Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/18313
Appears in Collections:Aquaculture Journal Articles
Peer Review Status: Refereed
Title: Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae
Authors: Kuhn, Jens H
Bao, Yiming
Bavari, Sina
Becker, Stephan
Bradfute, Steven
Brister, J Rodney
Bukreyev, Alexander A
Chandran, Kartik
Davey, Robert A
Dolnik, Olga
Dye, John M
Enterlein, Sven
Hensley, Lisa E
Honko, Anna N
Weidmann, Manfred
Contact Email: m.w.weidmann@stir.ac.uk
Issue Date: Jan-2013
Publisher: Springer
Citation: Kuhn JH, Bao Y, Bavari S, Becker S, Bradfute S, Brister JR, Bukreyev AA, Chandran K, Davey RA, Dolnik O, Dye JM, Enterlein S, Hensley LE, Honko AN & Weidmann M (2013) Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae, Archives of Virology, 158 (1), pp. 301-311.
Abstract: The task of international expert groups is to recommend the classification and naming of viruses. The International Committee on Taxonomy of Viruses Filoviridae Study Group and other experts have recently established an almost consistent classification and nomenclature for filoviruses. Here, further guidelines are suggested to include their natural genetic variants. First, this term is defined. Second, a template for full-length virus names (such as "Ebola virus H.sapiens-tc/COD/1995/Kikwit-9510621") is proposed. These names contain information on the identity of the virus (e.g., Ebola virus), isolation host (e.g., members of the species Homo sapiens), sampling location (e.g., Democratic Republic of the Congo (COD)), sampling year, genetic variant (e.g., Kikwit), and isolate (e.g., 9510621). Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). We suggest that these comprehensive names are to be used specifically in the methods section of publications. Suitable abbreviations, also proposed here, could then be used throughout the text, while the full names could be used again in phylograms, tables, or figures if the contained information aids the interpretation of presented data. The proposed system is very similar to the well-known influenzavirus nomenclature and the nomenclature recently proposed for rotaviruses. If applied consistently, it would considerably simplify retrieval of sequence data from electronic databases and be a first important step toward a viral genome annotation standard as sought by the National Center for Biotechnology Information (NCBI). Furthermore, adoption of this nomenclature would increase the general understanding of filovirus-related publications and presentations and improve figures such as phylograms, alignments, and diagrams. Most importantly, it would counter the increasing confusion in genetic variant naming due to the identification of ever more sequences through technological breakthroughs in high-throughput sequencing and environmental sampling.
Type: Journal Article
URI: http://hdl.handle.net/1893/18313
DOI Link: http://dx.doi.org/10.1007/s00705-012-1454-0
Rights: The publisher does not allow this work to be made publicly available in this Repository. Please use the Request a Copy feature at the foot of the Repository record to request a copy directly from the author. You can only request a copy if you wish to use this work for your own research or private study.
Notes: Additional co-authors: Peter B. Jahrling, Karl M. Johnson, Gary Kobinger, Eric M. Leroy, Mark S. Lever, Elke Mühlberger, Sergey V. Netesov, Gene G. Olinger, Gustavo Palacios, Jean L. Patterson, Janusz T. Paweska, Louise Pitt, Sheli R. Radoshitzky, Erica Ollmann Saphire, Sophie J. Smither, Robert Swanepoel, Jonathan S. Towner, Guido van der Groen, Viktor E. Volchkov, Victoria Wahl-Jensen, Travis K. Warren, Stuart T. Nichol
Affiliation: National Institutes of Health (US)
National Institutes of Health (US)
United States (US) Army - Medical Research Institute of Infectious Diseases
Philipps University of Marburg
University of New Mexico, USA
National Institutes of Health (US)
University of Texas Medical Branch
Albert Einstein College of Medicine of Yeshiva University
Texas Biomedical Research Institute
Philipps University of Marburg
United States (US) Army - Medical Research Institute of Infectious Diseases
Integrated BioTherapeutics Inc
Food and Drug Administration, USA
United States (US) Army - Medical Research Institute of Infectious Diseases
Aquaculture

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