Virus nomenclature below the species level: A standardized nomenclature for laboratory animal-adapted strains and variants of viruses assigned to the family Filoviridae

Jens H. Kuhn, Yiming Bao, Sina Bavari, Stephan Becker, Steven Bradfute, J. Rodney Brister, Alexander A. Bukreyev, Yíngyún Caì, Kartik Chandran, Robert A. Davey, Olga Dolnik, John M. Dye, Sven Enterlein, Jean Paul Gonzalez, Pierre Formenty, Alexander N. Freiberg, Lisa E. Hensley, Anna N. Honko, Georgy M. Ignatyev, Peter B. JahrlingKarl M. Johnson, Hans Dieter Klenk, Gary Kobinger, Matthew G. Lackemeyer, Eric M. Leroy, Mark S. Lever, Loreen L. Lofts, Elke Mühlberger, Sergey V. Netesov, Gene G. Olinger, Gustavo Palacios, Jean L. Patterson, Janusz T. Paweska, Louise Pitt, Sheli R. Radoshitzky, Elena I. Ryabchikova, Erica Ollmann Saphire, Aleksandr M. Shestopalov, Sophie J. Smither, Nancy J. Sullivan, Robert Swanepoel, Ayato Takada, Jonathan S. Towner, Guido van der Groen, Viktor E. Volchkov, Victoria Wahl-Jensen, Travis K. Warren, Kelly L. Warfield, Manfred Weidmann, Stuart T. Nichol

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

The International Committee on Taxonomy of Viruses (ICTV) organizes the classification of viruses into taxa, but is not responsible for the nomenclature for taxa members. International experts groups, such as the ICTV Study Groups, recommend the classification and naming of viruses and their strains, variants, and isolates. The ICTV Filoviridae Study Group has recently introduced an updated classification and nomenclature for filoviruses. Subsequently, and together with numerous other filovirus experts, a consistent nomenclature for their natural genetic variants and isolates was developed that aims at simplifying the retrieval of sequence data from electronic databases. This is a first important step toward a viral genome annotation standard as sought by the US National Center for Biotechnology Information (NCBI). Here, this work is extended to include filoviruses obtained in the laboratory by artificial selection through passage in laboratory hosts. The previously developed template for natural filovirus genetic variant naming (<virus name> <isolation host-suffix>/<country of sampling>/<year of sampling>/<genetic variant designation>-<isolate designation>) is retained, but it is proposed to adapt the type of information added to each field for laboratory animal-adapted variants. For instance, the full-length designation of an Ebola virus Mayinga variant adapted at the State Research Center for Virology and Biotechnology "Vector" to cause disease in guinea pigs after seven passages would be akin to "Ebola virus VECTOR/C.porcellus-lab/COD/1976/Mayinga-GPA-P7". As was proposed for the names of natural filovirus variants, we suggest using the full-length designation in databases, as well as in the method section of publications. Shortened designations (such as "EBOV VECTOR/C.por/COD/76/May-GPA-P7") and abbreviations (such as "EBOV/May-GPA-P7") could be used in the remainder of the text depending on how critical it is to convey information contained in the full-length name. "EBOV" would suffice if only one EBOV strain/variant/isolate is addressed.

Original languageEnglish (US)
Pages (from-to)1425-1432
Number of pages8
JournalArchives of Virology
Volume158
Issue number6
DOIs
StatePublished - Jun 2013

Fingerprint

Filoviridae
Laboratory Animals
Terminology
Viruses
Ebolavirus
Biotechnology
Names
Databases
Information Centers
Virology
Viral Genome
Information Storage and Retrieval
Publications
Guinea Pigs

ASJC Scopus subject areas

  • Virology

Cite this

Virus nomenclature below the species level : A standardized nomenclature for laboratory animal-adapted strains and 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.; Caì, Yíngyún; Chandran, Kartik; Davey, Robert A.; Dolnik, Olga; Dye, John M.; Enterlein, Sven; Gonzalez, Jean Paul; Formenty, Pierre; Freiberg, Alexander N.; Hensley, Lisa E.; Honko, Anna N.; Ignatyev, Georgy M.; Jahrling, Peter B.; Johnson, Karl M.; Klenk, Hans Dieter; Kobinger, Gary; Lackemeyer, Matthew G.; Leroy, Eric M.; Lever, Mark S.; Lofts, Loreen L.; Mühlberger, Elke; Netesov, Sergey V.; Olinger, Gene G.; Palacios, Gustavo; Patterson, Jean L.; Paweska, Janusz T.; Pitt, Louise; Radoshitzky, Sheli R.; Ryabchikova, Elena I.; Saphire, Erica Ollmann; Shestopalov, Aleksandr M.; Smither, Sophie J.; Sullivan, Nancy J.; Swanepoel, Robert; Takada, Ayato; Towner, Jonathan S.; van der Groen, Guido; Volchkov, Viktor E.; Wahl-Jensen, Victoria; Warren, Travis K.; Warfield, Kelly L.; Weidmann, Manfred; Nichol, Stuart T.

In: Archives of Virology, Vol. 158, No. 6, 06.2013, p. 1425-1432.

Research output: Contribution to journalArticle

Kuhn, JH, Bao, Y, Bavari, S, Becker, S, Bradfute, S, Brister, JR, Bukreyev, AA, Caì, Y, Chandran, K, Davey, RA, Dolnik, O, Dye, JM, Enterlein, S, Gonzalez, JP, Formenty, P, Freiberg, AN, Hensley, LE, Honko, AN, Ignatyev, GM, Jahrling, PB, Johnson, KM, Klenk, HD, Kobinger, G, Lackemeyer, MG, Leroy, EM, Lever, MS, Lofts, LL, Mühlberger, E, Netesov, SV, Olinger, GG, Palacios, G, Patterson, JL, Paweska, JT, Pitt, L, Radoshitzky, SR, Ryabchikova, EI, Saphire, EO, Shestopalov, AM, Smither, SJ, Sullivan, NJ, Swanepoel, R, Takada, A, Towner, JS, van der Groen, G, Volchkov, VE, Wahl-Jensen, V, Warren, TK, Warfield, KL, Weidmann, M & Nichol, ST 2013, 'Virus nomenclature below the species level: A standardized nomenclature for laboratory animal-adapted strains and variants of viruses assigned to the family Filoviridae', Archives of Virology, vol. 158, no. 6, pp. 1425-1432. https://doi.org/10.1007/s00705-012-1594-2
Kuhn, Jens H. ; Bao, Yiming ; Bavari, Sina ; Becker, Stephan ; Bradfute, Steven ; Brister, J. Rodney ; Bukreyev, Alexander A. ; Caì, Yíngyún ; Chandran, Kartik ; Davey, Robert A. ; Dolnik, Olga ; Dye, John M. ; Enterlein, Sven ; Gonzalez, Jean Paul ; Formenty, Pierre ; Freiberg, Alexander N. ; Hensley, Lisa E. ; Honko, Anna N. ; Ignatyev, Georgy M. ; Jahrling, Peter B. ; Johnson, Karl M. ; Klenk, Hans Dieter ; Kobinger, Gary ; Lackemeyer, Matthew G. ; Leroy, Eric M. ; Lever, Mark S. ; Lofts, Loreen L. ; Mühlberger, Elke ; Netesov, Sergey V. ; Olinger, Gene G. ; Palacios, Gustavo ; Patterson, Jean L. ; Paweska, Janusz T. ; Pitt, Louise ; Radoshitzky, Sheli R. ; Ryabchikova, Elena I. ; Saphire, Erica Ollmann ; Shestopalov, Aleksandr M. ; Smither, Sophie J. ; Sullivan, Nancy J. ; Swanepoel, Robert ; Takada, Ayato ; Towner, Jonathan S. ; van der Groen, Guido ; Volchkov, Viktor E. ; Wahl-Jensen, Victoria ; Warren, Travis K. ; Warfield, Kelly L. ; Weidmann, Manfred ; Nichol, Stuart T. / Virus nomenclature below the species level : A standardized nomenclature for laboratory animal-adapted strains and variants of viruses assigned to the family Filoviridae. In: Archives of Virology. 2013 ; Vol. 158, No. 6. pp. 1425-1432.
@article{4d787fb486c144a69e73ff97cfe3a5f5,
title = "Virus nomenclature below the species level: A standardized nomenclature for laboratory animal-adapted strains and variants of viruses assigned to the family Filoviridae",
abstract = "The International Committee on Taxonomy of Viruses (ICTV) organizes the classification of viruses into taxa, but is not responsible for the nomenclature for taxa members. International experts groups, such as the ICTV Study Groups, recommend the classification and naming of viruses and their strains, variants, and isolates. The ICTV Filoviridae Study Group has recently introduced an updated classification and nomenclature for filoviruses. Subsequently, and together with numerous other filovirus experts, a consistent nomenclature for their natural genetic variants and isolates was developed that aims at simplifying the retrieval of sequence data from electronic databases. This is a first important step toward a viral genome annotation standard as sought by the US National Center for Biotechnology Information (NCBI). Here, this work is extended to include filoviruses obtained in the laboratory by artificial selection through passage in laboratory hosts. The previously developed template for natural filovirus genetic variant naming ( ///-) is retained, but it is proposed to adapt the type of information added to each field for laboratory animal-adapted variants. For instance, the full-length designation of an Ebola virus Mayinga variant adapted at the State Research Center for Virology and Biotechnology {"}Vector{"} to cause disease in guinea pigs after seven passages would be akin to {"}Ebola virus VECTOR/C.porcellus-lab/COD/1976/Mayinga-GPA-P7{"}. As was proposed for the names of natural filovirus variants, we suggest using the full-length designation in databases, as well as in the method section of publications. Shortened designations (such as {"}EBOV VECTOR/C.por/COD/76/May-GPA-P7{"}) and abbreviations (such as {"}EBOV/May-GPA-P7{"}) could be used in the remainder of the text depending on how critical it is to convey information contained in the full-length name. {"}EBOV{"} would suffice if only one EBOV strain/variant/isolate is addressed.",
author = "Kuhn, {Jens H.} and Yiming Bao and Sina Bavari and Stephan Becker and Steven Bradfute and Brister, {J. Rodney} and Bukreyev, {Alexander A.} and Y{\'i}ngy{\'u}n Ca{\`i} and Kartik Chandran and Davey, {Robert A.} and Olga Dolnik and Dye, {John M.} and Sven Enterlein and Gonzalez, {Jean Paul} and Pierre Formenty and Freiberg, {Alexander N.} and Hensley, {Lisa E.} and Honko, {Anna N.} and Ignatyev, {Georgy M.} and Jahrling, {Peter B.} and Johnson, {Karl M.} and Klenk, {Hans Dieter} and Gary Kobinger and Lackemeyer, {Matthew G.} and Leroy, {Eric M.} and Lever, {Mark S.} and Lofts, {Loreen L.} and Elke M{\"u}hlberger and Netesov, {Sergey V.} and Olinger, {Gene G.} and Gustavo Palacios and Patterson, {Jean L.} and Paweska, {Janusz T.} and Louise Pitt and Radoshitzky, {Sheli R.} and Ryabchikova, {Elena I.} and Saphire, {Erica Ollmann} and Shestopalov, {Aleksandr M.} and Smither, {Sophie J.} and Sullivan, {Nancy J.} and Robert Swanepoel and Ayato Takada and Towner, {Jonathan S.} and {van der Groen}, Guido and Volchkov, {Viktor E.} and Victoria Wahl-Jensen and Warren, {Travis K.} and Warfield, {Kelly L.} and Manfred Weidmann and Nichol, {Stuart T.}",
year = "2013",
month = "6",
doi = "10.1007/s00705-012-1594-2",
language = "English (US)",
volume = "158",
pages = "1425--1432",
journal = "Archives of Virology",
issn = "0304-8608",
publisher = "Springer Wien",
number = "6",

}

TY - JOUR

T1 - Virus nomenclature below the species level

T2 - A standardized nomenclature for laboratory animal-adapted strains and 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 - Caì, Yíngyún

AU - Chandran, Kartik

AU - Davey, Robert A.

AU - Dolnik, Olga

AU - Dye, John M.

AU - Enterlein, Sven

AU - Gonzalez, Jean Paul

AU - Formenty, Pierre

AU - Freiberg, Alexander N.

AU - Hensley, Lisa E.

AU - Honko, Anna N.

AU - Ignatyev, Georgy M.

AU - Jahrling, Peter B.

AU - Johnson, Karl M.

AU - Klenk, Hans Dieter

AU - Kobinger, Gary

AU - Lackemeyer, Matthew G.

AU - Leroy, Eric M.

AU - Lever, Mark S.

AU - Lofts, Loreen L.

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 - Ryabchikova, Elena I.

AU - Saphire, Erica Ollmann

AU - Shestopalov, Aleksandr M.

AU - Smither, Sophie J.

AU - Sullivan, Nancy J.

AU - Swanepoel, Robert

AU - Takada, Ayato

AU - Towner, Jonathan S.

AU - van der Groen, Guido

AU - Volchkov, Viktor E.

AU - Wahl-Jensen, Victoria

AU - Warren, Travis K.

AU - Warfield, Kelly L.

AU - Weidmann, Manfred

AU - Nichol, Stuart T.

PY - 2013/6

Y1 - 2013/6

N2 - The International Committee on Taxonomy of Viruses (ICTV) organizes the classification of viruses into taxa, but is not responsible for the nomenclature for taxa members. International experts groups, such as the ICTV Study Groups, recommend the classification and naming of viruses and their strains, variants, and isolates. The ICTV Filoviridae Study Group has recently introduced an updated classification and nomenclature for filoviruses. Subsequently, and together with numerous other filovirus experts, a consistent nomenclature for their natural genetic variants and isolates was developed that aims at simplifying the retrieval of sequence data from electronic databases. This is a first important step toward a viral genome annotation standard as sought by the US National Center for Biotechnology Information (NCBI). Here, this work is extended to include filoviruses obtained in the laboratory by artificial selection through passage in laboratory hosts. The previously developed template for natural filovirus genetic variant naming ( ///-) is retained, but it is proposed to adapt the type of information added to each field for laboratory animal-adapted variants. For instance, the full-length designation of an Ebola virus Mayinga variant adapted at the State Research Center for Virology and Biotechnology "Vector" to cause disease in guinea pigs after seven passages would be akin to "Ebola virus VECTOR/C.porcellus-lab/COD/1976/Mayinga-GPA-P7". As was proposed for the names of natural filovirus variants, we suggest using the full-length designation in databases, as well as in the method section of publications. Shortened designations (such as "EBOV VECTOR/C.por/COD/76/May-GPA-P7") and abbreviations (such as "EBOV/May-GPA-P7") could be used in the remainder of the text depending on how critical it is to convey information contained in the full-length name. "EBOV" would suffice if only one EBOV strain/variant/isolate is addressed.

AB - The International Committee on Taxonomy of Viruses (ICTV) organizes the classification of viruses into taxa, but is not responsible for the nomenclature for taxa members. International experts groups, such as the ICTV Study Groups, recommend the classification and naming of viruses and their strains, variants, and isolates. The ICTV Filoviridae Study Group has recently introduced an updated classification and nomenclature for filoviruses. Subsequently, and together with numerous other filovirus experts, a consistent nomenclature for their natural genetic variants and isolates was developed that aims at simplifying the retrieval of sequence data from electronic databases. This is a first important step toward a viral genome annotation standard as sought by the US National Center for Biotechnology Information (NCBI). Here, this work is extended to include filoviruses obtained in the laboratory by artificial selection through passage in laboratory hosts. The previously developed template for natural filovirus genetic variant naming ( ///-) is retained, but it is proposed to adapt the type of information added to each field for laboratory animal-adapted variants. For instance, the full-length designation of an Ebola virus Mayinga variant adapted at the State Research Center for Virology and Biotechnology "Vector" to cause disease in guinea pigs after seven passages would be akin to "Ebola virus VECTOR/C.porcellus-lab/COD/1976/Mayinga-GPA-P7". As was proposed for the names of natural filovirus variants, we suggest using the full-length designation in databases, as well as in the method section of publications. Shortened designations (such as "EBOV VECTOR/C.por/COD/76/May-GPA-P7") and abbreviations (such as "EBOV/May-GPA-P7") could be used in the remainder of the text depending on how critical it is to convey information contained in the full-length name. "EBOV" would suffice if only one EBOV strain/variant/isolate is addressed.

UR - http://www.scopus.com/inward/record.url?scp=84878614566&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84878614566&partnerID=8YFLogxK

U2 - 10.1007/s00705-012-1594-2

DO - 10.1007/s00705-012-1594-2

M3 - Article

C2 - 23358612

AN - SCOPUS:84878614566

VL - 158

SP - 1425

EP - 1432

JO - Archives of Virology

JF - Archives of Virology

SN - 0304-8608

IS - 6

ER -