Filovirus refseq entries: Evaluation and selection of filovirus type variants, Type sequences, And names

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. FenimorePierre 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

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)3663-3682
Number of pages20
JournalViruses
Volume6
Issue number9
DOIs
StatePublished - 2014

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Names
Databases
Viruses
Information Centers
Information Storage and Retrieval
Virus Diseases
Biotechnology
Terminology
Disease Outbreaks
Sequence Analysis
Software
Genome
Costs and Cost Analysis
Population
Epidemiologists

Keywords

  • 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

ASJC Scopus subject areas

  • Infectious Diseases
  • Virology

Cite this

Kuhn, J. H., Andersen, K. G., Bào, Y., Bavari, S., Becker, S., Bennett, R. S., ... Nichol, S. T. (2014). Filovirus refseq entries: Evaluation and selection of filovirus type variants, Type sequences, And names. Viruses, 6(9), 3663-3682. https://doi.org/10.3390/v6093663

Filovirus refseq entries : Evaluation and selection of filovirus type variants, Type sequences, And names. / Kuhn, Jens H.; Andersen, Kristian G.; Bào, Yīmíng; Bavari, Sina; Becker, Stephan; Bennett, Richard S.; Bergman, Nicholas H.; Blinkova, Olga; Bradfute, Steven; Rodney Brister, J.; Bukreyev, Alexander; Chandran, Kartik; Chepurnov, Alexander A.; Davey, Robert A.; Dietzgen, Ralf G.; Doggett, Norman A.; Dolnik, Olga; Dye, John M.; Enterlein, Sven; Fenimore, Paul W.; Formenty, Pierre; Freiberg, Alexander N.; Garry, Robert F.; Garza, Nicole L.; Gire, Stephen K.; Gonzalez, Jean Paul; Griffiths, Anthony; Happi, Christian T.; Hensley, Lisa E.; Herbert, Andrew S.; Hevey, Michael C.; Hoenen, Thomas; Honko, Anna N.; Ignatyev, Georgy M.; Jahrling, Peter B.; Johnson, Joshua C.; Johnson, Karl M.; Kindrachuk, Jason; Klenk, Hans Dieter; Kobinger, Gary; Kochel, Tadeusz J.; Lackemeyer, Matthew G.; Lackner, Daniel F.; Leroy, Eric M.; Lever, Mark S.; Mühlberger, Elke; Netesov, Sergey V.; Olinger, Gene G.; Omilabu, Sunday A.; Palacios, Gustavo; Panchal, Rekha G.; Park, Daniel J.; Patterson, Jean L.; Paweska, Janusz T.; Peters, Clarence J.; Pettitt, James; Pitt, Louise; Radoshitzky, Sheli R.; Ryabchikova, Elena I.; Saphire, Erica Ollmann; Sabeti, Pardis C.; Sealfon, Rachel; Shestopalov, Aleksandr M.; Smither, Sophie J.; Sullivan, Nancy J.; Swanepoel, Robert; Takada, Ayato; Towner, Jonathan S.; Van Der Groen, Guido; Volchkov, Viktor E.; Volchkova, Valentina A.; Wahl-Jensen, Victoria; Warren, Travis K.; Warfield, Kelly L.; Weidmann, Manfred; Nichol, Stuart T.

In: Viruses, Vol. 6, No. 9, 2014, p. 3663-3682.

Research output: Contribution to journalArticle

Kuhn, JH, Andersen, KG, Bào, Y, Bavari, S, Becker, S, Bennett, RS, Bergman, NH, Blinkova, O, Bradfute, S, Rodney Brister, J, Bukreyev, A, Chandran, K, Chepurnov, AA, Davey, RA, Dietzgen, RG, Doggett, NA, Dolnik, O, Dye, JM, Enterlein, S, Fenimore, PW, Formenty, P, Freiberg, AN, Garry, RF, Garza, NL, Gire, SK, Gonzalez, JP, Griffiths, A, Happi, CT, Hensley, LE, Herbert, AS, Hevey, MC, Hoenen, T, Honko, AN, Ignatyev, GM, Jahrling, PB, Johnson, JC, Johnson, KM, Kindrachuk, J, Klenk, HD, Kobinger, G, Kochel, TJ, Lackemeyer, MG, Lackner, DF, Leroy, EM, Lever, MS, Mühlberger, E, Netesov, SV, Olinger, GG, Omilabu, SA, Palacios, G, Panchal, RG, Park, DJ, Patterson, JL, Paweska, JT, Peters, CJ, Pettitt, J, Pitt, L, Radoshitzky, SR, Ryabchikova, EI, Saphire, EO, Sabeti, PC, Sealfon, R, Shestopalov, AM, Smither, SJ, Sullivan, NJ, Swanepoel, R, Takada, A, Towner, JS, Van Der Groen, G, Volchkov, VE, Volchkova, VA, Wahl-Jensen, V, Warren, TK, Warfield, KL, Weidmann, M & Nichol, ST 2014, 'Filovirus refseq entries: Evaluation and selection of filovirus type variants, Type sequences, And names', Viruses, vol. 6, no. 9, pp. 3663-3682. https://doi.org/10.3390/v6093663
Kuhn, Jens H. ; Andersen, Kristian G. ; Bào, Yīmíng ; Bavari, Sina ; Becker, Stephan ; Bennett, Richard S. ; Bergman, Nicholas H. ; Blinkova, Olga ; Bradfute, Steven ; Rodney Brister, J. ; Bukreyev, Alexander ; Chandran, Kartik ; Chepurnov, Alexander A. ; Davey, Robert A. ; Dietzgen, Ralf G. ; Doggett, Norman A. ; Dolnik, Olga ; Dye, John M. ; Enterlein, Sven ; Fenimore, Paul W. ; Formenty, Pierre ; Freiberg, Alexander N. ; Garry, Robert F. ; Garza, Nicole L. ; Gire, Stephen K. ; Gonzalez, Jean Paul ; Griffiths, Anthony ; Happi, Christian T. ; Hensley, Lisa E. ; Herbert, Andrew S. ; Hevey, Michael C. ; Hoenen, Thomas ; Honko, Anna N. ; Ignatyev, Georgy M. ; Jahrling, Peter B. ; Johnson, Joshua C. ; Johnson, Karl M. ; Kindrachuk, Jason ; Klenk, Hans Dieter ; Kobinger, Gary ; Kochel, Tadeusz J. ; Lackemeyer, Matthew G. ; Lackner, Daniel F. ; Leroy, Eric M. ; Lever, Mark S. ; Mühlberger, Elke ; Netesov, Sergey V. ; Olinger, Gene G. ; Omilabu, Sunday A. ; Palacios, Gustavo ; Panchal, Rekha G. ; Park, Daniel J. ; Patterson, Jean L. ; Paweska, Janusz T. ; Peters, Clarence J. ; Pettitt, James ; Pitt, Louise ; Radoshitzky, Sheli R. ; Ryabchikova, Elena I. ; Saphire, Erica Ollmann ; Sabeti, Pardis C. ; Sealfon, Rachel ; Shestopalov, Aleksandr M. ; Smither, Sophie J. ; Sullivan, Nancy J. ; Swanepoel, Robert ; Takada, Ayato ; Towner, Jonathan S. ; Van Der Groen, Guido ; Volchkov, Viktor E. ; Volchkova, Valentina A. ; Wahl-Jensen, Victoria ; Warren, Travis K. ; Warfield, Kelly L. ; Weidmann, Manfred ; Nichol, Stuart T. / Filovirus refseq entries : Evaluation and selection of filovirus type variants, Type sequences, And names. In: Viruses. 2014 ; Vol. 6, No. 9. pp. 3663-3682.
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T1 - Filovirus refseq entries

T2 - Evaluation and selection of filovirus type variants, Type sequences, And names

AU - Kuhn, Jens H.

AU - Andersen, Kristian G.

AU - Bào, Yīmíng

AU - Bavari, Sina

AU - Becker, Stephan

AU - Bennett, Richard S.

AU - Bergman, Nicholas H.

AU - Blinkova, Olga

AU - Bradfute, Steven

AU - Rodney Brister, J.

AU - Bukreyev, Alexander

AU - Chandran, Kartik

AU - Chepurnov, Alexander A.

AU - Davey, Robert A.

AU - Dietzgen, Ralf G.

AU - Doggett, Norman A.

AU - Dolnik, Olga

AU - Dye, John M.

AU - Enterlein, Sven

AU - Fenimore, Paul W.

AU - Formenty, Pierre

AU - Freiberg, Alexander N.

AU - Garry, Robert F.

AU - Garza, Nicole L.

AU - Gire, Stephen K.

AU - Gonzalez, Jean Paul

AU - Griffiths, Anthony

AU - Happi, Christian T.

AU - Hensley, Lisa E.

AU - Herbert, Andrew S.

AU - Hevey, Michael C.

AU - Hoenen, Thomas

AU - Honko, Anna N.

AU - Ignatyev, Georgy M.

AU - Jahrling, Peter B.

AU - Johnson, Joshua C.

AU - Johnson, Karl M.

AU - Kindrachuk, Jason

AU - Klenk, Hans Dieter

AU - Kobinger, Gary

AU - Kochel, Tadeusz J.

AU - Lackemeyer, Matthew G.

AU - Lackner, Daniel F.

AU - Leroy, Eric M.

AU - Lever, Mark S.

AU - Mühlberger, Elke

AU - Netesov, Sergey V.

AU - Olinger, Gene G.

AU - Omilabu, Sunday A.

AU - Palacios, Gustavo

AU - Panchal, Rekha G.

AU - Park, Daniel J.

AU - Patterson, Jean L.

AU - Paweska, Janusz T.

AU - Peters, Clarence J.

AU - Pettitt, James

AU - Pitt, Louise

AU - Radoshitzky, Sheli R.

AU - Ryabchikova, Elena I.

AU - Saphire, Erica Ollmann

AU - Sabeti, Pardis C.

AU - Sealfon, Rachel

AU - Shestopalov, Aleksandr M.

AU - Smither, Sophie J.

AU - Sullivan, Nancy J.

AU - Swanepoel, Robert

AU - Takada, Ayato

AU - Towner, Jonathan S.

AU - Van Der Groen, Guido

AU - Volchkov, Viktor E.

AU - Volchkova, Valentina A.

AU - Wahl-Jensen, Victoria

AU - Warren, Travis K.

AU - Warfield, Kelly L.

AU - Weidmann, Manfred

AU - Nichol, Stuart T.

PY - 2014

Y1 - 2014

N2 - 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 [ ()////-], 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.

AB - 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 [ ()////-], 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.

KW - Bundibugyo virus

KW - cDNA clone

KW - Cuevavirus

KW - Ebola

KW - Ebola virus

KW - Ebolavirus

KW - Filovirid

KW - Filoviridae

KW - Filovirus

KW - Genome annotation

KW - ICTV

KW - International Committee on Taxonomy of Viruses

KW - Lloviu virus

KW - Marburg virus

KW - Marburgvirus

KW - Mononegavirad

KW - Mononegavirales

KW - Mononegavirus

KW - Ravn virus

KW - RefSeq

KW - Reston virus

KW - Reverse genetics

KW - Sudan virus

KW - Taï Forest virus

KW - Virus classification

KW - Virus isolate

KW - Virus nomenclature

KW - Virus strain

KW - Virus taxonomy

KW - Virus variant

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U2 - 10.3390/v6093663

DO - 10.3390/v6093663

M3 - Article

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VL - 6

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JO - Viruses

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