Virus nomenclature below the species level: A standardized nomenclature for filovirus strains and variants rescued from cDNA

Jens H. Kuhn, Yimíng Bào, Sina Bavari, Stephan Becker, Steven Bradfute, Kristina Brauburger, 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, Thomas Hoenen, Anna N. HonkoGeorgy M. Ignatyev, Peter B. Jahrling, Karl M. Johnson, Hans Dieter Klenk, Gary Kobinger, Matthew G. Lackemeyer, 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, 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, Valentina A. Volchkova, Victoria Wahl-Jensen, Travis K. Warren, Kelly L. Warfield, Manfred Weidmann, Stuart T. Nichol

    Research output: Contribution to journalArticle

    52 Scopus citations

    Abstract

    Specific alterations (mutations, deletions, insertions) of virus genomes are crucial for the functional characterization of their regulatory elements and their expression products, as well as a prerequisite for the creation of attenuated viruses that could serve as vaccine candidates. Virus genome tailoring can be performed either by using traditionally cloned genomes as starting materials, followed by site-directed mutagenesis, or by de novo synthesis of modified virus genomes or parts thereof. A systematic nomenclature for such recombinant viruses is necessary to set them apart from wild-type and laboratory-adapted viruses, and to improve communication and collaborations among researchers who may want to use recombinant viruses or create novel viruses based on them. A large group of filovirus experts has recently proposed nomenclatures for natural and laboratory animal-adapted filoviruses that aim to simplify the retrieval of sequence data from electronic databases. Here, this work is extended to include nomenclature for filoviruses obtained in the laboratory via reverse genetics systems. The previously developed template for natural filovirus genetic variant naming, <virus name> (<strain>/)<isolation host-suffix>/<country of sampling>/<year of sampling>/<genetic variant designation>-<isolate designation>, is retained, but we propose to adapt the type of information added to each field for cDNA clone-derived filoviruses. For instance, the full-length designation of an Ebola virus Kikwit variant rescued from a plasmid developed at the US Centers for Disease Control and Prevention could be akin to "Ebola virus H.sapiens-rec/COD/1995/Kikwit-abc1" (with the suffix "rec" identifying the recombinant nature of the virus and "abc1" being a placeholder for any meaningful isolate designator). Such a full-length designation should be used in databases and the methods section of publications. Shortened designations (such as "EBOV H.sap/COD/95/Kik-abc1") and abbreviations (such as "EBOV/Kik-abc1") 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)1229-1237
    Number of pages9
    JournalArchives of Virology
    Volume159
    Issue number5
    DOIs
    StatePublished - May 2014

    ASJC Scopus subject areas

    • Virology

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  • Cite this

    Kuhn, J. H., Bào, Y., Bavari, S., Becker, S., Bradfute, S., Brauburger, K., Rodney Brister, J., Bukreyev, A. A., Caì, Y., Chandran, K., Davey, R. A., Dolnik, O., Dye, J. M., Enterlein, S., Gonzalez, J. P., Formenty, P., Freiberg, A. N., Hensley, L. E., Hoenen, T., ... Nichol, S. T. (2014). Virus nomenclature below the species level: A standardized nomenclature for filovirus strains and variants rescued from cDNA. Archives of Virology, 159(5), 1229-1237. https://doi.org/10.1007/s00705-013-1877-2