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 “EBOVH.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.

Large-Scale Screening and Identification of Novel Ebola Virus and Marburg Virus Entry Inhibitors

“…For virus naming, we used the current recommendations of ICTV (32). The Zaire Ebola virus (EBOV) Mayinga strain with an insertion of green fluorescent protein (GFP) between the nucleoprotein (NP) and VP35 (33), which was a kind gift of Heinz Feldmann (NIH, Rocky Mountain Laboratory, Hamilton, MT), and the Marburg virus (MARV) Musoke strain were grown in Vero cells.…”

Development of a micro-neutralization assay for ebolaviruses using a replication-competent vesicular stomatitis hybrid virus and a quantitative PCR readout

“…The ebolavirus GP genes and their accession numbers are: EBOV.GP.Makona (KP096421), SUDV.GP (NC_006432), BDBV.GP (FJ217161), and RESTV.GP (NC_004161); we have adopted the revised nomenclature for ebolaviruses [34].…”

Chiropteran and Filoviruses in Africa: Unveiling an ancient history

“…(ICEBOV). The genus Marburgvirus accounts for a single species, Marburgvirus marburgvirus (formerly Lake Victoria marburgvirus), which consists of two very divergent "viruses": Marburg virus and Ravn virus, approximately 20% divergent at a genetic level (Carroll et al, 2013;Kuhn et al, 2010Kuhn et al, , 2013Towner et al, 2006Towner et al, , 2009. This is in contrast to the known diversity for Ebolavirus species, with Zaire ebolavirus having only a 2.7% nucleotide difference between sequences, Sudan ebolavirus 5.2%, and Reston ebolavirus 4.5% (Lauber and Gorbalenya, 2012;Carroll et al, 2013).…”