Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names
Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-ex...
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2014-09-01
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| Series: | Viruses |
| Subjects: | |
| Online Access: | http://www.mdpi.com/1999-4915/6/9/3663 |
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English |
| format |
Article |
| sources |
DOAJ |
| author |
Jens H. Kuhn Kristian G. Andersen Yīmíng Bào Sina Bavari Stephan Becker Richard S. Bennett Nicholas H. Bergman Olga Blinkova Steven Bradfute J. Rodney Brister Alexander Bukreyev Kartik Chandran Alexander A. Chepurnov Robert A. Davey Ralf G. Dietzgen Norman A. Doggett Olga Dolnik John M. Dye Sven Enterlein Paul W. Fenimore Pierre Formenty Alexander N. Freiberg Robert F. Garry Nicole L. Garza Stephen K. Gire Jean-Paul Gonzalez Anthony Griffiths Christian T. Happi Lisa E. Hensley Andrew S. Herbert Michael C. Hevey Thomas Hoenen Anna N. Honko Georgy M. Ignatyev Peter B. Jahrling Joshua C. Johnson Karl M. Johnson Jason Kindrachuk Hans-Dieter Klenk Gary Kobinger Tadeusz J. Kochel Matthew G. Lackemeyer Daniel F. Lackner Eric M. Leroy Mark S. Lever Elke Mühlberger Sergey V. Netesov Gene G. Olinger Sunday A. Omilabu Gustavo Palacios Rekha G. Panchal Daniel J. Park Jean L. Patterson Janusz T. Paweska Clarence J. Peters James Pettitt Louise Pitt Sheli R. Radoshitzky Elena I. Ryabchikova Erica Ollmann Saphire Pardis C. Sabeti Rachel Sealfon Aleksandr M. Shestopalov Sophie J. Smither Nancy J. Sullivan Robert Swanepoel Ayato Takada Jonathan S. Towner Guido van der Groen Viktor E. Volchkov Valentina A. Volchkova Victoria Wahl-Jensen Travis K. Warren Kelly L. Warfield Manfred Weidmann Stuart T. Nichol |
| spellingShingle |
Jens H. Kuhn Kristian G. Andersen Yīmíng Bào Sina Bavari Stephan Becker Richard S. Bennett Nicholas H. Bergman Olga Blinkova Steven Bradfute J. Rodney Brister Alexander Bukreyev Kartik Chandran Alexander A. Chepurnov Robert A. Davey Ralf G. Dietzgen Norman A. Doggett Olga Dolnik John M. Dye Sven Enterlein Paul W. Fenimore Pierre Formenty Alexander N. Freiberg Robert F. Garry Nicole L. Garza Stephen K. Gire Jean-Paul Gonzalez Anthony Griffiths Christian T. Happi Lisa E. Hensley Andrew S. Herbert Michael C. Hevey Thomas Hoenen Anna N. Honko Georgy M. Ignatyev Peter B. Jahrling Joshua C. Johnson Karl M. Johnson Jason Kindrachuk Hans-Dieter Klenk Gary Kobinger Tadeusz J. Kochel Matthew G. Lackemeyer Daniel F. Lackner Eric M. Leroy Mark S. Lever Elke Mühlberger Sergey V. Netesov Gene G. Olinger Sunday A. Omilabu Gustavo Palacios Rekha G. Panchal Daniel J. Park Jean L. Patterson Janusz T. Paweska Clarence J. Peters James Pettitt Louise Pitt Sheli R. Radoshitzky Elena I. Ryabchikova Erica Ollmann Saphire Pardis C. Sabeti Rachel Sealfon Aleksandr M. Shestopalov Sophie J. Smither Nancy J. Sullivan Robert Swanepoel Ayato Takada Jonathan S. Towner Guido van der Groen Viktor E. Volchkov Valentina A. Volchkova Victoria Wahl-Jensen Travis K. Warren Kelly L. Warfield Manfred Weidmann Stuart T. Nichol Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names Viruses Bundibugyo virus cDNA clone cuevavirus Ebola Ebola virus ebolavirus filovirid Filoviridae filovirus genome annotation ICTV International Committee on Taxonomy of Viruses Lloviu virus Marburg virus marburgvirus mononegavirad Mononegavirales mononegavirus Ravn virus RefSeq Reston virus reverse genetics Sudan virus Taï Forest virus virus classification virus isolate virus nomenclature virus strain virus taxonomy virus variant |
| author_facet |
Jens H. Kuhn Kristian G. Andersen Yīmíng Bào Sina Bavari Stephan Becker Richard S. Bennett Nicholas H. Bergman Olga Blinkova Steven Bradfute J. Rodney Brister Alexander Bukreyev Kartik Chandran Alexander A. Chepurnov Robert A. Davey Ralf G. Dietzgen Norman A. Doggett Olga Dolnik John M. Dye Sven Enterlein Paul W. Fenimore Pierre Formenty Alexander N. Freiberg Robert F. Garry Nicole L. Garza Stephen K. Gire Jean-Paul Gonzalez Anthony Griffiths Christian T. Happi Lisa E. Hensley Andrew S. Herbert Michael C. Hevey Thomas Hoenen Anna N. Honko Georgy M. Ignatyev Peter B. Jahrling Joshua C. Johnson Karl M. Johnson Jason Kindrachuk Hans-Dieter Klenk Gary Kobinger Tadeusz J. Kochel Matthew G. Lackemeyer Daniel F. Lackner Eric M. Leroy Mark S. Lever Elke Mühlberger Sergey V. Netesov Gene G. Olinger Sunday A. Omilabu Gustavo Palacios Rekha G. Panchal Daniel J. Park Jean L. Patterson Janusz T. Paweska Clarence J. Peters James Pettitt Louise Pitt Sheli R. Radoshitzky Elena I. Ryabchikova Erica Ollmann Saphire Pardis C. Sabeti Rachel Sealfon Aleksandr M. Shestopalov Sophie J. Smither Nancy J. Sullivan Robert Swanepoel Ayato Takada Jonathan S. Towner Guido van der Groen Viktor E. Volchkov Valentina A. Volchkova Victoria Wahl-Jensen Travis K. Warren Kelly L. Warfield Manfred Weidmann Stuart T. Nichol |
| author_sort |
Jens H. Kuhn |
| title |
Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names |
| title_short |
Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names |
| title_full |
Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names |
| title_fullStr |
Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names |
| title_full_unstemmed |
Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names |
| title_sort |
filovirus refseq entries: evaluation and selection of filovirus type variants, type sequences, and names |
| publisher |
MDPI AG |
| series |
Viruses |
| issn |
1999-4915 |
| publishDate |
2014-09-01 |
| description |
Sequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information’s (NCBI’s) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [<virus name> (<strain>)/<isolation host-suffix>/<country of sampling>/<year of sampling>/<genetic variant designation>-<isolate designation>], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences. |
| topic |
Bundibugyo virus cDNA clone cuevavirus Ebola Ebola virus ebolavirus filovirid Filoviridae filovirus genome annotation ICTV International Committee on Taxonomy of Viruses Lloviu virus Marburg virus marburgvirus mononegavirad Mononegavirales mononegavirus Ravn virus RefSeq Reston virus reverse genetics Sudan virus Taï Forest virus virus classification virus isolate virus nomenclature virus strain virus taxonomy virus variant |
| url |
http://www.mdpi.com/1999-4915/6/9/3663 |
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doaj-cd8d703b13bb4068a4fb369e9a6db0992020-11-24T21:29:10ZengMDPI AGViruses1999-49152014-09-01693663368210.3390/v6093663v6093663Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and NamesJens H. Kuhn0Kristian G. Andersen1Yīmíng Bào2Sina Bavari3Stephan Becker4Richard S. Bennett5Nicholas H. Bergman6Olga Blinkova7Steven Bradfute8J. Rodney Brister9Alexander Bukreyev10Kartik Chandran11Alexander A. Chepurnov12Robert A. Davey13Ralf G. Dietzgen14Norman A. Doggett15Olga Dolnik16John M. Dye17Sven Enterlein18Paul W. Fenimore19Pierre Formenty20Alexander N. Freiberg21Robert F. Garry22Nicole L. Garza23Stephen K. Gire24Jean-Paul Gonzalez25Anthony Griffiths26Christian T. Happi27Lisa E. Hensley28Andrew S. Herbert29Michael C. Hevey30Thomas Hoenen31Anna N. Honko32Georgy M. Ignatyev33Peter B. Jahrling34Joshua C. Johnson35Karl M. Johnson36Jason Kindrachuk37Hans-Dieter Klenk38Gary Kobinger39Tadeusz J. Kochel40Matthew G. Lackemeyer41Daniel F. Lackner42Eric M. Leroy43Mark S. Lever44Elke Mühlberger45Sergey V. Netesov46Gene G. Olinger47Sunday A. Omilabu48Gustavo Palacios49Rekha G. Panchal50Daniel J. Park51Jean L. Patterson52Janusz T. Paweska53Clarence J. Peters54James Pettitt55Louise Pitt56Sheli R. Radoshitzky57Elena I. Ryabchikova58Erica Ollmann Saphire59Pardis C. Sabeti60Rachel Sealfon61Aleksandr M. Shestopalov62Sophie J. Smither63Nancy J. Sullivan64Robert Swanepoel65Ayato Takada66Jonathan S. Towner67Guido van der Groen68Viktor E. Volchkov69Valentina A. Volchkova70Victoria Wahl-Jensen71Travis K. Warren72Kelly L. Warfield73Manfred Weidmann74Stuart T. Nichol75Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USAFAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USAInformation Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USAUnited States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USAInstitut für Virologie, Philipps-Universität Marburg, 35043 Marburg, GermanyNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USANational Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USAInformation Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USAUniversity of New Mexico, Albuquerque, NM 87131, USAInformation Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USADepartment of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USADepartment of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USAInstitute of Clinical Immunology, Russian Academy of Science, Siberian Branch, Novosibirsk, Novosibirsk Oblast, 630091, RussiaDepartment of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USAQueensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, AustraliaLos Alamos National Laboratory, Los Alamos, NM 87545, USAInstitut für Virologie, Philipps-Universität Marburg, 35043 Marburg, GermanyUnited States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USAIntegrated BioTherapeutics, Inc., Gaithersburg, MD 20878, USALos Alamos National Laboratory, Los Alamos, NM 87545, USAWorld Health Organization, 1211 Geneva, SwitzerlandDepartment of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USADepartment of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USAUnited States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USAFAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USAMetabiota, Inc., San Francisco, CA 94104, USADepartment of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USADepartment of Biological Sciences, College of Natural Sciences, and African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Lagos-Ibadan, Ogun State, NigeriaIntegrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USAUnited States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USANational Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USALaboratory for Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840 USAIntegrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USAFederal State Unitary Company "Microgen Scientific Industrial Company for Immunobiological Medicines", Ministry of Health of the Russian Federation, Moscow, 115088,RussiaIntegrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USAIntegrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USAPortland, OR 97222, USAIntegrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USAInstitut für Virologie, Philipps-Universität Marburg, 35043 Marburg, GermanySpecial Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2, CanadaNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USAIntegrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USANational Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USACentre International de Recherches Médicales de Franceville, B. P. 769, Franceville, GabonBiomedical Sciences Department, Dstl, Porton Down, Salisbury, Wiltshire SP4 0JQ, UKDepartment of Microbiology and National Emerging Infectious Diseases Laboratory, Boston University School of Medicine, Boston, MA 02118, USAResearch Center of Clinical and Experimental Medicine, Novosibirsk, Novosibirsk Region, 630090, RussiaIntegrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USADepartment of Medical Microbiology and Parasitology, College of Medicine of the University of Lagos, Idi-Araba, Private Mail Bag 12003, Lagos, NigeriaUnited States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USAUnited States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USAThe Broad Institute, Cambridge, MA 02142, USADepartment of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78227, USACenter for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg 2192, Gauteng, South AfricaDepartment of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USAIntegrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USAUnited States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USAUnited States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USAInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Novosibirsk Region, 630090, RussiaDepartment of Immunology and Microbial Science and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USAFAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USAComputer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USAResearch Center of Clinical and Experimental Medicine, Novosibirsk, Novosibirsk Region, 630090, RussiaBiomedical Sciences Department, Dstl, Porton Down, Salisbury, Wiltshire SP4 0JQ, UKVaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USAZoonoses Research Unit, University of Pretoria, Private bag X20 Hatfield, Pretoria 0028, South AfricaDivision of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Kita-ku, Sapporo, JapanViral Special Pathogens Branch, Division of High-Consequence Pathogens Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USAPrins Leopold Instituut voor Tropische Geneeskunde, 2000 Antwerp, BelgiumLaboratory of Molecular basis of viral pathogenicity, CIRI, Inserm U1111, Université de Lyon, UCB-Lyon-1, Ecole-Normale-Supérieure de Lyon, 69365 Lyon cedex 07, FranceLaboratory of Molecular basis of viral pathogenicity, CIRI, Inserm U1111, Université de Lyon, UCB-Lyon-1, Ecole-Normale-Supérieure de Lyon, 69365 Lyon cedex 07, FranceNational Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USAUnited States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USAUnither Virology, LLC, Silver Spring, MD 20910, USAInstitute of Aquaculture, University of Stirling FK9 4LA, UKViral Special Pathogens Branch, Division of High-Consequence Pathogens Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USASequence determination of complete or coding-complete genomes of viruses is becoming common practice for supporting the work of epidemiologists, ecologists, virologists, and taxonomists. Sequencing duration and costs are rapidly decreasing, sequencing hardware is under modification for use by non-experts, and software is constantly being improved to simplify sequence data management and analysis. Thus, analysis of virus disease outbreaks on the molecular level is now feasible, including characterization of the evolution of individual virus populations in single patients over time. The increasing accumulation of sequencing data creates a management problem for the curators of commonly used sequence databases and an entry retrieval problem for end users. Therefore, utilizing the data to their fullest potential will require setting nomenclature and annotation standards for virus isolates and associated genomic sequences. The National Center for Biotechnology Information’s (NCBI’s) RefSeq is a non-redundant, curated database for reference (or type) nucleotide sequence records that supplies source data to numerous other databases. Building on recently proposed templates for filovirus variant naming [<virus name> (<strain>)/<isolation host-suffix>/<country of sampling>/<year of sampling>/<genetic variant designation>-<isolate designation>], we report consensus decisions from a majority of past and currently active filovirus experts on the eight filovirus type variants and isolates to be represented in RefSeq, their final designations, and their associated sequences.http://www.mdpi.com/1999-4915/6/9/3663Bundibugyo viruscDNA clonecuevavirusEbolaEbola virusebolavirusfiloviridFiloviridaefilovirusgenome annotationICTVInternational Committee on Taxonomy of VirusesLloviu virusMarburg virusmarburgvirusmononegaviradMononegaviralesmononegavirusRavn virusRefSeqReston virusreverse geneticsSudan virusTaï Forest virusvirus classificationvirus isolatevirus nomenclaturevirus strainvirus taxonomyvirus variant |