Virus nomenclature below the species level: A standardized nomenclature for natural variants of viruses assigned to the family Filoviridae

Jens H. Kuhn, Yiming Bao, Sina Bavari, Stephan Becker, Steven Bradfute, J. Rodney Brister, Alexander Bukreyev, Kartik Chandran, Robert A. Davey, Olga Dolnik, John M. Dye, Sven Enterlein, Lisa E. Hensley, Anna N. Honko, Peter B. Jahrling, Karl M. Johnson, Gary Kobinger, Eric M. Leroy, Mark S. Lever, Elke MühlbergerSergey 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, Manfred Weidmann, Stuart T. Nichol

Research output: Contribution to journalArticle

63 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)301-311
Number of pages11
JournalArchives of Virology
Volume158
Issue number1
DOIs
StatePublished - 2013

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Filoviridae
Terminology
Names
Viruses
Ebolavirus
Democratic Republic of the Congo
Information Centers
Rotavirus
Viral Genome
Information Storage and Retrieval
Consensus Sequence
Biotechnology
Publications
Cell Culture Techniques
Databases
Guidelines

ASJC Scopus subject areas

  • Virology

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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; 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 journalArticle

Kuhn, JH, Bao, Y, Bavari, S, Becker, S, Bradfute, S, Brister, JR, Bukreyev, A, Chandran, K, Davey, RA, Dolnik, O, Dye, JM, Enterlein, S, Hensley, LE, Honko, AN, Jahrling, PB, Johnson, KM, Kobinger, G, Leroy, EM, Lever, MS, Mühlberger, E, Netesov, SV, Olinger, GG, Palacios, G, Patterson, JL, Paweska, JT, Pitt, L, Radoshitzky, SR, Saphire, EO, Smither, SJ, Swanepoel, R, Towner, JS, van der Groen, G, Volchkov, VE, Wahl-Jensen, V, Warren, TK, Weidmann, M & Nichol, ST 2013, 'Virus nomenclature below the species level: A standardized nomenclature for natural variants of viruses assigned to the family Filoviridae', Archives of Virology, vol. 158, no. 1, pp. 301-311. https://doi.org/10.1007/s00705-012-1454-0
Kuhn, Jens H. ; Bao, Yiming ; Bavari, Sina ; Becker, Stephan ; Bradfute, Steven ; Brister, J. Rodney ; Bukreyev, Alexander ; 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. / Virus nomenclature below the species level : A standardized nomenclature for natural variants of viruses assigned to the family Filoviridae. In: Archives of Virology. 2013 ; Vol. 158, No. 1. pp. 301-311.
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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.",
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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

AU - Chandran, Kartik

AU - Davey, Robert A.

AU - Dolnik, Olga

AU - Dye, John M.

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AU - Hensley, Lisa E.

AU - Honko, Anna N.

AU - Jahrling, Peter B.

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AU - Netesov, Sergey V.

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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

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