Viruses 2017, 9(5), 106; https://doi.org/10.3390/v9050106
Implementation of Objective PASC-Derived Taxon Demarcation Criteria for Official Classification of Filoviruses
Yīmíng Bào 1, Gaya K. Amarasinghe 2,†, Christopher F. Basler 3,†, Sina Bavari 4,†, Alexander Bukreyev 5,†, Kartik Chandran 6,†, Olga Dolnik 7,†, John M. Dye 4,†, Hideki Ebihara 8,†, Pierre Formenty 9,†
, Roger Hewson 10,†, Gary P. Kobinger 11,†, Eric M. Leroy 12,†, Elke Mühlberger 13,†, Sergey V. Netesov 14,†, Jean L. Patterson 15,†, Janusz T. Paweska 16,†, Sophie J. Smither 17,†, Ayato Takada 18,†, Jonathan S. Towner 19,†, Viktor E. Volchkov 20,†, Victoria Wahl-Jensen 21,† and Jens H. Kuhn 22,*,†
, Roger Hewson 10,†, Gary P. Kobinger 11,†, Eric M. Leroy 12,†, Elke Mühlberger 13,†, Sergey V. Netesov 14,†, Jean L. Patterson 15,†, Janusz T. Paweska 16,†, Sophie J. Smither 17,†, Ayato Takada 18,†, Jonathan S. Towner 19,†, Viktor E. Volchkov 20,†, Victoria Wahl-Jensen 21,† and Jens H. Kuhn 22,*,†
1
BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
2
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
3
Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30302-3965, USA
4
United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702-5011, USA
5
Department of Pathology, The University of Texas Medical Branch, Galveston, TX 77555-0144, USA
6
Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
7
Institute of Virology, Philipps University Marburg, 35032 Marburg, Germany
8
Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
9
World Health Organization, 1211 Geneva, Switzerland
10
Public Health England, Porton Down, Wiltshire, Salisbury SP4 0JG, UK
11
Department of Microbiology, Immunology & Infectious Diseases, Université Laval, Quebec City, QC G1V 0A6, Canada
12
Centre International de Recherches Médicales de Franceville, Institut de Recherche pour le Développement, BP 769 Franceville, Gabon
13
Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
14
Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia 630090
15
Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX 78245-0549, USA
16
Center for Emerging and Zoonotic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg 2131, Gauteng, South Africa
17
Chemical, Biological and Radiological Division, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
18
Division of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Sapporo 001-0020, Japan
19
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
20
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
21
National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD 21702, USA
22
Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
*
Author to whom correspondence should be addressed.
†
The members of the International Committee on Taxonomy of Viruses (ICTV) Filoviridae Study Group.
Academic Editor: Eric O. Freed
Received: 26 April 2017 / Revised: 26 April 2017 / Accepted: 2 May 2017 / Published: 11 May 2017
(This article belongs to the Collection Advances in Ebolavirus, Marburgvirus, and Cuevavirus Research)
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. View Full-TextKeywords:
cuevavirus; Ebola; ebolavirus; Filoviridae; filovirus; marburgvirus; Mononegavirales; virus taxonomy; virus classification; ICTV
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Bào, Y.; Amarasinghe, G.K.; Basler, C.F.; Bavari, S.; Bukreyev, A.; Chandran, K.; Dolnik, O.; Dye, J.M.; Ebihara, H.; Formenty, P.; Hewson, R.; Kobinger, G.P.; Leroy, E.M.; Mühlberger, E.; Netesov, S.V.; Patterson, J.L.; Paweska, J.T.; Smither, S.J.; Takada, A.; Towner, J.S.; Volchkov, V.E.; Wahl-Jensen, V.; Kuhn, J.H. Implementation of Objective PASC-Derived Taxon Demarcation Criteria for Official Classification of Filoviruses. Viruses 2017, 9, 106.
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