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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 301-311 |
| Number of pages | 11 |
| Journal | Archives of Virology |
| Volume | 158 |
| Issue number | 1 |
| DOIs | |
| State | Published - 2013 |
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ASJC Scopus subject areas
- Virology
Cite this
Virus nomenclature below the species level : A standardized nomenclature for natural variants of viruses assigned to the family Filoviridae. / 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.; Jahrling, Peter B.; Johnson, Karl M.; Kobinger, Gary; Leroy, Eric M.; Lever, Mark S.; Mühlberger, Elke; Netesov, Sergey V.; Olinger, Gene G.; Palacios, Gustavo; Patterson, Jean L.; Paweska, Janusz T.; Pitt, Louise; Radoshitzky, Sheli R.; Saphire, Erica Ollmann; Smither, Sophie J.; Swanepoel, Robert; Towner, Jonathan S.; van der Groen, Guido; Volchkov, Viktor E.; Wahl-Jensen, Victoria; Warren, Travis K.; Weidmann, Manfred; Nichol, Stuart T.
In: Archives of Virology, Vol. 158, No. 1, 2013, p. 301-311.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Virus nomenclature below the species level
T2 - A standardized nomenclature for natural variants of viruses assigned to the family Filoviridae
AU - Kuhn, Jens H.
AU - Bao, Yiming
AU - Bavari, Sina
AU - Becker, Stephan
AU - Bradfute, Steven
AU - Brister, J. Rodney
AU - Bukreyev, Alexander A.
AU - Chandran, Kartik
AU - Davey, Robert A.
AU - Dolnik, Olga
AU - Dye, John M.
AU - Enterlein, Sven
AU - Hensley, Lisa E.
AU - Honko, Anna N.
AU - Jahrling, Peter B.
AU - Johnson, Karl M.
AU - Kobinger, Gary
AU - Leroy, Eric M.
AU - Lever, Mark S.
AU - Mühlberger, Elke
AU - Netesov, Sergey V.
AU - Olinger, Gene G.
AU - Palacios, Gustavo
AU - Patterson, Jean L.
AU - Paweska, Janusz T.
AU - Pitt, Louise
AU - Radoshitzky, Sheli R.
AU - Saphire, Erica Ollmann
AU - Smither, Sophie J.
AU - Swanepoel, Robert
AU - Towner, Jonathan S.
AU - van der Groen, Guido
AU - Volchkov, Viktor E.
AU - Wahl-Jensen, Victoria
AU - Warren, Travis K.
AU - Weidmann, Manfred
AU - Nichol, Stuart T.
PY - 2013
Y1 - 2013
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84872261364&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84872261364&partnerID=8YFLogxK
U2 - 10.1007/s00705-012-1454-0
DO - 10.1007/s00705-012-1454-0
M3 - Article
C2 - 23001720
AN - SCOPUS:84872261364
VL - 158
SP - 301
EP - 311
JO - Archives of Virology
JF - Archives of Virology
SN - 0304-8608
IS - 1
ER -