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10.3390/v6093663
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Open AccessLetter

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

by
Jens H. Kuhn
1,*,#,¶,‡,
Kristian G. Andersen
2,
Yīmíng Bào
3,^,‡,
Sina Bavari
4,
Stephan Becker
5,
Richard S. Bennett
6,
Nicholas H. Bergman
6,
Olga Blinkova
3,‡,
Steven Bradfute
7,
J. Rodney Brister
3,^,‡,
Alexander Bukreyev
8,#,
Kartik Chandran
9,#,
Alexander A. Chepurnov
10,
Robert A. Davey
11,
Ralf G. Dietzgen
12,¶,
Norman A. Doggett
13,
Olga Dolnik
5,#,
John M. Dye
4,#,
Sven Enterlein
14,
Paul W. Fenimore
13,
Pierre Formenty
15,
Alexander N. Freiberg
8,
Robert F. Garry
17,
Nicole L. Garza
4,
Stephen K. Gire
2,
Jean-Paul Gonzalez
16,
Anthony Griffiths
11,
Christian T. Happi
18,
Lisa E. Hensley
1,
Andrew S. Herbert
4,
Michael C. Hevey
6,
Thomas Hoenen
19,
Anna N. Honko
1,
Georgy M. Ignatyev
20,
Peter B. Jahrling
1,
Joshua C. Johnson
1,
Karl M. Johnson
21,
Jason Kindrachuk
1,
Hans-Dieter Klenk
5,
Gary Kobinger
22,
Tadeusz J. Kochel
6,
Matthew G. Lackemeyer
1,
Daniel F. Lackner
6, 23,#,
Mark S. Lever
24,
Elke Mühlberger
25,#,
Sergey V. Netesov
26,#,
Gene G. Olinger
1,
Sunday A. Omilabu
27,
Gustavo Palacios
4,
Rekha G. Panchal
4,
Daniel J. Park
28, 11,#,
Janusz T. Paweska
29,#,
Clarence J. Peters
8,
James Pettitt
1,
Louise Pitt
4,
Sheli R. Radoshitzky
4, 30,
Erica Ollmann Saphire
31,#,
Pardis C. Sabeti
2,
Rachel Sealfon
32,
Aleksandr M. Shestopalov
26,
Sophie J. Smither
24,#,
Nancy J. Sullivan
33,
Robert Swanepoel
34,
Ayato Takada
35,#,
Jonathan S. Towner
36,#,
Guido Van der Groen
37,
Viktor E. Volchkov
38,#,
Valentina A. Volchkova
38,
Victoria Wahl-Jensen
6,
Travis K. Warren
4,#,
Kelly L. Warfield
39,
Manfred Weidmann
40 and
Stuart T. Nichol
36,*
1
Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
2
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
3
Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
4
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
5
Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany
6
National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA
7
University of New Mexico, Albuquerque, NM 87131, USA
8
Department of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA
9
Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
10
Institute of Clinical Immunology, Russian Academy of Science, Siberian Branch, Novosibirsk, Novosibirsk Oblast, 630091, Russia
11
Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
12
Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia
13
Los Alamos National Laboratory, Los Alamos, NM 87545, USA
14
Integrated BioTherapeutics, Inc., Gaithersburg, MD 20878, USA
15
World Health Organization, 1211 Geneva, Switzerland
16
Metabiota, Inc., San Francisco, CA 94104, USA
17
Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
18
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
19
Laboratory for Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840 USA
20
Federal State Unitary Company "Microgen Scientific Industrial Company for Immunobiological Medicines", Ministry of Health of the Russian Federation, Moscow, 115088,Russia
21
Portland, OR 97222, USA
22
Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2, Canada
23
Centre International de Recherches Médicales de Franceville, B. P. 769, Franceville, Gabon
24
Biomedical Sciences Department, Dstl, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
25
Department of Microbiology and National Emerging Infectious Diseases Laboratory, Boston University School of Medicine, Boston, MA 02118, USA
26
Research Center of Clinical and Experimental Medicine, Novosibirsk, Novosibirsk Region, 630090, Russia
27
Department of Medical Microbiology and Parasitology, College of Medicine of the University of Lagos, Idi-Araba, Private Mail Bag 12003, Lagos, Nigeria
28
The Broad Institute, Cambridge, MA 02142, USA
29
Center for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg 2192, Gauteng, South Africa
30
Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Novosibirsk Region, 630090, Russia
31
Department of Immunology and Microbial Science and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
32
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
33
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
34
Zoonoses Research Unit, University of Pretoria, Private bag X20 Hatfield, Pretoria 0028, South Africa
35
Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Kita-ku, Sapporo, Japan
36
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
37
Prins Leopold Instituut voor Tropische Geneeskunde, 2000 Antwerp, Belgium
38
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
39
Unither Virology, LLC, Silver Spring, MD 20910, USA
40
Institute of Aquaculture, University of Stirling FK9 4LA, UK
*
Authors to whom correspondence should be addressed.
#
Members of the 2012–2014 International Committee on Taxonomy of Viruses (ICTV) Filoviridae Study Group.
^
Members of the ICTV Data Subcommittee
National Center for Biotechnology Information (NCBI) Viral RefSeq Genomes Advisors for members of the order Mononegavirales.
‡
Members of the NCBI Genome Annotation Virus Working Group
Viruses 2014, 6(9), 3663-3682; https://doi.org/10.3390/v6093663
Received: 17 September 2014 / Accepted: 23 September 2014 / Published: 26 September 2014
(This article belongs to the Collection Advances in Ebolavirus, Marburgvirus, and Cuevavirus Research)
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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. View Full-Text
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 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
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited
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MDPI and ACS Style

Kuhn, J.H.; Andersen, K.G.; Bào, Y.; Bavari, S.; Becker, S.; Bennett, R.S.; Bergman, N.H.; Blinkova, O.; Bradfute, S.; Brister, J.R.; Bukreyev, A.; Chandran, K.; Chepurnov, A.A.; Davey, R.A.; Dietzgen, R.G.; Doggett, N.A.; Dolnik, O.; Dye, J.M.; Enterlein, S.; Fenimore, P.W.; Formenty, P.; Freiberg, A.N.; Garry, R.F.; Garza, N.L.; Gire, S.K.; Gonzalez, J.-P.; Griffiths, A.; Happi, C.T.; Hensley, L.E.; Herbert, A.S.; Hevey, M.C.; Hoenen, T.; Honko, A.N.; Ignatyev, G.M.; Jahrling, P.B.; Johnson, J.C.; Johnson, K.M.; Kindrachuk, J.; Klenk, H.-D.; Kobinger, G.; Kochel, T.J.; Lackemeyer, M.G.; Lackner, D.F.; Leroy, E.M.; Lever, M.S.; Mühlberger, E.; Netesov, S.V.; Olinger, G.G.; Omilabu, S.A.; Palacios, G.; Panchal, R.G.; Park, D.J.; Patterson, J.L.; Paweska, J.T.; Peters, C.J.; Pettitt, J.; Pitt, L.; Radoshitzky, S.R.; Ryabchikova, E.I.; Saphire, E.O.; Sabeti, P.C.; Sealfon, R.; Shestopalov, A.M.; Smither, S.J.; Sullivan, N.J.; Swanepoel, R.; Takada, A.; Towner, J.S.; Van der Groen, G.; Volchkov, V.E.; Volchkova, V.A.; Wahl-Jensen, V.; Warren, T.K.; Warfield, K.L.; Weidmann, M.; Nichol, S.T. Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names. Viruses 2014, 6, 3663-3682. https://doi.org/10.3390/v6093663

AMA Style

Kuhn JH, Andersen KG, Bào Y, Bavari S, Becker S, Bennett RS, Bergman NH, Blinkova O, Bradfute S, Brister JR, Bukreyev A, Chandran K, Chepurnov AA, Davey RA, Dietzgen RG, Doggett NA, Dolnik O, Dye JM, Enterlein S, Fenimore PW, Formenty P, Freiberg AN, Garry RF, Garza NL, Gire SK, Gonzalez J-P, Griffiths A, Happi CT, Hensley LE, Herbert AS, Hevey MC, Hoenen T, Honko AN, Ignatyev GM, Jahrling PB, Johnson JC, Johnson KM, Kindrachuk J, Klenk H-D, Kobinger G, Kochel TJ, Lackemeyer MG, Lackner DF, Leroy EM, Lever MS, Mühlberger E, Netesov SV, Olinger GG, Omilabu SA, Palacios G, Panchal RG, Park DJ, Patterson JL, Paweska JT, Peters CJ, Pettitt J, Pitt L, Radoshitzky SR, Ryabchikova EI, Saphire EO, Sabeti PC, Sealfon R, Shestopalov AM, Smither SJ, Sullivan NJ, Swanepoel R, Takada A, Towner JS, Van der Groen G, Volchkov VE, Volchkova VA, Wahl-Jensen V, Warren TK, Warfield KL, Weidmann M, Nichol ST. Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names. Viruses. 2014; 6(9):3663-3682. https://doi.org/10.3390/v6093663

Chicago/Turabian Style

Kuhn, Jens H.; Andersen, Kristian G.; Bào, Yīmíng; Bavari, Sina; Becker, Stephan; Bennett, Richard S.; Bergman, Nicholas H.; Blinkova, Olga; Bradfute, Steven; Brister, J. R.; Bukreyev, Alexander; Chandran, Kartik; Chepurnov, Alexander A.; Davey, Robert A.; Dietzgen, Ralf G.; Doggett, Norman A.; Dolnik, Olga; Dye, John M.; Enterlein, Sven; Fenimore, Paul W.; Formenty, Pierre; Freiberg, Alexander N.; Garry, Robert F.; Garza, Nicole L.; Gire, Stephen K.; Gonzalez, Jean-Paul; Griffiths, Anthony; Happi, Christian T.; Hensley, Lisa E.; Herbert, Andrew S.; Hevey, Michael C.; Hoenen, Thomas; Honko, Anna N.; Ignatyev, Georgy M.; Jahrling, Peter B.; Johnson, Joshua C.; Johnson, Karl M.; Kindrachuk, Jason; Klenk, Hans-Dieter; Kobinger, Gary; Kochel, Tadeusz J.; Lackemeyer, Matthew G.; Lackner, Daniel F.; Leroy, Eric M.; Lever, Mark S.; Mühlberger, Elke; Netesov, Sergey V.; Olinger, Gene G.; Omilabu, Sunday A.; Palacios, Gustavo; Panchal, Rekha G.; Park, Daniel J.; Patterson, Jean L.; Paweska, Janusz T.; Peters, Clarence J.; Pettitt, James; Pitt, Louise; Radoshitzky, Sheli R.; Ryabchikova, Elena I.; Saphire, Erica O.; Sabeti, Pardis C.; Sealfon, Rachel; Shestopalov, Aleksandr M.; Smither, Sophie J.; Sullivan, Nancy J.; Swanepoel, Robert; Takada, Ayato; Towner, Jonathan S.; Van der Groen, Guido; Volchkov, Viktor E.; Volchkova, Valentina A.; Wahl-Jensen, Victoria; Warren, Travis K.; Warfield, Kelly L.; Weidmann, Manfred; Nichol, Stuart T. 2014. "Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names" Viruses 6, no. 9: 3663-3682. https://doi.org/10.3390/v6093663

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