Virus nomenclature below the species level : a standardized nomenclature for filovirus strains and variants rescued from cDNA
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Date
Authors
Kuhn, Jens H.
Bao, Yımıng M.
Bavari, Sina
Becker, Stephan
Bradfute, Steven
Brauburger, Kristina
Brister, J. Rodney
Bukreyev, Alexander A.
Cai, Yıngyun
Chandran, Kartik
Journal Title
Journal ISSN
Volume Title
Publisher
Springer
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 laboratoryadapted
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.
Description
Keywords
Virus nomenclature, Species level, Filovirus strains, cDNA
Sustainable Development Goals
Citation
Kuhn, JH, Bao, YM, Bavari, S, Becker, S, Bradfute, S, Brauburger, K, Brister, JR, Bukreyev, AA, Cai, YY, Chandran, K, Davey, RA, Dolnik, O, Dye, JM, Enterlein, S, Gonzalez, JP, Formenty, P, Freiberg, AN, Hensley, LE, Hoenen, T, Honko, AN, Ignatyev, GM, Jahrling, PB, Johnson, KM, Klenk, HD, Kobinger, G, Lackemeyer, MG, Leroy, EM, Lever, MS, Muhlberger, 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, Volchkova, VA, Wahl-Jensen, V, Warren, TK, Warfield, KL, Weidmann, M & Nichol, ST 2014, 'Virus nomenclature below the species level : a standardized nomenclature for filovirus strains and variants rescued from cDNA', Archives of Virology, vol. 159, no. 5, pp. 1229-1237.