Viruses (Sep 2014)
Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names
- Jens H. Kuhn,
- Kristian G. Andersen,
- Yīmíng Bào,
- Sina Bavari,
- Stephan Becker,
- Richard S. Bennett,
- Nicholas H. Bergman,
- Olga Blinkova,
- Steven Bradfute,
- J. Rodney Brister,
- Alexander Bukreyev,
- Kartik Chandran,
- Alexander A. Chepurnov,
- Robert A. Davey,
- Ralf G. Dietzgen,
- Norman A. Doggett,
- Olga Dolnik,
- John M. Dye,
- Sven Enterlein,
- Paul W. Fenimore,
- Pierre Formenty,
- Alexander N. Freiberg,
- Robert F. Garry,
- Nicole L. Garza,
- Stephen K. Gire,
- Jean-Paul Gonzalez,
- Anthony Griffiths,
- Christian T. Happi,
- Lisa E. Hensley,
- Andrew S. Herbert,
- Michael C. Hevey,
- Thomas Hoenen,
- Anna N. Honko,
- Georgy M. Ignatyev,
- Peter B. Jahrling,
- Joshua C. Johnson,
- Karl M. Johnson,
- Jason Kindrachuk,
- Hans-Dieter Klenk,
- Gary Kobinger,
- Tadeusz J. Kochel,
- Matthew G. Lackemeyer,
- Daniel F. Lackner,
- Eric M. Leroy,
- Mark S. Lever,
- Elke Mühlberger,
- Sergey V. Netesov,
- Gene G. Olinger,
- Sunday A. Omilabu,
- Gustavo Palacios,
- Rekha G. Panchal,
- Daniel J. Park,
- Jean L. Patterson,
- Janusz T. Paweska,
- Clarence J. Peters,
- James Pettitt,
- Louise Pitt,
- Sheli R. Radoshitzky,
- Elena I. Ryabchikova,
- Erica Ollmann Saphire,
- Pardis C. Sabeti,
- Rachel Sealfon,
- Aleksandr M. Shestopalov,
- Sophie J. Smither,
- Nancy J. Sullivan,
- Robert Swanepoel,
- Ayato Takada,
- Jonathan S. Towner,
- Guido van der Groen,
- Viktor E. Volchkov,
- Valentina A. Volchkova,
- Victoria Wahl-Jensen,
- Travis K. Warren,
- Kelly L. Warfield,
- Manfred Weidmann,
- Stuart T. Nichol
Affiliations
- Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
- Kristian G. Andersen
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
- Yīmíng Bào
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
- Sina Bavari
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
- Stephan Becker
- Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany
- Richard S. Bennett
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA
- Nicholas H. Bergman
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA
- Olga Blinkova
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
- Steven Bradfute
- University of New Mexico, Albuquerque, NM 87131, USA
- J. Rodney Brister
- Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
- Alexander Bukreyev
- Department of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA
- Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Alexander A. Chepurnov
- Institute of Clinical Immunology, Russian Academy of Science, Siberian Branch, Novosibirsk, Novosibirsk Oblast, 630091, Russia
- Robert A. Davey
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia
- Norman A. Doggett
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Olga Dolnik
- Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany
- John M. Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
- Sven Enterlein
- Integrated BioTherapeutics, Inc., Gaithersburg, MD 20878, USA
- Paul W. Fenimore
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Pierre Formenty
- World Health Organization, 1211 Geneva, Switzerland
- Alexander N. Freiberg
- Department of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA
- Robert F. Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Nicole L. Garza
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
- Stephen K. Gire
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
- Jean-Paul Gonzalez
- Metabiota, Inc., San Francisco, CA 94104, USA
- Anthony Griffiths
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Christian T. Happi
- 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
- Lisa E. Hensley
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
- Andrew S. Herbert
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
- Michael C. Hevey
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA
- Thomas Hoenen
- Laboratory for Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840 USA
- Anna N. Honko
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
- Georgy M. Ignatyev
- Federal State Unitary Company "Microgen Scientific Industrial Company for Immunobiological Medicines", Ministry of Health of the Russian Federation, Moscow, 115088,Russia
- Peter B. Jahrling
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
- Joshua C. Johnson
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
- Karl M. Johnson
- Portland, OR 97222, USA
- Jason Kindrachuk
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
- Hans-Dieter Klenk
- Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany
- Gary Kobinger
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2, Canada
- Tadeusz J. Kochel
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA
- Matthew G. Lackemeyer
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
- Daniel F. Lackner
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA
- Eric M. Leroy
- Centre International de Recherches Médicales de Franceville, B. P. 769, Franceville, Gabon
- Mark S. Lever
- Biomedical Sciences Department, Dstl, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
- Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratory, Boston University School of Medicine, Boston, MA 02118, USA
- Sergey V. Netesov
- Research Center of Clinical and Experimental Medicine, Novosibirsk, Novosibirsk Region, 630090, Russia
- Gene G. Olinger
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
- Sunday A. Omilabu
- Department of Medical Microbiology and Parasitology, College of Medicine of the University of Lagos, Idi-Araba, Private Mail Bag 12003, Lagos, Nigeria
- Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
- Rekha G. Panchal
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
- Daniel J. Park
- The Broad Institute, Cambridge, MA 02142, USA
- Jean L. Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Janusz T. Paweska
- Center for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg 2192, Gauteng, South Africa
- Clarence J. Peters
- Department of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA
- James Pettitt
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
- Louise Pitt
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
- Sheli R. Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
- Elena I. Ryabchikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Novosibirsk Region, 630090, Russia
- Erica Ollmann Saphire
- Department of Immunology and Microbial Science and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Pardis C. Sabeti
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
- Rachel Sealfon
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Aleksandr M. Shestopalov
- Research Center of Clinical and Experimental Medicine, Novosibirsk, Novosibirsk Region, 630090, Russia
- Sophie J. Smither
- Biomedical Sciences Department, Dstl, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
- Nancy J. Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Robert Swanepoel
- Zoonoses Research Unit, University of Pretoria, Private bag X20 Hatfield, Pretoria 0028, South Africa
- Ayato Takada
- Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Kita-ku, Sapporo, Japan
- Jonathan S. Towner
- 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
- Guido van der Groen
- Prins Leopold Instituut voor Tropische Geneeskunde, 2000 Antwerp, Belgium
- Viktor E. Volchkov
- 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
- Valentina A. Volchkova
- 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
- Victoria Wahl-Jensen
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA
- Travis K. Warren
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
- Kelly L. Warfield
- Unither Virology, LLC, Silver Spring, MD 20910, USA
- Manfred Weidmann
- Institute of Aquaculture, University of Stirling FK9 4LA, UK
- Stuart T. Nichol
- 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
- DOI
- https://doi.org/10.3390/v6093663
- Journal volume & issue
-
Vol. 6,
no. 9
pp. 3663 – 3682
Abstract
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 [<virus name> (<strain>)/<isolation host-suffix>/<country of sampling>/<year of sampling>/<genetic variant designation>-<isolate designation>], 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.
Keywords
- 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
