, Volume 159, Issue 5, pp 1229-1237

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

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.

J. H. Kuhn, A. A. Bukreyev, K. Chandran, O. Dolnik, J. M. Dye, E. M. Leroy, E. Mühlberger, S. V. Netesov, J. L. Patterson, J. T. Paweska, E. O. Saphire, S. J. Smither, A. Takada, J. S. Towner, V. E. Volchkov, and T. K. Warren are Members of the International Committee on Taxonomy of Viruses (ICTV) Filoviridae Study Group.
The content of this publication does not necessarily reflect the views or policies of the US Department of the Army, the US Department of Defense or the US Department of Health and Human Services or of the institutions and companies affiliated with the authors. This work was funded in part by the Joint Science and Technology Office for Chem Bio Defense (proposal #TMTI0048_09_RD_T to SB). YC, JHK, and VWJ performed this work as employees of Tunnell Consulting, Inc., and MGL as an employee of Lovelace Respiratory Research Institute, both subcontractors to Battelle Memorial Institute under its prime contract with NIAID, under Contract No. HHSN272200700016I. This research was also supported in part by the Intramural Research Program of the NIH, National Library of Medicine (YB and JRB), and the Intramural Research Program of the NIH, NIAID (TH).