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

Kuhn, Jens H; Bào, Yīmíng; Bavari, Sina; Becker, Stephan; Bradfute, Steven; Brauburger, Kristina LU ; Rodney Brister, J; Bukreyev, Alexander A; Caì, Yíngyún and Chandran, Kartik, et al. (2014) In Archives of Virology 159(5). p.1229-1237
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... (More)
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. (Less)
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Archives of Virology
volume
159
issue
5
pages
1229 - 1237
publisher
Springer
external identifiers
  • scopus:84899932651
ISSN
1432-8798
DOI
10.1007/s00705-013-1877-2
language
English
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no
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298e9aa8-4f8e-46a1-b210-f81d345566e9 (old id 8728166)
date added to LUP
2016-02-25 10:34:06
date last changed
2017-10-22 03:08:16
@article{298e9aa8-4f8e-46a1-b210-f81d345566e9,
  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, &lt;virus name&gt; (&lt;strain&gt;/)&lt;isolation host-suffix&gt;/&lt;country of sampling&gt;/&lt;year of sampling&gt;/&lt;genetic variant designation&gt;-&lt;isolate designation&gt;, 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.},
  author       = {Kuhn, Jens H and Bào, Yīmíng and Bavari, Sina and Becker, Stephan and Bradfute, Steven and Brauburger, Kristina and Rodney Brister, J and Bukreyev, Alexander A and Caì, Yíngyún and Chandran, Kartik and Davey, Robert A and Dolnik, Olga and Dye, John M and Enterlein, Sven and Gonzalez, Jean-Paul and Formenty, Pierre and Freiberg, Alexander N and Hensley, Lisa E and Hoenen, Thomas and Honko, Anna N and Ignatyev, Georgy M and Jahrling, Peter B and Johnson, Karl M and Klenk, Hans-Dieter and Kobinger, Gary and Lackemeyer, Matthew G and Leroy, Eric M and Lever, Mark S and Mühlberger, Elke and Netesov, Sergey V and Olinger, Gene G and Palacios, Gustavo and Patterson, Jean L and Paweska, Janusz T and Pitt, Louise 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 Swanepoel, Robert and Takada, Ayato and Towner, Jonathan S and van der Groen, Guido and Volchkov, Viktor E and Volchkova, Valentina A and Wahl-Jensen, Victoria and Warren, Travis K and Warfield, Kelly L and Weidmann, Manfred and Nichol, Stuart T},
  issn         = {1432-8798},
  language     = {eng},
  number       = {5},
  pages        = {1229--1237},
  publisher    = {Springer},
  series       = {Archives of Virology},
  title        = {Virus nomenclature below the species level: a standardized nomenclature for filovirus strains and variants rescued from cDNA.},
  url          = {http://dx.doi.org/10.1007/s00705-013-1877-2},
  volume       = {159},
  year         = {2014},
}