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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

1
Integrated 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.
2
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. kandersen@oeb.harvard.edu.
3
Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. bao@ncbi.nlm.nih.gov.
4
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. sina.bavari.civ@mail.mil.
5
Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany. becker@staff.uni-marburg.de.
6
National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA. richard.bennett@nbacc.dhs.gov.
7
National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA. nicholas.bergman@nbacc.dhs.gov.
8
Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. olga.blinkova@nih.gov.
9
University of New Mexico, Albuquerque, NM 87131, USA. steven_bradfute@yahoo.com.
10
Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. jamesbr@ncbi.nlm.nih.gov.
11
Department of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA. alexander.bukreyev@utmb.edu.
12
Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA. kartik.chandran@einstein.yu.edu.
13
Integrated 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.
14
Integrated 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.
15
Integrated 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.
16
Integrated 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.
17
Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany. Dolnik@staff.uni-marburg.de.
18
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. john.m.dye1.civ@mail.mil.
19
Integrated 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.
20
Integrated 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.
21
Integrated 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.
22
Department of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA. anfreibe@utmb.edu.
23
Integrated 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.
24
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. Nicole.l.lackemeyer.ctr@mail.mil.
25
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. sgire@oeb.harvard.edu.
26
Integrated 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.
27
Integrated 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.
28
Integrated 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.
29
Integrated 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.
30
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. anderw.s.herbert.ctr@mail.mil.
31
National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA. michael.hevey@nbacc.dhs.gov.
32
Integrated 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.
33
Integrated 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.
34
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. g.m.ignatyev@microgen.ru.
35
Integrated 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.
36
Integrated 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.
37
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. microcaddis@gmail.com.
38
Integrated 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.
39
Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany. klenk@mailer.uni-marburg.de.
40
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. gary.kobinger@phac-aspc.gc.ca.
41
National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA. tadeusz.kochel@nbacc.dhs.gov.
42
Integrated 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.
43
National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA. daniel.lackner@nbacc.dhs.gov
44
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. eric.leroy@ird.fr.
45
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. mslever@mail.dstl.gov.uk.
46
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. muehlber@bu.edu.
47
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. nauka@nsu.ru.
48
Integrated 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.
49
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. steven_bradfute@yahoo.com.
50
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. gustavo.f.palacios.ctr@us.army.mil.
51
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. rekha.g.panchal.civ@mail.mil.
52
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. dpark@broadinstitute.org.
53
Integrated 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.
54
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. kartik.chandran@einstein.yu.edu.
55
Department of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA. cjpeters@UTMB.EDU.
56
Integrated 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.
57
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. louise.pitt@us.army.mil.
58
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. sheli.r.radoshitzky.ctr@mail.mil.
59
Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. lenryab@yandex.com.
60
Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. erica@scripps.edu.
61
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. pardis@broadinstitute.org.
62
Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. sealfon@gmail.com.
63
Novosibirsk State University, Novosibirsk, Novosibirsk Region, Russia, 630090. shestopalov2@mail.ru
64
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA. SJSMITHER@mail.dstl.gov.uk.
65
Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. njsull@mail.nih.gov.
66
Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. bobswanepoel@gmail.com.
67
Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. atakada@czc.hokudai.ac.jp.
68
Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. jit8@cdc.gov.
69
Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. steven_bradfute@yahoo.com.
70
Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. viktor.volchkov@inserm.fr.
71
Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. valentina.volchkova@inserm.fr.
72
National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA. victoria.jensen@nbacc.dhs.gov.
73
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. travis.k.warren.ctr@mail.mil.
74
Information Engineering Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. kartik.chandran@einstein.yu.edu.
75
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA. m.w.weidmann@stir.ac.uk.
76
IViral 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
PMCID:
PMC4189044
DOI:
10.3390/v6093663
[Indexed for MEDLINE]
Free PMC Article

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