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Filovirus RefSeq entries: evaluation and selection of filovirus type variants, type sequences, and names

Academic Article
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Overview

authors

  • Kuhn, J. H.
  • Andersen, Kristian G.
  • Bao, Y.
  • Bavari, S.
  • Becker, S.
  • Bennett, R. S.
  • Bergman, N. H.
  • Blinkova, O.
  • Bradfute, S.
  • Brister, J. R.
  • Bukreyev, A.
  • Chandran, K.
  • Chepurnov, A. A.
  • Davey, R. A.
  • Dietzgen, R. G.
  • Doggett, N. A.
  • Dolnik, O.
  • Dye, J. M.
  • Enterlein, S.
  • Fenimore, P. W.
  • Formenty, P.
  • Freiberg, A. N.
  • Garry, R. F.
  • Garza, N. L.
  • Gire, S. K.
  • Gonzalez, J. P.
  • Griffiths, A.
  • Happi, C. T.
  • Hensley, L. E.
  • Herbert, A. S.
  • Hevey, M. C.
  • Hoenen, T.
  • Honko, A. N.
  • Ignatyev, G. M.
  • Jahrling, P. B.
  • Johnson, J. C.
  • Johnson, K. M.
  • Kindrachuk, J.
  • Klenk, H. D.
  • Kobinger, G.
  • Kochel, T. J.
  • Lackemeyer, M. G.
  • Lackner, D. F.
  • Leroy, E. M.
  • Lever, M. S.
  • Muhlberger, E.
  • Netesov, S. V.
  • Olinger, G. G.
  • Omilabu, S. A.
  • Palacios, G.
  • Panchal, R. G.
  • Park, D. J.
  • Patterson, J. L.
  • Paweska, J. T.
  • Peters, C. J.
  • Pettitt, J.
  • Pitt, L.
  • Radoshitzky, S. R.
  • Ryabchikova, E. I.
  • Saphire, Erica Ollmann
  • Sabeti, P. C.
  • Sealfon, R.
  • Shestopalov, A. M.
  • Smither, S. J.
  • Sullivan, N. J.
  • Swanepoel, R.
  • Takada, A.
  • Towner, J. S.
  • van der Groen, G.
  • Volchkov, V. E.
  • Volchkova, V. A.
  • Wahl-Jensen, V.
  • Warren, T. K.
  • Warfield, K. L.
  • Weidmann, M.
  • Nichol, S. T.

publication date

  • September 2014

journal

  • Viruses-Basel  Journal

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 [ ()////-], 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.

subject areas

  • Databases, Nucleic Acid
  • Evolution, Molecular
  • Filoviridae
  • Humans
  • Selection, Genetic
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Research

keywords

  • Bundibugyo virus
  • Ebola
  • Ebola virus
  • Filoviridae
  • ICTV
  • International Committee on Taxonomy of Viruses
  • Lloviu virus
  • Marburg virus
  • Mononegavirales
  • Ravn virus
  • RefSeq
  • Reston virus
  • Sudan virus
  • Tai Forest virus
  • cDNA clone
  • cuevavirus
  • ebolavirus
  • filovirid
  • filovirus
  • genome annotation
  • marburgvirus
  • mononegavirad
  • mononegavirus
  • reverse genetics
  • virus classification
  • virus isolate
  • virus nomenclature
  • virus strain
  • virus taxonomy
  • virus variant
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Identity

PubMed Central ID

  • PMC4189044

International Standard Serial Number (ISSN)

  • 1999-4915

Digital Object Identifier (DOI)

  • 10.3390/v6093663

PubMed ID

  • 25256396
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Additional Document Info

start page

  • 3663

end page

  • 3682

volume

  • 6

issue

  • 9

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