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

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• 作者：Jens H. Kuhn (1)
  Yīmíng Bào (2)
  Sina Bavari (3)
  Stephan Becker (4)
  Steven Bradfute (5)
  Kristina Brauburger (6)
  J. Rodney Brister (2)
  Alexander A. Bukreyev (7)
  Yíngyún Caì (1)
  Kartik Chandran (8)
  Robert A. Davey (9)
  Olga Dolnik (4)
  John M. Dye (3)
  Sven Enterlein (10)
  Jean-Paul Gonzalez (11) (12)
  Pierre Formenty (13)
  Alexander N. Freiberg (7)
  Lisa E. Hensley (1)
  Thomas Hoenen (14)
  Anna N. Honko (3)
  Georgy M. Ignatyev (15)
  Peter B. Jahrling (1)
  Karl M. Johnson (16)
  Hans-Dieter Klenk (4)
  Gary Kobinger (17)
  Matthew G. Lackemeyer (1)
  Eric M. Leroy (18)
  Mark S. Lever (19)
  Elke Mühlberger (6)
  Sergey V. Netesov (20)
  Gene G. Olinger (3)
  Gustavo Palacios (3)
  Jean L. Patterson (9)
  Janusz T. Paweska (21)
  Louise Pitt (3)
  Sheli R. Radoshitzky (3)
  Elena I. Ryabchikova (22)
  Erica Ollmann Saphire (23)
  Aleksandr M. Shestopalov (20) (24)
  Sophie J. Smither (19)
  Nancy J. Sullivan (25)
  Robert Swanepoel (26)
  Ayato Takada (27)
  Jonathan S. Towner (28)
  Guido van der Groen (29)
  Viktor E. Volchkov (30)
  Valentina A. Volchkova (30)
  Victoria Wahl-Jensen (1)
  Travis K. Warren (3)
  Kelly L. Warfield (10)
  Manfred Weidmann (31)
  Stuart T. Nichol (28)
  
• 刊名：Archives of Virology
• 出版年：2014
• 出版时间：May 2014
• 年：2014
• 卷：159
• 期：5
• 页码：1229-1237
• 全文大小：
• 参考文献：1. Adams MJ, Carstens EB (2012) Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2012). Arch Virol 157:1411-422 CrossRef
  2. Calisher CH, van Regenmortel MHV (2009) Should all other biologists follow the lead of virologists and stop italicizing the names of living organisms? Zootaxa 2113:63-8
  3. Ebihara H, Takada A, Kobasa D, Jones S, Neumann G, Theriault S, Bray M, Feldmann H, Kawaoka Y (2006) Molecular determinants of Ebola virus virulence in mice. PLoS Pathog 2:e73 CrossRef
  4. Ebihara H, Theriault S, Neumann G, Alimonti JB, Geisbert JB, Hensley LE, Groseth A, Jones SM, Geisbert TW, Kawaoka Y, Feldmann H (2007) In vitro and in vivo characterization of recombinant Ebola viruses expressing enhanced green fluorescent protein. J Infect Dis 196(suppl. 2):S313–S322 CrossRef
  5. Enterlein S, Volchkov V, Weik M, Kolesnikova L, Volchkova V, Klenk HD, Mühlberger E (2006) Rescue of recombinant Marburg virus from cDNA is dependent on nucleocapsid protein VP30. J Virol 80:1038-043 CrossRef
  6. Enterlein S, Schmidt KM, Schümann M, Conrad D, Kr?hling V, Olejnik J, Mühlberger E (2009) The Marburg virus 3-noncoding region structurally and functionally differs from that of Ebola virus. J Virol 83:4508-519 CrossRef
  7. Feldmann H, Geisbert TW, Jahrling PB, Klenk H-D, Netesov SV, Peters CJ, Sanchez A, Swanepoel R, Volchkov VE (2005) Family / Filoviridae. In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (eds) Virus Taxonomy—Eighth Report of the International Committee on Taxonomy of Viruses. Elsevier/Academic Press, San Diego, pp 645-53
  8. Groseth A, Marzi A, Hoenen T, Herwig A, Gardner D, Becker S, Ebihara H, Feldmann H (2012) The Ebola virus glycoprotein contributes to but is not sufficient for virulence in vivo. PLoS Pathog 8:e1002847 CrossRef
  9. Hartman AL, Dover JE, Towner JS, Nichol ST (2006) Reverse genetic generation of recombinant Zaire Ebola viruses containing disrupted IRF-3 inhibitory domains results in attenuated virus growth in vitro and higher levels of IRF-3 activation without inhibiting viral transcription or replication. J Virol 80:6430-440 CrossRef
  10. Hartman AL, Bird BH, Towner JS, Antoniadou ZA, Zaki SR, Nichol ST (2008) Inhibition of IRF-3 activation by VP35 is critical for the high level of virulence of Ebola virus. J Virol 82:2699-704 CrossRef
  11. Hoenen T, Groseth A, de Kok-Mercado F, Kuhn JH, Wahl-Jensen V (2011) Minigenomes, transcription and replication competent virus-like particles and beyond: reverse genetics systems for filoviruses and other negative stranded hemorrhagic fever viruses. Antiviral Res 91:195-08 CrossRef
  12. Hoenen T, Shabman RS, Groseth A, Herwig A, Weber M, Schudt G, Dolnik O, Basler CF, Becker S, Feldmann H (2012) Inclusion bodies are a site of ebolavirus replication. J Virol 86:11779-1788 CrossRef
  13. Hoenen T, Groseth A, Callison J, Takada A, Feldmann H (2013) A novel Ebola virus expressing luciferase allows for rapid and quantitative testing of antivirals. Antiviral Res 99:207-13 CrossRef
  14. International Committee on Standardized Genetic Nomenclature for Mice (2011) Guidelines for Nomenclature of Mouse and Rat Strains. http://www.informatics.jax.org/mgihome/nomen/strains.shtml
  15. Kr?hling V, Dolnik O, Kolesnikova L, Schmidt-Chanasit J, Jordan I, Sandig V, Günther S, Becker S (2010) Establishment of fruit bat cells ( / Rousettus aegyptiacus) as a model system for the investigation of filoviral infection. PLoS Negl Trop Dis 4:e802 CrossRef
  16. Kuhn JH, Becker S, Ebihara H, Geisbert TW, Johnson KM, Lipkin WI, Negredo A, Netesov SV, Nichol ST, Palacios G, Peters CJ, Tenorio A, Volchkov VE, Jahrling PB (2010) Proposal for a revised taxonomy of the family / Filoviridae: classification, names of taxa and viruses, and virus abbreviations. Arch Virol 155:2083-103 CrossRef
  17. Kuhn JH, Becker S, Ebihara H, Geisbert TW, Jahrling PB, Kawaoka Y, Netesov SV, Nichol ST, Peters CJ, Volchkov VE, Ksiazek TG (2011) Family / Filoviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus Taxonomy—Ninth Report of the International Committee on Taxonomy of Viruses. Elsevier/Academic Press, London, pp 665-71
  18. Kuhn JH, Bao Y, Bavari S, Becker S, Bradfute S, Brister JR, Bukreyev AA, Caì Y, Chandran K, Davey RA, Dolnik O, Dye JM, Enterlein S, Gonzalez JP, Formenty P, Freiberg AN, Hensley LE, Honko AN, Ignatyev GM, Jahrling PB, Johnson KM, Klenk HD, Kobinger G, Lackemeyer MG, Leroy EM, Lever MS, Lofts LL, Mühlberger 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, Wahl-Jensen V, Warren TK, Warfield KL, Weidmann M, Nichol ST (2013) Virus nomenclature below the species level: a standardized nomenclature for laboratory animal-adapted strains and variants of viruses assigned to the family / Filoviridae. Arch Virol 158:1425-432 CrossRef
  19. Kuhn JH, Bao Y, Bavari S, Becker S, Bradfute S, Brister JR, Bukreyev AA, Chandran K, Davey RA, Dolnik O, Dye JM, Enterlein S, Hensley LE, Honko AN, Jahrling PB, Johnson KM, Kobinger G, Leroy EM, Lever MS, Mühlberger E, Netesov SV, Olinger GG, Palacios G, Patterson JL, Paweska JT, Pitt L, Radoshitzky SR, Saphire EO, Smither SJ, Swanepoel R, Towner JS, van der Groen G, Volchkov VE, Wahl-Jensen V, Warren TK, Weidmann M, Nichol ST (2013) Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family / Filoviridae. Arch Virol 158:301-11 CrossRef
  20. Lubaki NM, Ilinykh P, Pietzsch C, Tigabu B, Freiberg AN, Koup RA, Bukreyev A (2013) The lack of maturation of Ebola virus-infected dendritic cells results from the cooperative effect of at least two viral domains. J Virol 87:7471-485 CrossRef
  21. Martínez MJ, Biedenkopf N, Volchkova V, Hartlieb B, Alazard-Dany N, Reynard O, Becker S, Volchkov V (2008) Role of Ebola virus VP30 in transcription reinitiation. J Virol 82:12569-2573 CrossRef
  22. Martinez MJ, Volchkova VA, Raoul H, Alazard-Dany N, Reynard O, Volchkov VE (2011) Role of VP30 phosphorylation in the Ebola virus replication cycle. J Infect Dis 204(Suppl 3):S934–S940 CrossRef
  23. Mateo M, Carbonnelle C, Martinez MJ, Reynard O, Page A, Volchkova VA, Volchkov VE (2011) Knockdown of Ebola Virus VP24 impairs viral nucleocapsid assembly and prevents virus replication. J Infect Dis 204(Suppl 3):S892–S896 CrossRef
  24. Mateo M, Carbonnelle C, Reynard O, Kolesnikova L, Nemirov K, Page A, Volchkova VA, Volchkov VE (2011) VP24 is a molecular determinant of Ebola virus virulence in guinea pigs. J Infect Dis 204(Suppl 3):S1011–S1020 CrossRef
  25. Mittler E, Kolesnikova L, Herwig A, Dolnik O, Becker S (2013) Assembly of the Marburg virus envelope. Cell Microbiol 15:270-84 CrossRef
  26. Mpanju OM, Towner JS, Dover JE, Nichol ST, Wilson CA (2006) Identification of two amino acid residues on Ebola virus glycoprotein 1 critical for cell entry. Virus Res 121:205-14 CrossRef
  27. Neumann G, Feldmann H, Watanabe S, Lukashevich I, Kawaoka Y (2002) Reverse genetics demonstrates that proteolytic processing of the Ebola virus glycoprotein is not essential for replication in cell culture. J Virol 76:406-10 CrossRef
  28. Neumann G, Ebihara H, Takada A, Noda T, Kobasa D, Jasenosky LD, Watanabe S, Kim JH, Feldmann H, Kawaoka Y (2005) Ebola virus VP40 late domains are not essential for viral replication in cell culture. J Virol 79:10300-0307 CrossRef
  29. Prins KC, Delpeut S, Leung DW, Reynard O, Volchkova VA, Reid SP, Ramanan P, Cardenas WB, Amarasinghe GK, Volchkov VE, Basler CF (2010) Mutations abrogating VP35 interaction with double-stranded RNA render Ebola virus avirulent in guinea pigs. J Virol 84:3004-015 CrossRef
  30. Schmidt KM, Schümann M, Olejnik J, Kr?hling V, Mühlberger E (2011) Recombinant Marburg Virus expressing EGFP allows rapid screening of virus growth and real-time visualization of virus spread. J Infect Dis 204(Suppl 3):S861–S870 CrossRef
  31. Shabman RS, Hoenen T, Groseth A, Jabado O, Binning JM, Amarasinghe GK, Feldmann H, Basler CF (2013) An upstream open reading frame modulates Ebola virus polymerase translation and virus replication. PLoS Pathog 9:e1003147 CrossRef
  32. Theriault S, Groseth A, Neumann G, Kawaoka Y, Feldmann H (2004) Rescue of Ebola virus from cDNA using heterologous support proteins. Virus Res 106:43-0 CrossRef
  33. Towner JS, Paragas J, Dover JE, Gupta M, Goldsmith CS, Huggins JW, Nichol ST (2005) Generation of eGFP expressing recombinant Zaire ebolavirus for analysis of early pathogenesis events and high-throughput antiviral drug screening. Virology 332:20-7 CrossRef
  34. Volchkov VE, Volchkova VA, Mühlberger E, Kolesnikova LV, Weik M, Dolnik O, Klenk HD (2001) Recovery of infectious Ebola virus from complementary DNA: RNA editing of the GP gene and viral cytotoxicity. Science 291:1965-969 CrossRef
  35. Volchkova VA, Dolnik O, Martinez MJ, Reynard O, Volchkov VE (2011) Genomic RNA editing and its impact on Ebola virus adaptation during serial passages in cell culture and infection of guinea pigs. J Infect Dis 204(Suppl 3):S941–S946 CrossRef
  
• 作者单位：Jens H. Kuhn (1)
  Yīmíng Bào (2)
  Sina Bavari (3)
  Stephan Becker (4)
  Steven Bradfute (5)
  Kristina Brauburger (6)
  J. Rodney Brister (2)
  Alexander A. Bukreyev (7)
  Yíngyún Caì (1)
  Kartik Chandran (8)
  Robert A. Davey (9)
  Olga Dolnik (4)
  John M. Dye (3)
  Sven Enterlein (10)
  Jean-Paul Gonzalez (11) (12)
  Pierre Formenty (13)
  Alexander N. Freiberg (7)
  Lisa E. Hensley (1)
  Thomas Hoenen (14)
  Anna N. Honko (3)
  Georgy M. Ignatyev (15)
  Peter B. Jahrling (1)
  Karl M. Johnson (16)
  Hans-Dieter Klenk (4)
  Gary Kobinger (17)
  Matthew G. Lackemeyer (1)
  Eric M. Leroy (18)
  Mark S. Lever (19)
  Elke Mühlberger (6)
  Sergey V. Netesov (20)
  Gene G. Olinger (3)
  Gustavo Palacios (3)
  Jean L. Patterson (9)
  Janusz T. Paweska (21)
  Louise Pitt (3)
  Sheli R. Radoshitzky (3)
  Elena I. Ryabchikova (22)
  Erica Ollmann Saphire (23)
  Aleksandr M. Shestopalov (20) (24)
  Sophie J. Smither (19)
  Nancy J. Sullivan (25)
  Robert Swanepoel (26)
  Ayato Takada (27)
  Jonathan S. Towner (28)
  Guido van der Groen (29)
  Viktor E. Volchkov (30)
  Valentina A. Volchkova (30)
  Victoria Wahl-Jensen (1)
  Travis K. Warren (3)
  Kelly L. Warfield (10)
  Manfred Weidmann (31)
  Stuart T. Nichol (28)
  
  1. Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
  2. Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
  3. United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
  4. Institut für Virologie, Philipps-Universit?t Marburg, Marburg, Germany
  5. University of New Mexico, Albuquerque, NM, USA
  6. Department of Microbiology and National Emerging Infectious Diseases Laboratory, Boston University School of Medicine, Boston, MA, USA
  7. Department of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, USA
  8. Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
  9. Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
  10. Integrated BioTherapeutics, Inc., Gaithersburg, MD, USA
  11. Health Department, Institut de Recherche pour le Développement, Marseille, France
  12. Metabiota, Inc., San Francisco, CA, USA
  13. World Health Organization, Geneva, Switzerland
  14. Laboratory for Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
  15. Federal State Unitary Company “Microgen Scientific Industrial Company for Immunobiological Medicines- Ministry of Health of the Russian Federation, Moscow, Russia
  16. Bozeman, Montana, USA
  17. Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
  18. Centre International de Recherches Médicales de Franceville, Franceville, Gabon
  19. Biomedical Sciences Department, Dstl, Porton Down, Salisbury, Wiltshire, UK
  20. Novosibirsk State University, Novosibirsk, Novosibirsk Region, Russia
  21. Center for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg, Gauteng, South Africa
  22. Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Novosibirsk Region, Russia
  23. Department of Immunology and Microbial Science and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
  24. State Research Center of Virology and Biotechnology “Vector- Koltsovo, Novosibirsk Region, Russia
  25. Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
  26. Zoonoses Research Unit, University of Pretoria, Pretoria, South Africa
  27. Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan
  28. Centers for Disease Control and Prevention (CDC), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Division of High-Consequence Pathogens Pathology (DHCPP), Viral Special Pathogens Branch (VSPB), 1600 Clifton Road, Atlanta, GA, 30333, USA
  29. Prins Leopold Instituut voor Tropische Geneeskunde, Antwerp, Belgium
  30. Laboratoire des Filovirus, Inserm U758, Université de Lyon, UCB-Lyon-1, Ecole-Normale-Supérieure de Lyon, Lyon, France
  31. Universit?tsmedizin G?ttingen, Abteilung Virologie, G?ttingen, Germany
  
• ISSN：1432-8798

文摘

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.