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Viruses. 2017 May 11;9(5). pii: E106. doi: 10.3390/v9050106.

Implementation of Objective PASC-Derived Taxon Demarcation Criteria for Official Classification of Filoviruses.

Author information

1
BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. baoym@big.ac.cn.
2
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA. GAmarasinghe@path.wustl.edu.
3
Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30302-3965, USA. cbasler@gsu.edu.
4
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702-5011, USA. sina.bavari.civ@mail.mil.
5
Department of Pathology, The University of Texas Medical Branch, Galveston, TX 77555-0144, USA. alexander.bukreyev@utmb.edu.
6
Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA. kartik.chandran@einstein.yu.edu.
7
Institute of Virology, Philipps University Marburg, 35032 Marburg, Germany. Dolnik@staff.uni-marburg.de.
8
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702-5011, USA. john.m.dye1.civ@mail.mil.
9
Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA. Ebihara.Hideki@mayo.edu.
10
World Health Organization, 1211 Geneva, Switzerland. formentyp@who.int.
11
Public Health England, Porton Down, Wiltshire, Salisbury SP4 0JG, UK. Roger.Hewson@phe.gov.uk.
12
Department of Microbiology, Immunology & Infectious Diseases, Université Laval, Quebec City, QC G1V 0A6, Canada. gary.kobinger@crchudequebec.ulaval.ca.
13
Centre International de Recherches Médicales de Franceville, Institut de Recherche pour le Développement, BP 769 Franceville, Gabon. eric.leroy@ird.fr.
14
Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA. muehlber@bu.edu.
15
Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia 630090. netesov.s@nsu.ru.
16
Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78245-0549, USA. jpatters@TxBiomed.org.
17
Center for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg 2131, Gauteng, South Africa. januszp@nicd.ac.za.
18
Chemical, Biological and Radiological Division, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK. SJSMITHER@mail.dstl.gov.uk.
19
Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Sapporo 001-0020, Japan. atakada@czc.hokudai.ac.jp.
20
Viral 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 30329-4027, USA. jit8@cdc.gov.
21
Molecular Basis of Viral Pathogenicity, CIRI, INSERM U1111-CNRS UMR5308, Université de Lyon, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Lyon 69007, France. viktor.volchkov@inserm.fr.
22
National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA. victoria.jensen@nbacc.dhs.gov.
23
Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA. kuhnjens@mail.nih.gov.

Abstract

The mononegaviral family Filoviridae has eight members assigned to three genera and seven species. Until now, genus and species demarcation were based on arbitrarily chosen filovirus genome sequence divergence values (≈50% for genera, ≈30% for species) and arbitrarily chosen phenotypic virus or virion characteristics. Here we report filovirus genome sequence-based taxon demarcation criteria using the publicly accessible PAirwise Sequencing Comparison (PASC) tool of the US National Center for Biotechnology Information (Bethesda, MD, USA). Comparison of all available filovirus genomes in GenBank using PASC revealed optimal genus demarcation at the 55-58% sequence diversity threshold range for genera and at the 23-36% sequence diversity threshold range for species. Because these thresholds do not change the current official filovirus classification, these values are now implemented as filovirus taxon demarcation criteria that may solely be used for filovirus classification in case additional data are absent. A near-complete, coding-complete, or complete filovirus genome sequence will now be required to allow official classification of any novel "filovirus." Classification of filoviruses into existing taxa or determining the need for novel taxa is now straightforward and could even become automated using a presented algorithm/flowchart rooted in RefSeq (type) sequences.

KEYWORDS:

Ebola; Filoviridae; ICTV; Mononegavirales; cuevavirus; ebolavirus; filovirus; marburgvirus; virus classification; virus taxonomy

PMID:
28492506
PMCID:
PMC5454419
DOI:
10.3390/v9050106
[Indexed for MEDLINE]
Free PMC Article

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