Virology Division News

Archives of Virology

, Volume 159, Issue 5, pp 1229-1237

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

  • Jens H. KuhnAffiliated withIntegrated 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) Email author 
  • , Yīmíng BàoAffiliated withInformation Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
  • , Sina BavariAffiliated withUnited States Army Medical Research Institute of Infectious Diseases
  • , Stephan BeckerAffiliated withInstitut für Virologie, Philipps-Universität Marburg
  • , Steven BradfuteAffiliated withUniversity of New Mexico
  • , Kristina BrauburgerAffiliated withDepartment of Microbiology and National Emerging Infectious Diseases Laboratory, Boston University School of Medicine
  • , J. Rodney BristerAffiliated withInformation Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
  • , Alexander A. BukreyevAffiliated withDepartment of Pathology and Galveston National Laboratory, University of Texas Medical Branch
  • , Yíngyún CaìAffiliated withIntegrated 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)
    • , Kartik ChandranAffiliated withDepartment of Microbiology and Immunology, Albert Einstein College of Medicine
    • , Robert A. DaveyAffiliated withDepartment of Virology and Immunology, Texas Biomedical Research Institute
    • , Olga DolnikAffiliated withInstitut für Virologie, Philipps-Universität Marburg
    • , John M. DyeAffiliated withUnited States Army Medical Research Institute of Infectious Diseases
    • , Sven EnterleinAffiliated withIntegrated 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)Integrated BioTherapeutics, Inc.
    • , Jean-Paul GonzalezAffiliated withIntegrated 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)Health Department, Institut de Recherche pour le DéveloppementMetabiota, Inc.
    • , Pierre FormentyAffiliated withIntegrated 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)World Health Organization
    • , Alexander N. FreibergAffiliated withDepartment of Pathology and Galveston National Laboratory, University of Texas Medical Branch
    • , Lisa E. HensleyAffiliated withIntegrated 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)
    • , Thomas HoenenAffiliated withIntegrated 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)Laboratory for Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health
    • , Anna N. HonkoAffiliated withUnited States Army Medical Research Institute of Infectious Diseases
    • , Georgy M. IgnatyevAffiliated withIntegrated 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)Federal State Unitary Company “Microgen Scientific Industrial Company for Immunobiological Medicines”, Ministry of Health of the Russian Federation
    • , Peter B. JahrlingAffiliated withIntegrated 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)
    • , Karl M. JohnsonAffiliated withIntegrated 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)
    • , Hans-Dieter KlenkAffiliated withInstitut für Virologie, Philipps-Universität Marburg
    • , Gary KobingerAffiliated withIntegrated 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)Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada
    • , Matthew G. LackemeyerAffiliated withIntegrated 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)
    • , Eric M. LeroyAffiliated withIntegrated 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)Centre International de Recherches Médicales de Franceville
    • , Mark S. LeverAffiliated withIntegrated 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)Biomedical Sciences Department
    • , Elke MühlbergerAffiliated withDepartment of Microbiology and National Emerging Infectious Diseases Laboratory, Boston University School of Medicine
    • , Sergey V. NetesovAffiliated withInformation Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthNovosibirsk State University
    • , Gene G. OlingerAffiliated withUnited States Army Medical Research Institute of Infectious Diseases
    • , Gustavo PalaciosAffiliated withUnited States Army Medical Research Institute of Infectious Diseases
    • , Jean L. PattersonAffiliated withDepartment of Virology and Immunology, Texas Biomedical Research Institute
    • , Janusz T. PaweskaAffiliated withInformation Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthCenter for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service
    • , Louise PittAffiliated withUnited States Army Medical Research Institute of Infectious Diseases
    • , Sheli R. RadoshitzkyAffiliated withUnited States Army Medical Research Institute of Infectious Diseases
    • , Elena I. RyabchikovaAffiliated withInformation Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences
    • , Erica Ollmann SaphireAffiliated withInformation Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthDepartment of Immunology and Microbial Science and The Skaggs Institute for Chemical Biology, The Scripps Research Institute
    • , Aleksandr M. ShestopalovAffiliated withInformation Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthNovosibirsk State UniversityState Research Center of Virology and Biotechnology “Vector”
    • , Sophie J. SmitherAffiliated withIntegrated 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)Biomedical Sciences Department
    • , Nancy J. SullivanAffiliated withInformation Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthVaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health
    • , Robert SwanepoelAffiliated withInformation Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthZoonoses Research Unit, University of Pretoria
    • , Ayato TakadaAffiliated withInformation Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthDivision of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control
    • , Jonathan S. TownerAffiliated withInformation Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthCenters 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)
    • , Guido van der GroenAffiliated withInformation Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthPrins Leopold Instituut voor Tropische Geneeskunde
    • , Viktor E. VolchkovAffiliated withUnited States Army Medical Research Institute of Infectious DiseasesLaboratoire des Filovirus, Inserm U758, Université de Lyon, UCB-Lyon-1, Ecole-Normale-Supérieure de Lyon
    • , Valentina A. VolchkovaAffiliated withUnited States Army Medical Research Institute of Infectious DiseasesLaboratoire des Filovirus, Inserm U758, Université de Lyon, UCB-Lyon-1, Ecole-Normale-Supérieure de Lyon
    • , Victoria Wahl-JensenAffiliated withIntegrated 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)
    • , Travis K. WarrenAffiliated withUnited States Army Medical Research Institute of Infectious Diseases
    • , Kelly L. WarfieldAffiliated withIntegrated 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)Integrated BioTherapeutics, Inc.
    • , Manfred WeidmannAffiliated withUnited States Army Medical Research Institute of Infectious DiseasesUniversitätsmedizin Göttingen, Abteilung Virologie
    • , Stuart T. NicholAffiliated withInformation Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthCenters 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) Email author 

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.