Format

Send to:

Choose Destination
See comment in PubMed Commons below
Viruses. 2014 Sep 26;6(9):3663-82. doi: 10.3390/v6093663.

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

Author information

  • 1Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. kuhnjens@mail.nih.gov.
  • 2FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. kandersen@oeb.harvard.edu.
  • 3Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. bao@ncbi.nlm.nih.gov.
  • 4United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. sina.bavari.civ@mail.mil.
  • 5Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany. becker@staff.uni-marburg.de.
  • 6National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA. richard.bennett@nbacc.dhs.gov.
  • 7National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA. nicholas.bergman@nbacc.dhs.gov.
  • 8Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. olga.blinkova@nih.gov.
  • 9University of New Mexico, Albuquerque, NM 87131, USA. steven_bradfute@yahoo.com.
  • 10Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. jamesbr@ncbi.nlm.nih.gov.
  • 11Department of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA. alexander.bukreyev@utmb.edu.
  • 12Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA. kartik.chandran@einstein.yu.edu.
  • 13Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. alexa.che.purnov@gmail.com.
  • 14Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. rdavey@txbiomed.org.
  • 15Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. r.dietzgen@uq.edu.au.
  • 16Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. doggett@lanl.gov.
  • 17Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany. Dolnik@staff.uni-marburg.de.
  • 18United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. john.m.dye1.civ@mail.mil.
  • 19Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. sven.enterlein@gmail.com.
  • 20Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. paulf@lanl.gov.
  • 21Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. formentyp@who.int.
  • 22Department of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA. anfreibe@utmb.edu.
  • 23Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. steven_bradfute@yahoo.com.
  • 24United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. Nicole.l.lackemeyer.ctr@mail.mil.
  • 25FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. sgire@oeb.harvard.edu.
  • 26Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. : jpgonzalez@metabiota.com.
  • 27Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. agriffiths@txbiomed.org.
  • 28Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. chappi@hsph.harvard.edu.
  • 29Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. lisa.hensley@nih.gov.
  • 30United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. anderw.s.herbert.ctr@mail.mil.
  • 31National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA. michael.hevey@nbacc.dhs.gov.
  • 32Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. kartik.chandran@einstein.yu.edu.
  • 33Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. anna.honko@nih.gov.
  • 34FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. g.m.ignatyev@microgen.ru.
  • 35Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. jahrlingp@niaid.nih.gov.
  • 36Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. joshua.johnson@nih.gov.
  • 37FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. microcaddis@gmail.com.
  • 38Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. kindrachuk.kenneth@nih.gov.
  • 39Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany. klenk@mailer.uni-marburg.de.
  • 40FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. gary.kobinger@phac-aspc.gc.ca.
  • 41National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA. tadeusz.kochel@nbacc.dhs.gov.
  • 42Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. matthew.lackemeyer@nih.gov.
  • 43National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA. daniel.lackner@nbacc.dhs.gov
  • 44FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. eric.leroy@ird.fr.
  • 45FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. mslever@mail.dstl.gov.uk.
  • 46FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. muehlber@bu.edu.
  • 47FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. nauka@nsu.ru.
  • 48Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. gene.olinger@nih.gov.
  • 49FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. steven_bradfute@yahoo.com.
  • 50United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. gustavo.f.palacios.ctr@us.army.mil.
  • 51United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. rekha.g.panchal.civ@mail.mil.
  • 52FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. dpark@broadinstitute.org.
  • 53Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. jpatters@txbiomed.org.
  • 54FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. kartik.chandran@einstein.yu.edu.
  • 55Department of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA. cjpeters@UTMB.EDU.
  • 56Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA. james.pettitt@nih.gov.
  • 57United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. louise.pitt@us.army.mil.
  • 58United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. sheli.r.radoshitzky.ctr@mail.mil.
  • 59Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. lenryab@yandex.com.
  • 60Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. erica@scripps.edu.
  • 61FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. pardis@broadinstitute.org.
  • 62Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. sealfon@gmail.com.
  • 63Novosibirsk State University, Novosibirsk, Novosibirsk Region, Russia, 630090. shestopalov2@mail.ru
  • 64FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. SJSMITHER@mail.dstl.gov.uk.
  • 65Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. njsull@mail.nih.gov.
  • 66Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. bobswanepoel@gmail.com.
  • 67Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. atakada@czc.hokudai.ac.jp.
  • 68Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. jit8@cdc.gov.
  • 69Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. steven_bradfute@yahoo.com.
  • 70Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. viktor.volchkov@inserm.fr.
  • 71Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. valentina.volchkova@inserm.fr.
  • 72National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA. victoria.jensen@nbacc.dhs.gov.
  • 73United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. travis.k.warren.ctr@mail.mil.
  • 74Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. kartik.chandran@einstein.yu.edu.
  • 75United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. m.w.weidmann@stir.ac.uk.
  • 76IViral 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, USA. stn1@cdc.gov.

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.

PMID:
25256396
[PubMed - indexed for MEDLINE]
PMCID:
PMC4189044
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Multidisciplinary Digital Publishing Institute (MDPI) Icon for PubMed Central
    Loading ...
    Write to the Help Desk