CLASSIFICATION OF VIRUSES
- Early efforts were concentrated on the pathogenic properties, organ tropisms, ecological and transmission characteristics.
- Bawden (1940's) for the first time proposed that viruses be grouped on the basis of shared virion properties. Included were Herpesvirus, Myxovirus, Poxvirus and some plant filamentous viruses.
- Several individuals and committees independently advanced classification schemes resulting in confusion overcompeting, conflicting schemes.
- It became clear (and it is now) that virus classification and nomenclature are topics that give riseto very strongly held opinions.
"The world, said Paul Valery, is equally threatened with two catastrophes: order and disorder. So is virology."
The International Committee on Nomenclature of Viruses (ICNV) Became the International Committee on Taxonomy of Viruses (ICTV)
- It operates under the auspices of the Virology Division of the International Union of Microbiological Societies.
- It has six subcommittees, 45 study groups, and over 500 participating virologists.
- Created in 1973 from the need for a universal taxonomic system.
- Virion characteristics are considered and weighted as criteria for making divisions into families, in some casessub-families, and genera.
- Does not consider phylogenetic relationships. Viruses leave no fossils (except perhaps within arthropods andother creatures embedded in amber).
- Until recently, the scheme did not use any hierarchical level higher than that of family, but now one order (Mononegavirales) has been approved.
- The relative hierarchy and weight assigned to each characteristic used in defining taxa is set arbitrarily.
- It still influenced by prejudgments of relationships that according to Fenner (1974) "we would like to believe(from an evolutionary standpoint), but are unable to prove".
Present Taxonomic Organization of Viruses
1 order
71 families (24 infect humans and animals)
11 subfamilies
164 genera, including many floating genera
4,000 member viruses
- Lower hierarchical levels, such as subspecies, strain, variant, and so forth, are established by internationalspecialty groups and by culture collections.
- The system still contains hundreds of unassigned viruses, largely because of la lack of data.
- Some taxonomically unresolved families are still floating like Artevirus and Deltavirus.
The Universal System of Virus Taxonomy
Virus Orders
- Represent groupings of families of viruses that share common characteristics and are distinct from other orders and families.
- Designated by names with the suffix -virales.
- Only one order has been approved by the ICTV: Mononegavirales comprises the families Paramyxoviridae, Rhabdoviridae, and Filoviridae.
- ICTV moves slowly in the approval of orders, limiting use to those instances where there is good evidenceof phylogenetic relationship among the member families.
Virus Families
- Represent groupings of genera that share common characteristics and are distinct from the member virusesof other families.
- Designated by names with the suffix -viridae.
- Despite concerns about the arbitrariness of early criteria for creating these taxa, most of the original familiesstill remain intact.
- Most of the families of viruses have distinct virion.morphology, genome structure, strategies of replication,and phylogenetic independence or separation.
- This level in the taxonomy hierarchy now seems stable.
- It is the benchmark of the entire universal taxonomy system.
Virus Sub-families
- Designated by terms with the suffix -virinae.
- In the families Poxviridae, Herpesviridae, Parvoviridae, and Paramyxoviridae, subfamilies have been introducedto allow for a more complex hierarchy of taxa.
Virus Genera
- Represents groupings of species that share common characteristics and are distinct from the member virusesof other genera.
- Designated by terms with the suffix -virus.
- As more viruses are discovered and studied, there is pressure in many families to use smaller and smaller genetic,structural, or other differences to create new genera.
Virus Species
It is the most important hierarchical level in classification, but with the viruses it has proved to be the most difficult to address.
After years of controversy, the ICTV has adopted van Regenmortel's (1991) definition:
'A virus species is defined as a polythetic class of viruses that constitutes areplicating lineage and occupies a particular ecological niche'
Members of a polythetic class are defined by more than one property, and no single property is essential or necessary.
Problem still exists in deciding whether a particular virus should be designated as a species or as a strain....
Some viruses have already been designated as 'species' (Sindbis, Newcastle, poliovirus 1, vaccinia, Fidji disease,and tomato spotted wilt virus).
The Usage of Formal Taxonomic Nomenclature
- The first letters of virus family, subfamily, and genus names are capitalized.
- The genus and species names are printed in italics (underlined when typewritten).
- Species designations are not capitalized.
- Virus nomenclature would not involve the use of Latinized binomial terms.
- The terms Herpesvirus varicellae, Flavivirus fabricis have been abandoned.
- In informal vernacular usage, virus family, subfamily, genus, and species names are written in lower case script;they are not capitalized, nor are they printed in italics or underlined (....the picornavirus family,...the enterovirus genus....).
Examples of Full Formal Taxonomic Terminology
Family Poxviridae, subfamily Chordopoxvirinae, genus Orthopoxvirus, vaccinia virus.
Family Herpesviridae, subfamily Alphaherpesvirinae, genus Simplexvirus, human herpesvirus 2 (herpes simplex virus 2).
Family Picornaviridae, genus Enterovirus, poliovirus 1.
Order Mononegavirales, family Rhabdoviridae, genus Lyssavirus, rabies virus.
Family Bunyaviridae, genus Tospovirus, tomato spotted wilt virus.
Family Bromoviridae, genus Bromovirus, brome mosaic virus.
Genus Sobermovirus, southern bean mosaic virus.
Family Totiviridae, genus Totivirus, Saccharomyces cerevisae virus L-A.
Family Tectiviridae, genus Tectivirus, enterobacteria phage PRD.
Some Properties of Viruses Used in Taxonomy
To describe a virus comprehensively, approximately 500 to 700 characters must be determined.
Virion Properties
Virion size
Virion shape
Presence or absence and nature of spikes
Presence or absence of an envelope
Capsid symmetry and structure
Physico-Chemical and Physical Properties
Virion molecular mass (Mr)
Virion buoyant density (in CsCl, sucrose,etc.)
Virion sedimentation coefficient
pH stability
Thermal stability
Cation stabililty (Mg2+, Mn2+)
Solvent stability
Detergent stability
Irradiation stability
Genome
Type of nucleic acid (DNA or RNA)
Size of genome in kb/kbp
Strandedness: ss or ds
Linear or circular
Sense (+ or -ve or ambisense)
Number and size of segments
Nucleotide sequence
Presence of repetitive sequence elements
Presence of isomerization
G&C content ratio
Presence or absence and type of 5' terminal cap
Presence or absence and type of 3' terminal poly (A) tract
Proteins
Number, size, and functional activities of structural proteins.
Number, size, and functional activities of non-structural proteins.
Details of special functional activities of proteins, e.g. transcriptase, reverse trascriptase, hemagglutinin, neuraminidase.
Aminoacid sequence
Other protein properties (glycosylation, etc.)
Lipids
Content, character, etc.
Carbohydrates
Content, character, etc.
Genome organization and replication
Genome organization
Strategy of replication
Number and position of open reading frames
Transcriptional characteristics
Translational characteristics
Site of accumulation of virion proteins
Site of virion assembly
Site and nature of maturation and release
Other Properties
Antigenic Properties
Serological relationships, especially as obtained in reference centers.
Biological Properties
Natural host range
Mode of transmission in nature
Vector relationships
Geographic distribution
Pathogenicity, association with disease
Tissue tropisms, pathology, histopathology
The ICTV Database
The number of viruses occupying geographic and/or host niches as pathogens or silent passangers of humans, plants, invertebrates, protozoa, fungi and bacteria is very large.
ICTV recognizes more than 4000.
It has been estimated than more than 30,000 viruses, virus strains, and subtypes are being tracked in various specialtylabs, reference centers, culture collections, and some international agencies.
ICTV has a virus database - ICTV database (ICTVdb) - available to all virologists worldwide to develop and manage theuniversal system for virus taxonomy
Databases Interphased with the ICTVdb
- The plant virus database operated at the Australian National University of Canberra, Australia.
- The Virus Identification Data Exchange (VIDE) Project.
- The Veterinary Virus Database operated by CSIRO. The VIREF project.
- The Arbovirus Database operated by the American Committee on Arthropod-borne Viruses (ACAV) by the Centers for Disease Control in Ft. Collins (CO).
- VIDE is the most advanced as it involves a worldwide network of more than 200 collaborating plant virologists.Data for more than 890 plant viruses in 55 genera.