, Novosibirsk,Novosibirsk Oblast, 630091, Russia;Integrated BioTherapeutics, Inc., Gaithersburg, MD 20878, USA;Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA;Laboratory for Virology, Division of Intramural Research,National Institute for Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT59840 USA;Laboratory of Molecular basis of viral pathogenicity, CIRI, Inserm U1111, Université de Lyon, UCB-Lyon-1, Ecole-Normale-Supérieure de Lyon, 69365 Lyon cedex 07, France;Los Alamos National Laboratory, Los Alamos, NM 87545, USA;Metabiota, Inc., San Francisco, CA 94104, USA;National Biodefense Analysis and Countermeasures Center, Fort Detrick,Frederick, MD 21702, USA;Portland, OR 97222, USA;Prins Leopold Instituut voor Tropische Geneeskunde, 2000 Antwerp, Belgium;Queensland Alliance for Agriculture and Food Innovation, The University of Queensland,St. Lucia, QLD 4072, Australia;Research Center of Clinical and Experimental Medicine, Novosibirsk, Novosibirsk Region, 630090, Russia;Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2, Canada;The Broad Institute, Cambridge, MA 02142, USA;United States Army Medical Research Institute of Infectious Diseases, Fort Detrick,Frederick, MD 21702, USA;Unither Virology, LLC, Silver Spring, MD 20910, USA;University of New Mexico, Albuquerque, NM 87131, USA;Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA;Viral Special Pathogens Branch, Division of High-Consequence Pathogens Pathology,National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA;World Health Organization, 1211 Geneva, Switzerland;Zoonoses Research Unit, University of Pretoria, Private bag X20 Hatfield, Pretoria 0028, South Africa;

关键词: Bundibugyo virus;    cDNA clone;    cuevavirus;    Ebola;    Ebola virus;    ebolavirus;    filovirid;    Filoviridae;    filovirus;    genome annotation;    ICTV;    International Committee on Taxonomy of Viruses;    Lloviu virus;    Marburg virus;    marburgvirus;    mononegavirad;    Mononegavirales;    mononegavirus;    Ravn virus;    RefSeq;    Reston virus;    reverse genetics;    Sudan virus;    Taï Forest virus;    virus classification;    virus isolate;    virus nomenclature;    virus strain;    virus taxonomy;    virus variant;   

DOI  :  10.3390/v6093663

来源: DOAJ

【 摘 要 】

Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis.Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information’s (NCBI’s) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [ ()////-], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences.

【 授权许可】

Unknown